**The evolution, homeostasis and reproduction (first) lecture

To regard man, the most ephemeral and rapidly evolving of all species, as the final and unsurpassable achievement of creation, especially in his present-day particularly dangerous and disagreeable stage of development, is certainly the most arrogant and dangerous of all untenable doctrines. If I thought of man as the final image of God, I should not know what to think of God. But when I consider that our ancesters, at a time fairly recent in relation to earth's history, were perfectly ordinary apes, closely related to chimpanzees, I see a glimmer of hope. It does not require considerable optimism to assume that from us human beings something better and higher may evolve. Far from seeing in man the irrevocable and unsurpassable image of God, I assert--more modestly and, I believe, in greater awe of the Creation and its infinite possibilities--that the long-sought missing link between animals and the really humane being is ourselves!
-Konrad Lorenz, On Aggression

Biology is the study of life on Earth.

Assignment
Audesirk, Audesirk and Byers, Chapter 1, Many selections throughout text

Today's musical selection
Sam Cooke "What a wonderful world" ("Don't know much about biology...")

What is unique to life?

Fig. 1-2
Cell membrane contains protoplasm and somehow inside, cells are "alive."
(1) Complex - Cells have very complex macromolecules (DNA, RNA, protein).
In general, entropy (disorder) increases [we will return to this point in a later lecture]. However, in Biology, small systems are defined, enclosed in cells, that defy this generalization
(2) Movement, Responsiveness (irritability, sensitivity, excitability)
(3) Development, Growth, Form
(4) Metabolism - exchange energy
-Catabolic (breakdown)
-Anabolic (build-up)
*(6) Homeostasis (regulation)
Example#1 Thermostat, servo mechanism, negative feedback.
Example#2 Weight regulation 1 cookie/day = 25 lb/yr
*(7) Evolution is major unifying principle
Life on Earth is 3 1/2 billion yrs old (and presumably all organisms have common ancestor)
History from primordial "soup" of molecules to biology, extinctions, etc.
*(8) Reproduction -
"Survival" in biology is to and reproduce and produce fertile offspring.
Example#1- One species definition: Reproduce, fertile offspring
Horse - donkey (differenty species) mate to produce the mule -- the mule is sterile: Mule, (here is my late friend's dad proudly posing with his Missouri mules)
Example#2- Consider this: so much energy is devoted to reproduction that reproductive structures constitute most of the human diet. Oh? Well, grain, fruit (and vegetables that are fruits), dairy products and eggs.

The virus story

Figure E9-1
To tell the next story, let us introduce reproduction in the bacteriophage (a virus that "eats" bacteria). Is a virus alive? Compare the terms "infectious" with "living." Is the virus the oldest form of life because it is so simple? (Made up of just Protein and DNA) No, it cannot be because it is a Parasite and therefore could not exits until its host existed.


Figure E9-2
(Alfred Hershey & Martha Chase 1952 work) radioactive sulfur seen in protein coat of bacteriophage, radioactive phosphorus seen in bacteria where DNA is orchestrating the manufacture of new virus.

"Is it animal, vegetable or mineral"
- a question on an old quiz show called "20 questions"

Fig. 1-11
Kingdoms (At one time, 2 kingdoms were proposed (plants and animals), but there were problems, for instance some organisms have properties of both kingdoms. Now 5 are generally accepted.

Sometimes more are also proposed. How can the number of kingdoms be subject to debate? Classification is not an exact science.
5 Kingdoms:

Kingdoms and domains

Monera (prokaryotes) are very diverse (2 of the 3 domains)

These cells do not have a nucleus. The suffix "karyote" refers to the nucleus, and comes up in words like "perikaryon" (the part of a nerve cell near its nucleus) and "karyotype" (the chromosomal constitution of a cell).
The other four kingdoms have eukaryotic cells.
Protista (single celled "plants" and "animals") are also very diverse
Fungi
Plantae
Animalia

Do they make their own food?

Fig. 1-10
Fig. 28.1
Autotroph vs. Heterotroph (self- other-feeder)
Food web (from ecology chapter)

Phylogeny vs Taxonomy

Fig 18-5
Fig. 18-6
Fig. 24-1
Taxonomy is sometimes called "Systematics" and is based on the Linnean system (Linnaeus 1705-1778 botanist)

Table 18-1
Kingdom - Phylum - Class - Order - Family - Genus - Species

(phylogeny and systematics.) Here, domain is more inclusive than kingdom
Genus - Species: binomial nomenclature
Phylum = Division for plants fungi bacteria
Homo sapiens people
Drosophila melanogaster fruit flies
Canis familiaris dogs
In phylogeny we try to draw conclusions (and diagrams) of how related organisms are.

Figure 18-5
There can be various levels of artistic license in such evolutionary diagrams.

Here is a display at the Carnegie museum in Pittsburgh. It is actually a graph. Diversity is on the X axis (abscissa). That diversity in this example is the location on Earth. The Y axis (ordinate) is time with long ago on the bottom and now on top and split up into epochs of the geological time scale (Eocene, etc.). Of note is that animals lower in the diagram are not just "simpler" animals of today. Rather, today's animals are only at the top, and some further down may be extinct, for instance, horses in the New World until they were re-introduced.

Such a diagram branches out, hence the term "divergent evolution," a concept so fundamental that you should see it now even though evolution will be covered in detail in the last quarter of the semester. One very fundamental concept is that of homology. The wing of a bird and the flipper of a porpoise are homologous and are descended from the same common structure that led to your arm and hand.

Molecular biologists borrowed this strategy and produce divergent evolution diagrams of their own (at first much to the chagrin of the comparative anatomists).

Levels of analysis

Fig. 1-1
element - molecule - organelle - cell - tissue - organ -
organ system - organism - population - biosphere

Questions used in 2007 & 2008 relating to this outline

These days, autotrophs are almost exclusively
(a) herbivores.
*(b) photosynthetic.
(c) predators.
(d) prokaryotes.
(e) ruminants.

I said that a phylogenetic diagram was like a graph. What is on the ordinate (Y-axis)?
(a) binomial nomenclature
(b) bacteria on the left, people on the right
(c) kingdom on the left, species on the right
(d) the independent variable
*(e) time from long ago to present

Comparative anatomy shows similarities in human and bird forelimbs, since humans and birds had a common ancestor. The forelimbs are called
(a) metabolic.
(b) metazoans.
(c) homeostatic.
*(d) homologous.
(e) prokaryotic.

You look at an amoeba in the microscope. Where might you put it in a phylogenetic diagram of eukaryotes?
(a) at the middle at the bottom.
*(b) at the left at the top.
(c) right next to Drosophila melanogaster.
(d) beside all the others that have the nitrogen-containing polysaccharide chitin.
(e) with ancient organisms.

In the food web, high level consumers (predators) would be considered to be
(a) more evolved than anybody else.
*(b) heterotrophs.
(c) lacking in catabolic metabolism.
(d) higher in entropy than any other organism.
(e) ruminants.

The mule was used as an example to show
(a) some organisms of the past are now extinct.
(b) the forelimbs of vertebrates are not homologous.
(c) the dangers of anabolic steroids.
(d) not all reproducing "organisms" are considered to be alive.
*(e) the horse and donkey are different species.

In the Hershey-Chase Experiment, phosphorus and sulfur were used because phosphorus is found in ____________ while sulfur is found in ______________.
(a) Cell membrane, Lipids
(b) Vesicles, Proteins
*(c) DNA, Proteins
(d) Proteins, RNA
(e) Bacteria, Lipids

Why don't most people gain or lose a lot of weight rapidly?
*(a) They eat the right amount.
(b) They count calories rather than kilocalories.
(c) They adjust their caloric loss through the urine to compensate for overeating or undereating.
(d) Antidiuretic hormone (ADH) regulates weight.
(e) Parathormone (PTH) mediates the storage of extra energy.

Terms like Homo sapiens
(a) demonstrate the concept of homology.
*(b) are derived from the Linnean system of taxonomy.
(c) tell you the phylogeny.
(d) tell us the kingdom and phylum in Latin.
(e) relate tissues to organs.

I said that the tree of life is like a graph. What is on the X-axis (abscissa) of the tree of life?
A) Binomial nomenclature.
B) The species is on the left and the genus is on the right.
C) Catabolic is on the left and metabolic is on the right.
*D) Diversity.
E) The dependent variable.

Disorder increases according to the second law of thermodynamics.
A) Homeostasis is the word biologists use for disorder.
B) This is exemplified by anabolic reactions.
*C) Although biology is complex, this law still applies to the whole universe.
D) Entropy is the fundamental unifying principle in biology.
E) Comparative anatomy was used to demonstrate that disorder applies to biology.

Your lab partner tells you that the Paramecium cell you see in the microscope is very primitive. You offer the following correction:
*A) They are present-day organisms with a 3 & 1/2 billion year geneology just like you.
B) Viruses (not Paramecia) are primitive, but cells arose later (than viruses) in the history of life.
C) Because they have photosynthesis, they must be very old.
D) Although Paramecia are prokaryotes without organelles, they are autotrophic.
E) Bacteriophage have infected those Paramecia.

What kind of an organism is a bacteriophage?
A) It is a eukaryote.
B) Scientists consider it to be a predator in the food chain.
C) It is an autotroph.
D) It is a bacterium.
*E) It is not an organism since it is not cellular.

Radioactive phosphorus vs. radioactive sulfur were used by Hershey and Chase
A) to identify membrane glycolipids.
*B) to show that DNA, not protein, is the hereditary macromolecule.
C) to diagnose brain tumors.
D) to show that water dissolves hydrophobic ions.
E) to show the age of fossils and rocks.

Untreated diabetic patients
*A) are the only people who excrete calories.
B) are the only people who have catabolic metabolism.
C) have resistance to malaria.
D) were classified by Linnaeus.
E) are protostomes.

In one table I showed you, it was claimed that bacteria and protists could be either autotrophic or heterotrophic. This dichotomy applies to
A) whether the organism is diploid or haploid
*B) whether they make their own food.
C) presence of a nucleus.
D) embryonic development.
E) whether they are gymnosperms or tracheophytes.



Questions used in 2002 relating to this outline (as well as other outlines)

You were presented with the classification of the wolf (Animalia - Chordata - Mammalia - Carnivora - Canidae - Canis - lupis). Which group would have the most species in it?
*(a) phylum
(b) class
(c) order
(d) family
(e) genus

What happens when bacteriophage T2 infects a bacterium?
(a) Phage RNA enters the cell.
*(b) Only viral DNA enters the bacterium.
(c) Only viral protein enters the bacterium.
(d) The entire virus, enzymes and membranes and all, enter.
(e) The virus injects a poison into the bacterium to kill it.

About how long ago did the first cells appear?
(a) 3.5 million years
*(b) 3.5 billion years
(c) after photosynthesis evolved
(d) not until there was sexual reproduction
(e) 1.5 billion years ago when eukaryotes came into existence

"Membership" in this group is sometimes defined by ability to mate and bear fertile offspring:
(a) species.
(b) genus.
(c) family.
(d) order.
(e) class.

Bacteriophage were used
(a) to obtain temperature resistant enzyme for PCR.
(b) to make a cDNA library.
(c) by Hershey and Chase to show that DNA but not protein was the hereditary material.
(d) to show that the lac operon is regulated by presence of lactose.
(e) for gene therapy.


This page was last revised 6/8/09

**The strong inference (scientific method) lecture

"Strong Inference"

I keep six honest serving men
(They taught me all I knew);
Their names are What and Why and When
And How and Where and Who. - Kipling

If I have seen further, is is by standing on the shoulders of giants
-Sir Isaac Newton Letter to Robert Hooke 5 February 1675

A dwarf standing on the shoulders of a giant may see farther than a giant himself
- Robert Burton (1577-1640) The anatomy of melancholy

Assignment
Audesirk et al., Chapter 1, pp. 610-611 & 629 (also pay attention to several figures and readings in other chapters)

Today's musical selection
Tina Turner One of the living

Nature of scientific inquiry

Fig. 1-4
Scientific inquiry and scientific method is based on observation - systematic, objective, repeatable

Figure 14-7
You cannot always manipulate things, example: studying the fossil record.
But you can make observations like the similarities in the forelimbs of birds and mammals.

Think about high school geometry. In the text book, there are "postulates" that we assume must be true and "theorems" that can be proven. In the home work, there are "if - then" problems in which something iis assumed ("if"), a conclusion ("then") can be worked out by applying the theorems and postulates step-by step.

There are various kinds of science.
Some scientists make models (mathematical or electrical) of biological systems that have predictive value. Other scientists collect descriptive data that further substantiates a global theory.

Fig. 1-10
(Already shown in first lecture outline)
Model: energy flow in biology

Is there one right kind of science?

"Strong inference" is the title of a paper by John R. Platt (Science, 146, 347-353, 1964) in which he criticizes some approaches to science. Here are some quotes:
"...some fields of science are moving forward much faster than others"
"Those rapidly moving fields are fields where a particular method of doing scientific research is systematically used and taught, an accumulative method of inductive inference that is so effective that I think it should be given the name of 'strong inference.'"
"Strong inference consistds of...:
(1) Devising alternative hypotheses;
and
(2) Devising a crucial experiment ... with alternative outcomes ... each of which will ... exclude one or more of the hypotheses"
"It is like climbing a tree."
"[focus] on the exclusion of a hypothesis"
"How small and elegant an experiment can you perform?
"You must study the simplest system you think has properties you are interested in." (attributed to C. Levinthal
"...there is no such thing as proof in science... science advances only by disproofs." (attributed to Karl Popper

Doing an experiment

In an experiment:
An independent variable is what we manipulate, typically graphed on the abscissa (X-axis)
A dependent variable is what we measure, typically graphed on the ordinate (Y-axis)
Control - other variables are to be controlled
The population is everything out there
The sample is what, out of the population, we measure (to make inferences about the population)
Sampling - random sampling is best
Descriptive statistics gives us averages (means)
as well as measurements of how variable the data are (standard deviations)
In inferential statistics we propose a null hypothesis vs. an alternative hypothesis.

Doing statistics

Hypotheses are small questions. You "test" these hypotheses - answers (in the form of "rejecting the null hypothesis") are never certain but rather involve an acceptably low probability (usually 5%) of being wrong, hence the involvement of statistics in experimental design.

Enter (stage left): Statistics

"There are three kinds of lies: lies, damn lies and statistics"
Benjamin Disraeli (quoted in Mark Twain's autobiography, Chapter 29)

Enter (stage left) The normal distribution

Figure 15-13
(I just needed a picture showing the normal distribution)
Figure 15-13 will be shown again in the context of genetic basis of evolution

Figure
Area under the curve = 1
Middle of the curve is the mean, 0 in the "standard" normal distribution
variation is indicated by standard deviation
z-score indicates the number of standard deviations away from the mean the a score is
About 5% of the curve is 2 or more standard deviations from the mean

Central limit theorem:
The distribution of sample averages approaches the normal distribution as the sample size increases
(It's a theorem, that means it can be proven, it's not just an idea)

"The results are significant beyond the 0.05 level." (This its typical) This means that the results could have happened by chance (rather than because of our independent variable) 5% of the time

"It has been proven beyond a shadow of a doubt using the scientific method" - Nonsense!

Collect more data, and you will be more certain. You can only reject the null hypothesis. You can not accept (or prove) the null hypothesis. In other words, "absence of data is not the same as data of absence."

Thought problem & story

Suppose someone says that a certain plant is extinct. How can he know? To state that for certain would require examination of every square inch of the Earth. Most naturalists admit that they can say for (fairly) certain if a bird species is gone. The reason is that birds are so conspicuous and that there are so many well-trained bird-watchers. Birds do go extinct! Here is a SLIDE I took at the Smithsonian natural history museum of Martha, the last passenger pigeon who died 1 pm Sept 1, 1914 at the Cincinnatti Zoo. The famous ornithologist Audubon, saw them darken the skies hundreds of times during their migration. However, the ivory-billed woodpecker was considered extinct after its last sighting in 1944. Then it was (presumably) seen again in 2004 (although there remains some uncertainty.

"We have no evidence showing that (whatever)" - Nonsense!

In summary, the step-by-step progress of science involves statistics, and asking the right questions, that can be answered appropriately. A course in advanced statistics is usually called "experimental design" because you cannot even do the right experiment without the right design, controls, and statistics in mind.


Your faculty are scientists

"Publish or perish." Perhaps you have heard that expression. In my opinion, "a university is a community of scholars dedicated to the acquisition and disemination of knowledge." Faculty are expected to do research as well as to teach courses and are usually granted tenure only if their research publications are favorably viewed by their peers (at other universities)

Watch out!

Sometimes "scientists" are not completely honest when there is a conflict of interest

Personalities

Fig. E9-3
Science is a human endeavor.
See story on p. 155 about Maurice Wilkins and Rosalind Franklin
See story on p. 156 about James Watson and Frances Crick
1962 Nobel Prize in Physiology and Medicine
American chemist Linus Pauling might have made discovery but he was not allowed to go to a meeting where data were presented because of strong anti-Communist movement in the US in the early 1950's

Scientific revolutions

Book by Thomas Kuhn (1962)
"paradigm" - set of beliefs shared by the scientific community
When too many contradictions accumulate - "paradigm shift"

Questions used in 2007 & 20008 relating to this outline

I said that "absence of data is not the same as data of absence" to paraphrase
(a) "the sample must be random."
(b) "observations must be unbiased."
*(c) "you never accept the null hypothesis."
(d) "not all science is based on experiments."
(e) "publish or perish."

Description of a hypothesis:
(a) It unifies all the observations in a field.
*(b) It should be stated in a way so that it can be disproved.
(c) Like a postulate in geometry, we must assume it is true.
(d) Like a theorem in geometry, it can be proved.
(e) It is used to describe a process and to make predictions.

It is reasonable to hypothesize that the average height of the Bio 110 class can be estimated by the average of the Tuesday morning lab because
(a) students were not biased when they did those measurements.
(b) we controlled all other variables in this experiment.
*(c) there is no reason to think it is not a random sample.
(d) we measured a population, not a sample, Tuesday morning.
(e) height is an independent variable.

The normal distribution is used because
*(a) it can be proven that the sample means are normally distributed.
(b) it is how the independent variable is related to the dependent variable.
(c) it is systematic, objective and repeatable.
(d) it is the best description of how postulates and theorems work in a high school geometry "if-then" homework problem.
(e) it is the best way to graph homology on a taxonomic tree.

The ivory-billed woodpecker
(a) has wings that are not homologous to human forelimbs.
(b) is dangerous because it has prions.
(c) was found on the Galapagos by Darwin.
*(d) was thought to be extinct but may not be.
(e) became extinct in the Old World and then was re-introduced from the New World.

Why do scientists study a sample instead of a population?
A) A sample is more accurate.
B) A population is random.
*C) A population is too big to study.
D) The sample is like a theorem while the population is like postulate.
E) Only with the sample can you prove the null hypothesis.

Which is true about the discovery of the structure of DNA?
A) American Linus Pauling discovered it.
B) Nobody believes Watson and Crick's model because they had a conflict of interest.
C) It's primary structure is the sequence of amino acids in it.
*D) The Nobel Prize went to three men, and Rosalind Franklin did not share the award.
E) It can be altered by exposure to the abnormal structure of a prion.

The null hypothesis
A) is the same as a law.
B) is the same as a model.
C) is the same as a theory.
*D) cannot be accepted, it can only be be rejected.
E) allows us to have a "paradigm shift" (scientific revolution).

I want to test a drug, so I do a clinical trial. I give half the subjects the drug and half the people a "placebo" (a dud). Why?
A) The placebo guarantees that the researchers do not have a conflict of interest.
B) The placebo guarantees that the sample is random.
C) The placebo guarantees that the observations are repeatable.
D) If we are testing a diabetes drug, we should give overweight people the drug and thin people the placebo.
*E) The people getting the placebo serve as the control group.

I calculate the mean from my sample. What is true about the sample mean?
*A) The distribution of sample means is described by the normal distribution.
B) It is the same as the standard deviation.
C) It is the same as the median.
D) It is the same as the population mean.
E) It is one of the controlled variables.

What is the significance of the "tails" (more than 2 standard deviations from the mean) of the normal distribution?
A) Homology is in the tails while analogy is in the rest of the distribution.
B) If it is in the tails, scientists consider it to be a law, while the rest of the distribution is a model.
*C) It has to do with disproving the null hypothesis.
D) The tail on the left is the dependent variable and the tail on the right is the independent variable.
E) The mean is in the tail on the left while the median is in the tail on the right.


Question used in 2002 relating to this outline

A small scientific question which the typical biologist "tests" with an experiment is called a
(a) theory.
*(b) hypothesis.
(c) model.
(d) correlation.
(e) law.


This page was last revised 6/8/09

**The chemistry and water lecture

"Water, water everywhere
And all the boards did shrink
Water, water everywhere
nor any drop to drink."

-Samuel Taylor Coleridge
The rime of the ancient mariner

CHEMISTRY:

Assignment
Audesirk, Audesirk and Byers, Chapter 2 (and a table in chapter 34)

Today's musical selection
Tom Lehrer, the elements

"Inorganic chemistry" is an expression for first year college chemistry.
Second year college chemistry is "organic chemistry," the chemistry of carbon (C) based molecules.
In Bio 110, we have the good fortune of summarizing these 2 yrs of chemistry in a few lectures!

Substance is composed of Mass (matter), and Energy is also important, but, in biology, we will focus only on that energy which is biologically useful.

INORGANIC CHEMISTRY

From the Los Alamos National Labs (periodic table)

Figure 2-1
Atoms = Elements
There are 3 particles.
electrons and the nucleus (Protons and Neutrons)

Table 2-1
Periodic table - elements - O, C, H, Ca, P, K, S, ... are most abundant in life
There are also trace materials like iron and zinc.

1. Protons determine the atomic number (integers in order, top of each box on the periodic table).
2. Neutrons plus protons determne weight (bottom of box).

Isotopes
These are not integers because there are several isotopes such as 3H (tritium), 14C. The 14 is a superscript, and this is pronounced "C-14." Isotopes are radioactive, and decay with a characteristic half-life. In biology, radioactive isotopes are used for radiocarbon dating and to label molecules (radioactive tracers) and for autoradiography (exposing film),...

Box E2-1
...and
PET scan (positron emission tomography)

3. electrons, virtually no mass, involved in bonding of two major types:

Figure 2-6a
(a) covalent bonding

Fig. 2-4
(b) NaCl splits to Na+ (sodium) and Cl- (chloride) ions that are attracted to each other because of opposite charges

Figure 2-3
If light is absorbed by a pigment, the electron is excited, and, if the molecule fluoresces, the exctation in the electron comes back down; electrons are very important for how biological energy is stored (photosynthesis) and how it is released (cellular respiration)

Water

The body is approxamately 2/3 water. In addition, as you will see repeatedly this semester, water is incorporated into many organic molecules.

Molecules - the next higher level of integration above atoms, generally aggregates of atoms linked by covalent bonds. Because water is so fundamental, we start with water as an example molecule.

Figure 2-6b
H2O has covalent bonds, but there is some separation of charge, making it a polar molecule
Water is very important as a solvent, in reactions, and in temperature regulation.
As a polar solvent, it dissolves charged molecules or ions.


Figure 2-14
A small fraction of water molecules split to H+ and OH- "ions", ...

Figure 2-15
pH
...and if there is an excess of H+, the solution is an acid; if OH- predominates, it is a base. The pH scale runs from 0 (acid) to 7 neutral to 14 base (alkaline). The pH = -log [H+].


Other important properties of water:
(1) It has a very high specific heat measured in calories (1 cal is the energy to heat water 1oC); units of energy (the "calories" you "count" when dieting are actually kcal). In this regard, big bodies of water can moderate the climate (cooler in summer, warmer in the winter), the "sea climate."
(2) It has an extremely high heat of vaporization (about 540 cal/g, actually 576 at 37oC), important in body cooling via sweating and panting.
(3) It organizes matter by adhesion and cohesion and because molecules can be hydrophilic or hydrophobic.

Figure 2-12
Consider a container of Italian dressing, where the oil floats on the watery liquid, and the oil is organized into small spheres when the bottle is shaken well

Oxygen - an integrative story

Pineapple juice (or other acidic juices like lemon juice) keeps the potato slice on the right from turning brown.
(The acidity blocks an enzyme that causes oxidation of the amino acid tyroosine.)
In general, oxygen is a necessary evil, necessary because we need it for metabolism, evil because oxidation is "biological rusting."

Table 34.3
Vitamin E (tocophorol) [and several otther nutrients] are antioxidants.

Preview of coming attractions (concerning oxygen)
(1) aerobic metabloism
(2) absent in primordial atmosphere
(3) precursor of Ozone (blocks ultraviolet light from Sun)

Questions used in 2007 & 2008 relating to this outline

What do we mean by 14C when carbon usually has 6 protons and 6 neutrons?
(a) The difference between 12 and 14 is made up by two extra electrons.
(b) This carbon has 7 protons and 7 neutrons.
(c) 14C is a famous polar solvent.
(d) This is a charged ion.
*(e) It wouldn't be carbon if it didn't have 6 protons, so it must have 8 neutrons.

It is true that hydrogen and oxygen are covalently bound in water, but that is not the whole truth. Why not?
(a) Water is not polar.
(b) If the pH is 7, it can never be true.
*(c) Water can divide to hydroxyl and hydrogen ions.
(d) Water fluoresces.
(e) Water cannot become part of an organic molecule.

After an electron is excited, energy may be released when the electron drops back to its lower energy shell. How is this energy release witnessed?
(a) NaCl is covalently bound.
(b) The pH gets lower.
(c) By ADP converting to ATP plus inorganic phosphate.
(d) By the half life.
*(e) Light is emitted.

It takes 1 calorie to raise the temperature of 1 ml of water 1 oC. Why is sweating so useful to cool you when you are hot?
(a) The half life of sweat is different
(b) Water organizes hydrophobic and hydrophilic molecules
(c) Water is needed for hydrolysis.
*(d) The heat of vaporization is way more than 1 calorie.
(e) Some water is incorporated into organic molecules.

In biology, sodium is found in what form?
(a) As a radioactive isotope.
(b) As a high, i.e. acidic, pH.
(c) In pentoses.
(d) Covalently bound to chloride.
*(e) As an ion.

"Oxygen has 8 protons and 8 neutrons." True in general, but why is the atomic mass 15.999 instead of 16?
*(a) Perhaps some atoms have less than 8 neutrons.
(b) Perhaps some atoms have less than 8 protons.
(c) Because there are not enough electrons.
(d) Oxygen is the backbone of organic molecules because it makes four bonds.
(e) Oxygen molecules that are in hydrocarbons have less.

Electrons are important in pigments and also for
(a) atomic weight.
(b) the "sea climate."
(c) hydrophobicity.
(d) the resting potential
*(e) chemical bonding.

Atoms or molecules that have gained or lost electrons are termed
A) acids.
B) bases.
C) polymers.
*D) ions.
E) radioactive.

If a substance measures 7 on the pH scale, that substance
*A) has equal concentrations of H+ and OH- ions.
B) is exemplified by stomach acid.
C) is alkaline.
D) probably lacks OH- ions.
E) is basic.

Which four elements make up approximately 96% of living matter?
A) carbon, sulfur, phosphorus, helium
*B) carbon, hydrogen, nitrogen, oxygen
C) carbon, sodium, chlorine, magnesium
D) carbon, oxygen, sulfur, calcium
E) oxygen, hydrogen, calcium, sodium

In what way is 14C, used in radiocarbon dating fossils, different from normal carbon?
A) Its atomic weight is lower.
B) It has more protons.
*C) It has more neutrons.
D) It is oxidized.
E) It is an ion

If you cut open a potato, it will turn brown if you do not dip it into pineapple juice (or something else acidic) because of an enzyme, an amino acid and what else?
*A) oxygen
B) nitrogen
C) carbon
D) sulfur
E) phosphorus

What determines the atomic number of an atom?
A) number of electrons if it is an ion
B) total number of protons, neutrons and electrons
C) arrangement of neutrons in the atomic nucleus
*D) number of protons in the atomic nucleus
E) the total number of protons plus neutrons

The way that light from the Sun interacts with matter is
A) to change the pH.
B) to create positron emission tomography.
C) change the atomic weight.
D) convert a neutron into a proton.
*E) excite an electron.

Polar covalent bonds form
A) after the half-life has occurred.
*B) when electrons are shared, but unequally (example: water).
C) ions are formed.
D) an acid and base are combined.
E) charged atoms are attracted to each other.

Sweating is a useful cooling mechanism for humans because
*A) water takes up a great deal of heat in changing from its liquid state to its gaseous state.
B) it takes one calorie to heat one milliliter of water one degree Centigrade.
C) water can exist in three states at temperatures common on Earth.
D) water is an outstanding solvent.
E) water ionizes readily.

Questions used in 2002 relating to this outline (and other outlines)

One reason that membrane lipids are arranged the way they are is because of
(a) essential amino acids.
(b) ionic bonds.
*(c) hydrophobic fatty acids.
(d) hydrolysis of bonds.
(e) the half life.

A given element with a given integer atomic number might not have an integer atomic weight because of
*(a) a variable number of neutrons.
(b) a variable number of protons.
(c) unsaturated bonds.
(d) the fact that light excites the electron orbitals.
(e) covalent bonds.

Because of the half-life of 14C, you may be able to determine
(a) whether your solvent is a polar solvent.
(b) whether an organism is a prokaryote or a eukaryote.
(c) whether a reaction is anaerobic.
*(d) the age of a fossil.
(e) number of amino acids in a protein.

Charged atoms such as Na+ are called
(a) isotopes.
*(b) ions.
(c) covalent bonds.
(d) molecules.
(e) neutrons.

All of the following are used in living systems. Which is least abundant?
(a) carbon
(b) nitrogen
(c) hydrogen
*(d) iron
(e) oxygen


This page was last revised 6/9/09

**The organic chemistry lecture

"He said science was going to discover the basic secret of life someday," the bartender put in. He scratched his head and frowned. "Didn't I read in the paper the other day where they'd found out what it was?"
"I missed that," I murmured.
"I saw that," said Sandra. "About two days ago."
"That's right," said the bartender.
"What is the secret of life?" I asked.
"I forget," said Sandra.
"Protein," the bartender declared. "They found out something about protein."
"Yeah," said Sandra, "that's it."

-Kurt Vonnegut, Jr. Cat's Cradle

Assignment
Audesirk, Audesirk & Byers Chapter 3

Today's musical selection
Bush The chemicals between us

ORGANIC CHEMISTRY
is the chemistry of carbon (C) which makes 4 bonds.
In "Star Trek" (the first movie), people were called "carbon based units" by the alien.

Hydrocarbon

(Hydro-carbon - prefix suggests hydrogen, suffix suggests carbon).
They are hydrophobic and nonpolar.
CH4 methane, - natural gas
Fossil fuel, but also in primordial atmosphere, oddly
Gasoline has typically 8 carbons (octane) and is fluid. Long chains are thick, like oil and vasoline.
nonpolar, hydrophobic

Carbohydrate

Figure 3-4
(Carbo-hydrate is also sort of a compound word, carbon, but note that "hydrate" suggests water, not hydrogen) - the general formula is Cn(H2O)n
Monosaccharides
Hexose (hex = 6 [carbons], "-ose" always means sugar)- glucose, the most famous monosaccaccharide, is good to illustrate that monosaccharides usually assume a ring structure

Figire 3-6
Pentose - ribose, deoxyribose (that are in RNA and DNA) are famous

Figure 3-7
Compound dehydration synthesis, hydrolysis (hydro-water, lysis-breakdown)
In digestion, macromolecules are broken down to monomers.
Disaccharide - sucrose, lactose (milk)

Lactose
in milk, so all babies can digest it
Europeans evolved with dairy husbandry and so can enjoy milk as adults
Many Asians and Africans cannot
later we will see that the lac operon controls enzymes for lactose utilization in bacteria

Figure 3-8
Polysaccharides starch (plant), glycogen (glyco-sugar, gen-give birth to) (animal)
alpha 1-4 linkage
Carbohydrates are used for energy.

Figure 3-9
Carbohydrates are used for structure: cellulose (beta-1,4 glucoses), the most plentiful biological molecule on Earth,
Carbohydrates are used for bulk since people cannot digest fiber, but termites & cattle can. This introduces the topic of symbiosis (living together) and mutualism (where it is to the benefit of both organisms since, for termites, zooflagellates, which are protozoa, break down cellulose and for cattle, bacteria do the job.

Other functions
Carbohydrates are used for structure in some proteins
Carbohydrates contribute to exoskeleton in arthropods, a polymer called chitin that has some nitrogen and is also in cell walls of fungi

Lipids

(fats) store more energy (2x sugar) 1 tablespoon of sugar is 50, fat 100 "Calories" = kilocaloriies

Figure 3-11
Glycerol & 3 fatty acids (16-24 C long) - triglyceride ester bonds
note the dehydration synthesis
The -COOH defines an organic acid such as a fatty acid, otherwise the molecule is a hydrocarbon.
C-C (single bond) vs. C=C (double bond) unsaturated (vs saturated with H's), with several, it is referred to as "polyunsaturated" PUFA = polyunsaturated fatty acid
Animal fats tend to be saturated, bad for arteries leads to atherosclerosis; vs vegetable fats better.

Figure 3-15
Polar phospholipids - contribute to membranes because polar group is hydrophilic and fatty acid (acyl) tail is hydrophobic
polar-glycerol-FA1-FA2 (more double bonds, fluidity)
Here are some famous fatty acids: stearic C18, Oleic-18:1
There are also glycolipids with sugar attached to lipid in membranes.

Figure 3-16
Steroids-cholesterol - fit into membranes and serve as precursors for hormones,
especially "sex hormones" like testosterone, progesterone, estrogen
Howard Cossel "anabolic steroids" (metabolic: catabolic vs anabolic) - androgens, the hormones like testosterone that favor nitrogen retention (muscle growth)
Salts of cholesterol are in bile (from liver) that acts like a detergent to emulsify fats to aid in digestion.
Interestingly, cholesterol is required in animals and is an "essential" nutrient in insects that cannot synthesize it; too much bad in people, and that can be controlled by diet though people also biosynthesize cholesterol.

Other functions
Waxes: fatty acid + long chain alcohol (instead of glycerol) prevent water loss also used for structure in nbee hive.
Blubber, especially in warm blooded cetaceans, serves as insulation.
In summary, lipids are used for energy, structure, hormones, insulation, water loss, digestion

Proteins

Proteins and nucleic acids make up 2/3 of dry weight of the body
short = "Peptides", medium = polypeptide, long = "protein" (hundreds, thousands)
Proteins are very important because chains of amino acids can be very complex

Figure 3-18
Amino acid
The general formula is NH2-CR-COOH - amino ( -NH2 ) and acid ( -COOH ).

Figure 3-20
Peptide bonds involves -NH2 and -COOH getting linked with a dehydration synthesis.

There are about 20 amino acids (alphabet of 20 letters)
R group varies
If you made a peptide 4 amino acids long, there would be 20 x 20 x 20 x 20 = 160,000 different possibilities, hence the complexity.
About half of the amino acids are "essential" meaning that they cannot be made by metabolic conversion from other molecules and thus need to be eaten - corn is notoriously low in tryptophan and methionine).

Structure:
primary (the sequence)
secondary (alpha helix, beta pleated sheet)
tertiary structure (disulfide and other bonds)
quaternary structure (chains interact with each other)
(here is a really important example - hemoglobin - which has 2 alpha subunits and 2 beta subunits.)

Beyond 4 levels
There are so many levels of protein structure above these 4, glycosylation (adding a sugar), phosphorylation, chopping fragments out of the protein, and other post-translational modifications, that you will have to wait until a more advanced course to really focus on them.

Protein diversity makes for individuality, and at the level of the immune system, proteins (antigens) determine self vs non-self.

Proteins can serve for:
Structure (example keratin which is in hair)
Enzymes - Their names end in the suffix -ase), that are catalysts (molecules that influece the rate of a reaction).
Antibodies (used against antigens)
Storage
Transport (example hemoglobin)
Motility and contraction
Hormones and neurotransmitters (often smaller fragments of a larger precursor, a prohormone)
Receptors (for hormones and neurotransmitter)
Energy - though the use of protein for energy is not efficient and NH3, released in catabolism of amino acids, is toxic and must be eliminated, sometimes as urea, sometimes as uric acid.
Venoms, toxins

Questions used in 2007 and 2008 relating to this outline

If it were in a polyunsaturated fatty acid, how many bonds does a carbon have?
(a) 1
(b) 2
(c) 3
*(d) 4
(e) 5

Explain "corn is not a good source of essential amino acids."
(a) It does not have all 15 amino acids.
(b) The proteins of corn have been hydrolyzed.
*(c) It does not have all the amino acids required in the human diet.
(d) These are the amino acids used for energy in catabolism.
(e) Corn is missing pyruvate, a very important amino acid.

The dehydration synthesis combines [A] to [B] in fat molecules
(a) [A] carbohydrate; [B] water
(b) [A] one amino acid; [B] another
(c) [A] one amino acid; [B] ammonia
(d) [A] glycogen; [B] glucose
*(e) [A] glycerol; [B] fatty acids

The lipids in membranes have two fatty acids. In place of the third, there is a
(a) glycerol.
(b) steroid.
*(c) polar group.
(d) hydrocarbon.
(e) saturated amino acid.

Lipids store twice as much energy as carbohydrates. How is that energy measured?
*(a) in "calories"
(b) by the length of the chain
(c) by tonicity (hypertonic, isotonic, hypotonic)
(d) by the first law of thermodynamics
(e) by oxidation - reduction

What is considered bulk or fiber for humans but can be used for energy by termites and cattle?
*(a) cellulose
(b) those amino acids that are not essential
(c) disaccharides
(d) long chain fatty acids
(e) It depends on whether the humans in question are lactose intolerant.

What kind of molecule is octane?
(a) a monosaccharide
*(b) a hydrocarbon
(c) glycogen
(d) a steroid
(e) a polypeptide

What kind of molecule is ribose?
*(a) a pentose
(b) an enzyme
(c) chitin
(d) a polysaccharide
(e) an anabolic steroid

Which of the following is NOT an organic molecule?
A) a polypeptide
B) nucleic acid
C) cellulose
*D H2O
E) a monounsaturated fatty acid

Macromolecules are synthesized by removing (what?) from the building blocks?
A) carbon.
B) covalent bonds.
*C) water.
D) oxygen.
E) peptides.

Which of the following correctly matches an organic polymer with its respective monomers?
*A) protein and amino acids
B) carbohydrates and polysaccharides
C) hydrocarbon and monosaccharides
D) polar phospholipid and steroids
E) glycerol and glycogen

The fiber in your diet is really
A) a polypeptide.
B) a polyunsaturated fatty acid.
C) starch.
D) keratin, a structural protein.
*E) a polysaccharide.

In a biological membrane, the phospholipids are arranged with the fatty acid chains facing the interior of the membrane. As a result, the interior of the membrane is
*A) hydrophobic.
B) hydrophilic.
C) charged.
D) polar.
E) filled with water.

When hemoglobin is shown as two alpha chains linked to two beta chains, this represents which level of protein organization?
A) glycosylation
B) posttranslational modifications
C) primary structure
*D) quaternary structure
E) phosphorylation

What type of chemical reaction results in the breakdown of organic polymers into their respective subunits?
A) dehydration
B) oxidation
C) reduction
D) ionization
*E) hydrolysis

Where is glycogen stored in vertebrate animals?
A) brain and kidneys
*B) liver and muscles
C) heart and bones
D) pancreas and blood
E) adipose tissue

The group of biological molecules most diverse in structure is
A) disaccharides.
B) lipids.
*C) proteins.
D) polyunsaturated fatty acids
E) steroids


Questions used in 2002 relating to this outline (and other outlines)

One reason that membrane lipids are arranged the way they are is because of
(a) essential amino acids.
(b) ionic bonds.
*(c) hydrophobic fatty acids.
(d) hydrolysis of bonds.
(e) the half life.

Which would have the greatest potential for variability?
(a) a nucleotide 3 base pairs long
*(b) a peptide 3 amino acids long
(c) a hydrocarbon 3 carbons long
(d) a glycogen chain 3 glucose molecules long
(e) ATP

Those amino acids your metabolism cannot synthesize from other amino acids are called
(a) polyunsaturated.
(b) isotopes.
(c) vital.
(d) exerogonic.
*(e) essential.

Certain chemical modifications of a protein are called "post-translational."
(a) Post-translational modifications include "high" levels of structural organization such as alpha helix vs. beta pleated sheet.
(b) "Post-translational" would be the term applied to the association of two alpha subunits and two beta subunits in hemoglobin.
(c) "Post-translational" refers to the sequence of amino acids coded in that protein's "gene" (DNA coding sequence).
(d) For a protein to become an antigen (a non-self protein), it must be modified post-translationally.
*(e) "Post-translational" is after the manufacture of protein from a template of mRNA.

Steroids are
(a) hydrophilic.
(b) hydrocarbons.
(c) carbohydrates.
(d) triglycerides.
*(e) lipids.

In terms of biological reactions, what is the opposite of dehydration synthesis?
(a) transcription
(b) anabolic metabolism
(c) entropy
(d) photosynthesis
*(e) hydrolysis

Which does NOT have nitrogen in it?
(a) deoxyribonucleic acid
(b) chitin
*(c) starch
(d) protein
(e) urea

Kilocalories, those "calories" you count when you are dieting, are a measurement of
(a) water content of food and drink you consume.
(b) amino acid content of food.
*(c) energy available in food.
(d) relative fat content of food.
(e) relative carbohydrate content of food.

People with type I diabetes mellitus need to inject insulin
(a) because they have a mutation that puts valine in the 6th amino acid position of the beta chain of hemoglobin.
*(b) that is a protein hormone.
(c) because it is an enzyme used in digestion.
(d) to replace the missing gonadal steroids.
(e) to activate the sodium-potassium pump.

Enzymes are indicated by the suffix
(a) -ose.
*(b) -ase.
(c) -eic.
(d) -some.
(e) -karyote.

What type of molecule is cellulose?
(a) triglyceride
(b) nucleic acid
(c) polypeptide
(d) polyunsaturated fatty acid
*(e) carbohydrate

Vegetable oils would be higher (than animal fats) in
*(a) fatty acids with double bonds.
(b) triglycerides in which each acyl group is saturated with as many -H's as possible.
(c) all essential amino acids.
(d) uric acid.
(e) mutations.

Triglycerides with some double bonds are called
(a) enzymatic.
(b) ionic.
*(c) polyunsaturated.
(d) hydrolytic.
(e) radioactive.

Which does not have sugar in it?
(a) starch
(b) glycoproteins and glycolipids
(c) glycogen
*(d) testosterone
(e) sucrose

Which is not true about hemoglobin?
(a) It contains iron.
(b) It is in red blood cells.
(c) It is altered in sickle cell anemia.
*(d) It is an enzyme that makes DNA from a template of mRNA.
(e) It is a protein used for the transport of oxygen.

Reactions by which amino acids are used for energy, yielding nitrogenous wastes, might be referred to as:
*(a) catabolic.
(b) anabolic.
(c) prokaryotic.
(d) eukaryotic.
(e) autotrophic.

Which is NOT a carbohydrate?
(a) lactose
*(b) cholesterol
(c) glycogen
(d) Cn(H2O)n
(e) chitin

Enzymes function for
(a) motility.
(b) energy storage.
*(c) catalysis.
(d) attacking antigens.
(e) storage of hereditary information.

The liver bile salts that are secreted into the intestines are most closely related to
(a) cellulose.
(b) membrane glycolipids.
(c) ATP.
*(d) cholesterol.
(e) antibodies.

About how many different amino acids are used by living things?
(a) 10
*(b) 20
(c) 40
(d) 64
(e) 100

Arrangement of membrane lipids depends largely on
*(a) polar and hydrophobic portions of the molecules.
(b) ions.
(c) collagen.
(d) hydrolysis.
(e) radioactivity.

The term "unsaturated," as in "polyunsaturated" refers to
(a) whether all of the essential amino acids are there.
(b) whether an electron is missing.
(c) whether the third nucleotide in the codon is required to specify the amino acid.
(d) whether an element has an extra neutron.
*(e) whether there are double bonds.


This page was last revised 6/17/09

**The cell lecture

Amoebas are very small
Oh ah ee oo there's absolutely no strife
living the timeless life
I don't need a wife
living the timeless life
If I need a friend I just give a wriggle
Split right down the middle
And when I look there's two of me
Both as handsome as can be
Oh here we go slithering, here we go slithering and squelching on
-Incredible string band, A very cellular song

Cell Biology

Assignment
Audesirk, Audesirk & Byers Chapter 4

Today's musical selection
Five blobs - The blob

Figure E42a
Euglena complex Eukaryotic cell - self sufficient, swim, see, photosynthesize

Figure 4-20
Prokaryote

Figure 4-3
Eukaryote

Figure E42c
Protozoan (Paramecium)
vs. Metazoan complex, starts as 1 cell.

Figure 4-10
divide (Mitoses) - daughter cells
become specialized

control of gene expression (in multicellular organism):
(1) different genes turned on in different cells (and at different times)
(2) ALL CELLS HAVE SAME GENES - CELLS DIFFERENT BY WHICH GENES ARE TURNED ON
(3) but this can be fairly permanent, developmental change in gene regulation

Figure 4-1
Microscopy:
gives relative sizes and emphasizes the importance of light and electron microscopy.

Dyes (that absorb light) are used to highlight substructures in cells. Consider, for instance, the word "chromosome" which translates to "colored body."

Similarly, electron dense materials, heavy metals like osmium, uranium and lead create an electron density in the EM.

Since I have done some EM, I offer these pictures to give you a feeling of how EM is done. Sections are cut with an ultramicrotome using a diamond knife and sections, floated onto water are picked up on small copper grids. The grid is put into an evacuated column in the EM (like Figure E41c), and, at low magnification, a ribbon of sections can be seen.

Figure. 4-2
The cell membrane is a selective barrier to polar, charged, hydrophilic molecules and ions. These need to be pumped at the expense of energy or come through specific channels (pore molecules) through the membrane (more later in membrane coverage).

Eukaryotic cells have specific little bodies that are the small cell parallel of organs in the body, and hence they are called "organelles."

Figure 4-4
plant cell, note cell wall, plasmodesmata, chloroplasts and large vacuole.

Figure 4-3 (again)
animal cell. Below, we will go through the following structures one at a time: nucleus, endoplasmic reticulum (rough and smooth), Golgi apparatus, flagellum

Figure 4-9a
Nucleus - double envelope with pores

Figure 4-12
Ribosomes & RER (rough endoplasmic reticulum) where mRNA is translated into protein, "rough" describing the ribosomes that can be seen in the electron microscope. Also, here is an EM from my work showing RER.

Figure 4-12 (continued)
There is also smooth ER where reactions other than protein synthesis take place, such as steroid hormone synthesis, detoxification of substances in liver. Liver hepatocytes detoxify. Barbiturates induce an increase in the "microsomal fraction," smooth ER as seen after grinding and spinning down in a centriguge tube

Figure 4-11
Also free ribosomes and polysomes in the cytoplasm that make proteins that go to different places.
Protein synthesis - goes at 10 amino acids per second

Figure 4-13
Golgi apparatus receives vesicles from ER (at cis face) and send secretory products that bleb off (from trans side) reactions after protein synthesis (post-translational modification of proteins) take place in Golgi complex.

Figure 4-14
It is very interesting to consider the different routings for different proteins in the cell.
this figure ("sidedness of the plasma membrane") reminds us that inside the ER, Golgi complex, or vesicle is outside the cell, much like inside the gut is outside the body.

FigureE4-2d
Figure 4-17
Mitochondria has a inner and outer membranes, the inner one with shelves called cristae.
The function of the mitochondrion in ATP production

Theory that mitochondria (and chloroplasts), with their double membranes, are evolved from prokaryotes, engulfed into eukaryotic cells; They have some genes.

Also mitochondria are intimastely involved in programmed cell death (apoptosis)

Figure 4-18
chloroplast with 2 membranes plus granum with thylakoid membranes, frets and stroma. Note that the pigmernts for photosynthesis, in order to be absorbed by light, are deployed in multiple layers of membranes.

Figure 4-15
Lysosomes, need to introduce phagocytosis (phag - eat as in hyperphagic, eating too much, or bacteriophage, a virus that infects bacteria)
Lysosomes merge and digest.
This also applies to autophagy, where cell eats itself in a process of turnover of its components.
Here is a picture from my own work of lysosomes merging with recycled membranes in the Drosophila visual receptor,

Figure 4-7
Microtubules
flagella and cilia - "9 + 2" arrangement
Paramecia swimming cilia - beat reverses when bump

Figure 4-8
sperm flagella, cilia to clear mucus from trachea

Figure 4-6
Microfilaments
(will be covered in muscle lectures)
also many other functions, streaming and anchoring of cytoplasm

Questions used in 2007 and 2008 relating to this outline

Posttranslational modifications are changes that are made to
(a) phage.
(b) cells when they are being prepared for microscopy.
(c) bacterial DNA.
(d) mitochondria.
*(e) proteins.

The Golgi apparatus receives vesicles from
(a) chromosomes.
(b) the nucleolus.
*(c) the rough endoplasmic reticulum.
(d) the cell wall.
(e) autophagy.

To "attack" antigens, an antibody
(a) uses phagocytosis.
(b) injects its RNA into the cell.
(c) must be polyunsaturated
(d) must reside within the lysosome.
*(e) is put out of the cell by exocytosis.

The primary structure of a protein
(a) depends on whether it is a "self" vs. a "non-self" protein.
(b) has to do with whether there is an alpha helix or a beta sheet.
*(c) depends on the sequence of amino acids.
(d) depends on glycosylation.
(e) is exemplified by the alpha and beta chains in hemoglobin.

ATP, is made
(a) by chopping out fragments from a protein.
*(b) in cytoplasm and mitochondria.
(c) during apotosis.
(d) by plasmids.
(e) by smooth endoplasmic reticulum.

Euglena
(a) have a cell wall made of chitin.
(b) are metazoans with different genes active in different cells of the body.
(c) are so small that they can only be seen in the electron microscope.
*(d) have photosynthesis.
(e) are prokaryotes.

Mitochondria and chloroplasts are thought to have originated about 1.5 billion years ago
(a) when the microsomal fraction assembled into the smooth endoplasmic reticulum.
(b) as vesicles that blebbed off of the Golgi apparatus.
*(c) when prokaryotes became engulfed into the primordial eukaryotic cell.
(d) because of a mass extinction.
(e) because of genetic drift.

Ribosomes exist as free ribosomes, polysomes, and
(a) attached to the basal body.
(b) attached to the Golgi complex.
(c) attached to the chromosomes.
*(d) attached to the rough endoplasmic reticulum.
(e) in the spindle apparatus.

In phagocytosis, a food vacuole (endosome) merges with
*(a) a lysosome.
(b) a cilium.
(c) a microfilament.
(d) plasmodesmata.
(e) a nephridium.

Ribosomes are the site of synthesis of
A) DNA.
B) phagocytosis.
C) ATP.
D) nucleoli.
*E) proteins.

Which of the following is associated with rough endoplasmic reticulum?
A) chlorophyll
*B) ribosomes
C) cholesterol
D) microtubules
E) mitosis

What is not characteristic of a prokaryotic cell?
A) a cell membrane
*B) a nuclear membrane
C) a cell wall
D) plasmids
E) DNA

Receptors are membrane proteins that would be synthesized on ribosomes
*A) on the rough endoplasmic reticulum
B) on the smooth endoplasmic reticulum
C) on the Golgi complex
D) in the chloroplast
E) in the nucleus

Which organelle does one expect to be most abundant in cells that need lots of biological energy like cardiac muscle cells?
A) vacuoles
B) lysosomes
C) Golgi complexes
D) smooth ER
*E) mitochondria

If all the lysosomes within a cell suddenly ruptured, what could occur?
A) If it were a prokaryotic cell, it would become a eukaryotic cell.
B) If it were a Paramecium, it would swim backwards.
*C) The macromolecules in the cell cytoplasm would be broken down.
D) Antibody proteins would be exocytosed.
E) Proteins would be translated from DNA in vesicles.

Cells that primarily produce steroid hormones, as well as liver cells that destroy toxins, have large quantities of
A) apoptosis.
*B) smooth endoplasmic reticulum.
C) cell walls.
D) heavy metals.
E) flagella

The Golgi packages materials into ________ for transport or exocytosis.
A) cilia
B) plasmids
*C) vesicles
D) vacuoles
E) nucleoli

Which organelle would a white blood cell use to destroy a bacterium it has phagocytosed?
A) nucleus
B) mitochondrion
*C) lysosome
D) polysome
E) flagellum

Which order describes the flow between endoplasmic reticulum (ER), exocytotic vesicles, and Golgi apparatus in the export of protein from the cell?
A) From Golgi to ER to vesicle.
*B) From ER to Golgi to vesicles.
C) From vesicles to Golgi to ER.
D) From Golgi to vesicle to ER.
E) From vesicles to ER to Golgi.

Questions used in 2002 relating to this outline (and other outlines)

Ribosomes might be situated (A-where?) and serve (B-what function?).
(a) A in the nucleus; B to store genetic information.
(b) A in the Golgi apparatus; B to deliver energy.
*(c) A in the rough endoplasmic reticulum; B to synthesize proteins.
(d) A in the plasmalemma; B to mediate transcription.
(e) A in the desmosome; B to carry the genetic code for each protein.

Lysosomes would function to
(a) make glucose from CO2 and H2O using energy from light.
(b) modify proteins coming from the endoplasmic reticulum.
(c) allow cells to move ("swim").
*(d) break down membrane-enclosed cellular waste or food.
(e) carry oxygen from the lungs to the tissues.

In which cellular organelle is most of the ATP produced from thorough glucose catabolism?
(a) nucleus
(b) rough endoplasmic reticulum
*(c) mitochondrion
(d) flagellum
(e) chloroplast

If a biochemist grinds up liver and isolates microsomes as fraction in the centrifuge tube, what would this organelle with enzymes for detoxifying alcohol, drugs or toxins, be as seen in an electron microscope?
*(a) smooth endoplasmic reticulum
(b) tight junction
(c) nuclear envelope
(d) microtubules
(e) contractile vacuole

When you see dark areas in transmission electron microscopy or what appear to be membrane proteins in freeze-fracture, you are actually seeing
(a) colored dyes such as those that make chromosomes to appear as colored bodies.
*(b) heavy metals such as osmium, lead, uranium and platinum.
(c) individual molecules.
(d) the effects of radioactive isotopes.
(e) covalent and ionic bonds.


This page was last revised 6/18/09

**The membrane lecture

MEMBRANES

Assignment
Audesirk, Audesirk & Byers Chapter 5

Today's musical selection
Ray Charles America the Beautiful

Lipid biochemistry:

Figure 5-10
Get a good source of membranes: red blood cells (erythrocytes) from adult human have only plasmalemma. Gorter and Grendel showed in1925 that there was enough lipid to make two layers.
Put red blood cells into distilled water, they burst from hyposmotic shock and become only "ghosts" - membrane only.

Membrane structure

Figure 5-3
shows hydrophobic vs hydrophilic aspect of polar phospholipid
bilayer (Davson-Danielli)

Figure 5-2
shows the chemical structure of a polar phospholipid)

Figure 5-1
Fluid mosaic Singer and Nicolson
Proteins (channels, pumps, receptors, etc.) among lipids

Figure 5-4
Double bonds make more fluid, cholesterol makes less fluid.

Techniques to study membranes

Freeze fracture EM. Membrane is ripped in half, and membrane proteins are shadowed.

Picture I made freeze fracture replicas with this apparatus. Specimen is prepared, frozen to liquid nitrogen temperature, put inside a vacuum, smashed with a razor, blasted from an angle with a platinum gun (to shadow protein with electron dense metal), blasted from above with a carbon gun (to hold replica together), then the tissue is dissolved away.

Here, from my research, is an example of how things look. Picture shows visual membranes in Drosophila. High vitamin A has membranes full of protein (rhodopsin) while vitamin A deprivation eliminates this protein.

Membrane lipid types

Membrane lipids are composed of:
(1) Phospholipids such as phosphatidylcholine (lecithin)
I did some research on the phospholipids of the Drosophila head. Using radioactively lbeled phosphate, many different phospholipids are visualized after they have been separated on a TLC (thin layer chromatography) plate.
Amphipathic
(2) Cholesterol
(3) Glycolipids such as one that accumulates in Tay-Sachs, a hereditary lysosomal storage disease,1/30 Am. Jews carry, recessive, fatal at 6 mo - 5 yr
The sugar groups of glycoproteins and glycolipids are on the outside of the membrane.

Signal transduction

It used to be thought that lipids just sit there. In the 1980's it became clear that they turn over metabolically and that some products of membrane lipid turnover are important mediators of intracellular signalling. This is very fundamental and will come up repeatedly in biology.


How do molecules get across the membrane?

Diffusion
Lipid makes a barrier to anything polar
(steroid hormones can go in)
Channels (for ions, electrical conductances)

Figure 5-12
how pump molecule uses ATP to make sodium and potassium gradients.

Bulk transport

Figure 5-15
phagocytosis - cell eating
pinocytosis - cell drinking

Figure 5-16
Exocytosis

Figure 5-14
receptor mediated endocytosis - clathrin coated

Figure 5-19
Also holes in membranes from one cell to another are important:
(1) Gap junctions (animals)
(2) Plasmodesmata (plants)

shows some other functions of membrane proteins

(1) in addition to transport,
(2) many enzymes are on the membrane
(3) receptors for hormones, neurotransmitters and developmental signals are on the membrane.

Figure 5-18
(4) cells are joined by proteins
(5) cells communicate by proteins
(6) cells hook to extracellular proteins by proteins

Questions used in 2007 and 2008 relating to this outline

A red blood cell ghost was used to study
(a) lysosomal storage diseases.
(b) nuclei.
*(c) membranes.
(d) the genetic code.
(e) the action potential.

A TLC (thin layer chromatography) plate could be used to
(a) model continental drift.
(b) allow Cl- (chloride ions) to pass out of the cell.
(c) demonstrate phagocytosis.
(d) visualize proteins in a carbon-platinum replica of the membrane.
*(e) separate membrane lipids chemically.

Clathrin coated pits are part of what process?
(a) meiosis
(b) apoptosis
(c) hydrolysis
*(d) endocytosis
(e) transcription

It would take energy in the form of ATP to transport Ca2+ ions from [A] to [B].
(a) [A] coated pit; [B] coated vesicle
*(b) [A] inside the cell; [B] outside the cell
(c) [A] microfilament; [B] microtubule
(d) [A] omega figure; [B] coated pit
(e) [A] nucleus; [B] rough endoplasmic reticulum

The function of a gap junction is
(a) to hold cells together.
*(b) allow confluence of cytoplasm of adjacent cells.
(c) receptor mediated endocytosis.
(d) to allow a white blood cell to "eat" bacteria.
(e) to make the plant cell wall permeable.

Pseudopods might be used by Amoebae to eat Paramecia by a process called
(a) exocytosis.
(b) phosphorylation
(c) hydrophobicity.
(d) autoradiography.
*(e) phagocytosis.

Which is true about glycolipids?
(a) They are the rigid motile elements of cilia and flagella.
(b) They are the universal currency of biological energy.
(c) They are phosphorylated peptides.
*(d) They accumulate in victims of Tay-Sachs disease.
(e) Phosphatidylcholine is the predominant type.

Tight junctions are used
*(a) to keep layers of cells from leaking.
(b) to hold the tRNA to the DNA.
(c) in the Kreb's cycle.
(d) in flagella.
(e) to coat vesicles used in bulk transport.

The central concept of the fluid mosaic model is that
*(a) there is enough lipid in membranes to make two layers.
(b) mRNA can pass freely from the cytoplasm to the nucleus.
(c) ions can pass through the hydrophobic layer.
(d) 38 pyruvates are made from one glycogen.
(e) the cell membrane is the only membrane in eukaryotic cells.

Phospholipids
*A) are found in cell membranes.
B) are completely hydrophilic.
C) are completely hydrophobic.
D) are made in the mitochondria.
E) allow water and ions to move from outside the cell into the cell.

In general, which of the following is largely responsible for moving substances across the plasma membrane?
A) the bilayer of lipids
B) carbohydrates
*C) proteins
D) nucleic acids
E) cytoskeleton

Which of the following would not be found in a membrane?
*A) cellulose
B) cholesterol
C) phospholipid
D) channel protein
E) receptor protein

Glucose gets into the cell
A) by drifting through the lipid bilayer like steroid hormones do.
*B) with the aid of transport proteins.
C) only when ADP plus phosphate is converted into ATP.
D) with the help of a protein named clathrin.
E) by exocytosis.

What does a cell use exocytosis for?
A) to move away from danger
B) to create identical "daughter" cells
C) to keep a layer of cells from leaking (between the cells) like a sieve.
D) to move bad cholesterol (LDL) into the cell
*E) to release substances from the cell

What is not characteristic of a prokaryotic cell?
A) a cell membrane
*B) a nuclear membrane
C) a cell wall
D) plasmids
E) DNA

Receptors are membrane proteins that would be synthesized on ribosomes
*A) on the rough endoplasmic reticulum
B) on the smooth endoplasmic reticulum
C) on the Golgi complex
D) in the chloroplast
E) in the nucleus

The feature that creates a barrier to the movement of ions across the membrane is
A) channel proteins
B) cellulose
C) lactase
*D) fatty acids
E) vitamin E

How are plasma membranes BEST described?
A) a double layer of phospholipid molecules with hydrophobic tails directed toward the cytoplasm of the cell
B) a single layer of phospholipid molecules with water molecules attached along one side
C) a double layer of phospholipid molecules with hydrophilic heads directed toward each other
*D) a double layer of phospholipid molecules with hydrophobic tails oriented toward each other
E) a single layer of phospholipids with tails pointed to the inside of the cell

Within the fluid mosaic of a plasma membrane, what is the role of proteins?
A) They bind estrogen and testosterone since these molecules cannot cross the membrane.
B) They are the site of ADP formation.
C) They cause arteriosclerosis.
D) They are the site of transcription.
*E) They serve as channels and receptors and for transport.

The dominant type of lipid found in cell membranes is
A) the ribosome.
B) vitamin A.
*C) phospholipid.
D) a glycoprotein.
E) the type that accumulates in Tay-Sach's Disease.

Glucose gets into the cell
A) through coated pits
*B) with the aid of proteins.
C) when ADP plus phosphate is converted into ATP.
D) with the help of clathrin.
E) by exocytosis.

If red blood cells are taken from the body and placed into a hypotonic solution (like distilled water), what happens to the cells?
*A) The cells swell and burst because water moves into the cells.
B) The cells shrivel up because water leaves the cells.
C) Gap junctions will form.
D) "Good cholesterol" (LDL) will be transported.
E) Desmosomes and tight junctions will form.

Sometimes, the cytoplasm of a cell will have too many calcium (Ca2+) ions. How does the cell re-establish its normal calcium homeostasis?
A) by receptor-mediated endocytosis
B) phagocytosis
C) osmosis
D) through plasmodesmata
*E) active transport

The electric signal goes from one myocardial (heart muscle) cell to the next through
A) coated pits.
B) desmosomes.
*C) gap junctions.
D) glycolipids.
E) active transporters that utilize ATP.


Questions used in 2002 relating to this outline (and other outlines)

One reason that membrane lipids are arranged the way they are is because of
(a) essential amino acids.
(b) ionic bonds.
*(c) hydrophobic fatty acids.
(d) hydrolysis of bonds.
(e) the half life.

A cell's membrane consists principally of two layers of
(a) hydrocarbon.
(b) disaccharides.
(c) cellulose.
*(d) lipid.
(e) collagen.

This page was last revised 7/8/08

**The metabolism lecture

Any plant or man who dies
adds to Nature's compost heap
becomes the manure without which
nothing could grow nothing could be created
Death is simply part of the process
Every death even the cruellest death
Drowns in the total indifference of Nature
Nature herself would watch unmoved
if we destroyed the entire human race
I hate Nature
-Peter Weiss ... Marat ...Sade 1965

Assignment
Audesirk, Audesirk & Byers Chapters 6 & 8

Today's musical selection
Jay and the Americans - Only in America

Metabolism

Metabolism is the general term for two kinds of reactions:
(1) catabolic reactions (breakdown)
and
(2) anabolic reactions (constructive)

Energy saved mostly through photosynthesis (Chapter 7, does not fit in this one semester)
released through "respiration" ("respiration" applies to breathing and cellularrespiration)

Figure 6-8
ADP plus phosphate <-> ATP involved in storage and release of energy
ATP made of Adenine, ribose and 3 phosphates, energy stored in 3rd phosphate bond

Figure 6-5
"Burning" glucose


Figure 6-3
substrates (reactants)-> products

Figure 6-13
Simplified metabolic pathways
Reminder: enzymes are named with suffix "-ase."

Figure 6-14
overcome energy of activation - catalysts - enzymes

Energy

Energy - kinetic and potential (later, discussing bioelectricity, potential will also be Volts)
First law of thermodynamics - energy of universe is constant
Second law - things become more disordered
Humanities: a 10 page science fiction story Isaac Asimov, The last Question in which it is asked what happens after the universe is dissipated.)
Energy flows as entropy increases.
In general, heat is waste and not useful.
BTU's (British thermal units, which can be converted to calories) imply that energy and heat are related.
Heat stored in energies of covalent bonds in kcal / mol
Free energy can be used for work = what is stored in bonds minus what is wasted as heat

Figure 6-3
Exerogonic,
e.g. cellular respiration C6H12O6 -> 6CO2 +6H2O + energy
the free energy is 686 kcal/mol

ATP

Figure 8-10
Store glucose energy into ATP
ATP to ADP
38 of them generated when respiration is complete
40.3% efficient, the rest is heat, usually considered as waste but useful in temperature regulation in warm blooded animals, homoiotherms, homeotherms.

It is easy to mistakenly think that energy use is only by muscles. However, a lot of the body's energy is used in transport and in reactions. ATP transfers its 3rd phosphate to molecules and the phosphate is then released as inorganic phosphate to be eventually added to ADP to make ATP.

Figure 6-19
Optimum tempreature for human enzyme may be near 37oC, body temperature. For a thermophilic bacterium, it may be very high, useful in PCR (polymerase chain reaction). Also, optimum pH for pepsin (proteolytic enzyme in stomach) is acidic while for amylase (polysaccharide enzyme in saliva) is slightly basic.

Biological Energy

Reminder - "count" "calories"= kcal
2000 per day for a sedentary woman
Important that we do not lose calories (through urine or feces) except through urine in untreated diabetes.

Figure (Chapter 6 opener)
(also Chapter 6 case study, energy unleashed, p. 101 and revisited, p. 113)
Marathon - 3000 Cal aerobic. 100 yd dash -anaerobic

Figure 6-10
ATP's 3rd phosphate bond has lots of energy, and breaking that bond releases the energy, but interestingly, how cells use energy is to put that phosphate from ATP onto a molecule like an ion pump or muscle's myosin molecule.

We get our energy mostly from (1) glucose, (2) glycogen (glyco-sugar, gen-give rise to) in muscle for use in muscle and in liver for glucose release to blood, (3) amino acids (with NH3 as waste), or (4) fat (mostly fatty acids are chopped down 2 carbons at a time to give acetic acid into acetyl CoA in the Kreb's cycle).

photosynthesis to make glucose, cellular respiration to release energy
Reaction [for glucose, C6(H2O)6]: C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O

Overview

Figure 8-10
Overall, 1 glucose can give up to 38 ATP's, a few from glycolysis and the rest from the mitochondrion

Glycolysis

Figure 8-2
glycolysis
NAD+ plus 2 H <-> NADH in oxidation - reduction reactions as a way to carry electrons.
lose electrons - oxidation (NAD+ is oxidized)
nicotinamide adenine dinucleotide
add electrons - reduction (NADH is reduced)

Figure 8-1
Glycolysis is a compound word
glyco-sugar,
lysis-splitting.
Glucose is split into 2 pyruvic acids
Use 2 ATP's make 4, net 2 make 2 NADH's plus 2 H+'s, the H+'s come from from "sugar"

Anaerobic glycolysis

Figure 8-4
without oxygen, make ethanol or lactate (lactic acid).
Anaerobic glycolysis is used to deliver ATP quickly but wastefully (squandering glucose).
Make ATP's but need to regenerate NAD+ from NADH] to make.
Lactic acid contributes to fatigue in muscle and oxygen debt, and the liver eventually reconverts.
Anaerobic cellular "respiration" is needed in times of extreme exertion because the heart (cardiac output) is the limiting factor in delivery of oxygen to muscle.
Lactic acid is also made by bacteria in yogurt, sour cream, and cheese.

Krebs cycle

Figure 8-9
Pyruvic acids generate 2 acetic acids, become Acetyl CoA's.
Kreb's cycle = citric acid cycle = TCA (tricarboxylic acid cycle)
Takes place in the mitochondrion
A few ATP's are made plus NADH's and FADH2 are generated
Notice that CO2 is generated here.

The1953 Nobel prize in Physiology and Medicine was divided equally, one half awarded to: SIR HANS ADOLF KREBS for his discovery of the citric acid cycle and the other half to: FRITZ ALBERT LIPMANN for his discovery of co-enzyme A and its importance for intermediary metabolism.

Electron transport

Figure 8-8
sugar-H2 + NAD+ -> (DEHYDROGENASE) "sugar" + NADH + H+
(in other words, H is split to H+ and e-)
Electron transport and oxidative phosphorylation use oxygen
cytochromes - these are iron - containing pigments (iron is in the form of heme)
Iron is not abundant, but it is important in biology.
NADH and FADH2 give electrons to cytochromes and oxygen

Protons pumped, then flow down gradient making ATP's.
Something like an ion pump (we will cover that a lot later in the semester) in reverse is how most ATP is made, H+ (pH, proton) gradient runs through that molecule, like water running through turbines generating electricity, to generate electricity

Questions used in 2007 and 2008 relating to this outline

"Thermophilic" is a term applied to
(a) warm blooded animals.
(b) enzymes like pepsin that function well in stomach acid.
(c) entropy.
*(d) bacteria whose enzymes are used in PCR (the polymerase chain reaction).
(e) counting calories.

Hydrogen ions are pumped across a membrane, then, when they run back, they generate ATP. This is a simplified statement of
(a) thermodynamics.
(b) anaerobic glycolysis.
(c) the role of lactic acid in fatigue.
*(d) the electron transport chain.
(e) translation.

686 kcal per mole describes
(a) acetyl CoA.
*(b) energy from glucose breakdown.
(c) NAD+ and NADH.
(d) homeotherms.
(e) urea formation resulting from amino acid catabolism.

"Exerogonic" is a term applied to
(a) cell drinking.
(b) the "central dogma" of cell biology.
*(c) reactions.
(d) protein synthesis.
(e) apoptosis.

About what fraction of ATP is made by glycolysis when respiration is aerobic?
*(a) 1/16
(b) 1/4
(c) 1/2
(d) 3/4
(e) 15/16

In the delivery of biological energy
(a) sucrase gets used up when it generates glucose and fructose.
(b) the mitochondria use CO2 to produce O2.
(c) heat and entropy are captured and stored in ADP.
(d) glucose is taken into muscle (when insulin is low) where it is converted into triglycerides.
*(e) phosphate is typically transferred from ATP to another molecule.

Questions used in 2002 relating to this outline (and other outlines)

In the delivery of biological energy
(a) sucrase gets used up when it generates glucose and fructose.
*(b) phosphate is typically transferred from ATP to another molecule.
(c) heat and entropy are captured and stored in ADP.
(d) the end-product feeds back to inhibit the rate-limiting enzyme.
(e) the mitochondria use CO2 to produce O2

A reaction that requires oxygen is called
(a) autotrophic.
(b) fermentation.
(c) anabolic.
(d) reduction.
*(e) aerobic.

Kilocalories, those "calories" you count when you are dieting, are a measurement of
(a) water content of food and drink you consume.
(b) amino acid content of food.
*(c) energy available in food.
(d) relative fat content of food.
(e) relative carbohydrate content of food.

The fundamental function of aerobic respiration in cells is
(a) production of glucose.
*(b) the release of energy.
(c) storage of entropy.
(d) the replication of DNA.
(e) biosynthesis of triglycerides.

In which cellular organelle is most of the ATP produced from thorough glucose catabolism?
(a) nucleus
(b) rough endoplasmic reticulum
*(c) mitochondrion
(d) flagellum
(e) chloroplast

If animal muscle cells are depleted of sufficient levels of oxygen during use, anaerobic glycolysis will result and pyruvic acid will be converted into
*(a) lactic acid.
(b) carbon dioxide.
(c) glucose.
(d) glycogen.
(e) oxygen.

Energy that is not converted to useful energy is usually given off as
A) radioactivity.
B) ATP.
C) pH.
*D) heat.
E) ethanol.

At the end of glycolysis, the original carbons of the glucose molecule form
A) carbon dioxide.
B) hydrogen ions (H+) plus electrons (e-).
*C) two molecules of pyruvic acid.
D) two fatty acid chains.
E) sucrose.

H+ (hydrogen ions) run across a membrane protein to generate most of the ATP
A) during glycolysis.
B) during fermentation.
C) during the Krebs cycle
D) when pyruvic acid is converted to Acetyl CoA.
*E) in the mitochondrion.

Entropy is a measure of
A) anabolic reactions.
B) enzymes.
C) fermentation.
D) lactic acid.
*E) disorder.

During glycolysis, the net production of ATP is
A) one molecule.
*B) two molecules.
C) 34 molecules.
D) 36 molecules.
E) 38 molecules.

A "high-energy" bond in an ATP molecule is located between
*A) the second and third phosphate groups.
B) acetic acid and acetyl CoA.
C) the cytoplasm and the mitochondrion.
D) the production of CO2 and the production of H2O.
E) pyruvate and lactic acid

Why are enzymes important?
A) They are carbohydrates.
B) They are the basis of the laws of thermodynamics.
C) They are the universal "currency" of energy in biological systems.
*D) They catalyze reactions at body temperature
E) They are only important in the laboratory in PCR (polymerase chain reactions).

When the breakdown of glucose happens with insufficient oxygen,
A) water and carbon dioxide are formed.
B) NH3 is formed.
C) that is when the electron transport chain is used
*D) it is called anaerobic glycolysis.
E) it is called the Krebs cycle

What results if glucose is metabolized under aerobic conditions (the reactions are allowed to go to completion)?
A) Acetic acid comes out of the mitochondrion to become ethanol.
*B) 36 or 38 ATP molecules are made.
C) Oxygen is not used since it is not available.
D) Lactic acid is formed in muscle.
E) Carbon dioxide plus water are converted to glucose.

This page was last revised 6/24/09

**The DNA lecture

DNA - the molecule of heredity

Assignment
Audesirk, Audesirk & Byers Chapter 9, part of Chapter 10 and several figures from other chapters

Today's musical selection
Waltz round the cycle

History

Figure 9-1
It was not until the 1940's that it was proved that DNA was the material of heredity.
(work of Griffith and Avery) S (smooth) bacteria kill mouse, R (rough) not, DNA from S can transform R to make them deadly.

Central dogma

Figure 10-3
One "gene" codes for one "protein"
Central Dogma (of cell biology)
DNA (nucleus, virus) ONE GENE
->transcription->
mRNA (nucleus to cytoplasm in eukaryotic cell)
->translation->
Protein ONE PROTEIN

Figure E19-2a
retrovirus, like HIV, makes DNA from a template of RNA using an enzyme called reverse transcriptase.

Figure 10-2
RNA's: m (messenger), r (ribosomes), t (transfers aa's)

Table 10-1
Nucleic acids: nucleotide = sugar, PO4 & base (no essential nucleic acids)
Sugar (ribose or deoxyribose), phosphate (PO4), base
4 bases in DNA: Adenine, Guanine, Thymine, Cytosine
4 bases in RNA: The same except Uracil instead of Thymine
purines - A & G, pyrimidines - C, T, U

How can DNA lead to so much biological variability?

Two in a row nucleotides in a row would give 4 x 4 = 16 possibilities.
This is < 20, the number of amino acids, so 2 would not be enough for code.
It takes a longer macromolecule of DNA to code for a protein than the protein it codes for.

Table 10-3
(The genetic code)
4 x 4 x 4 - there is a 3 letter word (codon) consisting of 4 letters for each amino acid.
However 4 x 4 x 4 = 64 is more than enough (redundant) and the word for this is degeneracy, in that there are several codes for certain of the amino acids.

DNA has a built in way to reproduce itself accurately...

Figure 9-6
DNA is a double helix, with A across from T and C across from G
this pairing is essential for DNA to reproduce itself.
DNA is quite stable and accurate in its replication.

...and to orchestrate transcription and translation

Figure 10-9
In making RNA, the same pairing applies except that U is across from A.

More detail on DNA replication

Figure E9-7
each strand contains all the information necessary, put into action by each strand being capable of organizing the other strand; but instead of the two strands separating entirely and generating the daughter strand, numerous bubbles form where the parental strand is copied at the replication fork.

5'->3' direction replication fork
enzymes:
DNA helicase and leading strand DNA polymerase
lagging strand:
DNA polymerase makes one piece at a time
DNA ligase puts pieces together

Mutations

Figure 12-29
Sickle-cell anemia

Figure 9-8
DNA is quite stable and accurate in its replication. However, sometimes factors such as chemical mutagens and ionizing radiation cause alterations called mutations. In the fully evolved organism, mutations are usually deliterious, but they can sometimes create an advantage. On the evolutionary time scale, mutations have been the driving force of divergent evolution and adaptive radiation.

Disorder which turns human red blood cells (erythrocytes) sickle shaped (sickle cell anemia) is caused by a mutation substituting Val for Glu at amino acid #6 in the beta chain of hemoglobin. This disorder is high in African-American of equatorial African origin. Homozygous, it is very bad, but heterozygous, it confers resistance to malaria.

Orientation for using microscopes in cell lab (and other labs)

Fig. 1 - Start with the lowest power objective with the stage all the way up
Fig. 2 - Best to use your left hand on the focus knobs...
Fig. 3 - ...so that your right hand is available to move the slide

To find and focus your specimen:
(1) put a landmark, like the edge of the cover slip or a highly stained part of the slide in the light beam
(2) [from the stage up position with the lowest power objective, see above] move the slide's landmark back and forth (right hand) (or up and down) continuously while moving the stage down (left hand)
(3) when the landmark is in focus, find the specimen
(4) the microscope is parfocal, meaning that you can then go to higher power objectives and be reasonably close to focus

Questions used in 2007 and 2008 relating to this outline

In the genetic code, how many different triplets are there?
(a) 3
(b) 4
(c) 16
(d) 20
*(e) 64

What substance from S bacteria convert R bacteria into a form that is lethal to mice?
*(a) DNA
(b) NADH
(c) Glycogen
(d) ATP
(e) Protein

In transcription,
(a) mRNA is used to make protein.
(b) the ribosomes are used.
*(c) DNA is used to make mRNA.
(d) the anticodon is matched to the codon.
(e) RNA is used to make DNA.

HIV (human immunodeficiency virus)
(a) remains outside the cell like a bacteriophage.
(b) is made up of DNA and protein.
(c) is the only virus (or organism) with degeneracy in its genetic code.
(d) works backwards by using anticodons instead of codons.
*(e) uses reverse transcriptase.

How might a complementary vs. a template DNA strand differ?
(a) Across from U would be A.
*(b) Across from A would be T.
(c) Across from C would be C.
(d) Across from G would be glycine.
(e) Across from DNA would be RNA.

Replication forks would be used in conjunction with
*(a) DNA polymerase.
(b) translation.
(c) reverse transcriptase.
(d) sickle cells.
(e) heterozygous mutations.

A ribosome is used to assist in the process of
(a) transcription.
(b) copying DNA into mRNA.
*(c) translation.
(d) conversion of ATP to ADP.
(e) dehydration synthesis.

Transfer RNA (tRNA) is used in the process of
(a) oxidative phosphorylation.
(b) exocytosis.
(c) producing a karyotype.
(d) crossing over.
*(e) translation.

Which is NOT true about HIV (Human Immunodeficiency Virus)?
(a) It goes into the cell it infects.
*(b) It belongs to the kingdom of protista.
(c) Causing AIDS, it preferentially depletes helper T cells.
(d) Its hereditary material is RNA.
(e) Reverse transcriptase is already present.

A ribosome is used to assist in the process of
(a) transcription.
(b) copying DNA into mRNA.
*(c) translation.
(d) conversion of ATP to ADP.
(e) dehydration synthesis.

Transfer RNA (tRNA) is used in the process of
(a) oxidative phosphorylation.
(b) exocytosis.
(c) producing a karyotype.
(d) crossing over.
*(e) translation.

Which is NOT true about HIV (Human Immunodeficiency Virus)?
(a) It goes into the cell it infects.
*(b) It belongs to the kingdom of protista.
(c) Causing AIDS, it preferentially depletes helper T cells.
(d) Its hereditary material is RNA.
(e) Reverse transcriptase is already present.

Because of degeneracy of the DNA code,
A) the HIV retrovirus disobeys central dogma.
B) most mutations are bad.
C) both strands can be used for DNA to reproduce itself, but only one strand can be used to code for a specific protein.
D) it takes four nucleotides in a row to determine one amino acid.
*E) it might be possible to have a mutation in the DNA without changing the protein it codes for.

Which is NOT true about hemoglobin?
A) It contains iron.
B) It is in red blood cells.
C) It is altered in sickle cell anemia.
*D) It is an enzyme that makes DNA from a template of mRNA.
E) It is a protein used for the transport of oxygen.

Which would have the greatest potential for variability?
*A) a peptide 3 amino acids long
B) a nucleotide chain 3 base pairs long
C) a hydrocarbon 3 carbons long
D) a glycogen chain 3 glucose molecules long
E) ATP

What was the main point of Griffith's experiments with pneumonia in mice?
A) A mutation is how the R strain becomes the S strain.
B) DNA was reverse transcribed into RNA using DNA ligase.
C) Protein carries the code for heredity.
D) RNA is translated into DNA.
*E) There is a substance present in dead bacteria that can cause a heritable change in living bacteria.

DNA has
A) A, U, G, and C bases.
B) only purines.
C) anticodons.
*D) C, T, A, and G bases.
E) all 5 bases: A, U, G, T, and C.

The DNA of a certain organism has guanine as 30% of its bases. What percentage of its bases would be adenine?
A) 0%
B) 10%
*C) 20%
D) 30%
E) 40%

For the DNA sequence GCCTAT in the template DNA strand, the sequence found in the complementary DNA strand is
*A) CGGATA.
B) GCCATA.
C) CGGAUA.
D) ATTCGC.
E) GCCTAT.

How does the Watson and Crick model of DNA structure help explain DNA replication?
A) Uracil is always across from Thymine.
*B) Precise base pairing allows the base sequence to be copied.
C) Methionine is the amino acid for the stop codon.
D) Some amino acids are purines and these are mutated to different amino acids, pyrimidines.
E) It doesn't; DNA never replicates.

A stretch of DNA 10 nucleotides long can have how many possible sequences of the four bases?
A) one
B) four
C) ten
D) hundreds
*E) way more than any of the above

Questions used in 2002 relating to this outline (and other outlines)

Which would have the greatest potential for variability?
(a) a nucleotide 3 base pairs long
*(b) a peptide 3 amino acids long
(c) a hydrocarbon 3 carbons long
(d) a glycogen chain 3 glucose molecules long
(e) ATP

Which nucleotide base is used in RNA but not DNA?
(a) cytosine
(b) adenine
(c) thymine
*(d) uracil
(e) guanine

Ribosomes might be situated (A-where?) and serve (B-what function?).
(a) A in the nucleus; B to store genetic information.
(b) A in the Golgi apparatus; B to deliver energy.
*(c) A in the rough endoplasmic reticulum; B to synthesize proteins.
(d) A in the plasmalemma; B to mediate transcription.
(e) A in the desmosome; B to carry the genetic code for each protein.

Making mRNA from a template of DNA is called
(a) respiration.
(b) glycolysis.
(c) motility.
*(d) transcription.
(e) fluorescence.

Because of degeneracy of the DNA code,
(a) the HIV retrovirus disobeys central dogma.
(b) most mutations are bad.
(c) both strands can be used for DNA to reproduce itself, but only one strand can be used to code for a specific protein.
(d) it takes four nucleotides in a row to determine one amino acid.
*(e) it might be possible to have a mutation in the DNA without changing the protein it codes.

Which is a purine base of a nucleotide?
*(a) adenine
(b) ribose
(c) phenylalanine
(d) lactic acid
(e) actin

Which is not true about hemoglobin?
(a) It contains iron.
(b) It is in red blood cells.
(c) It is altered in sickle cell anemia.
*(d) It is an enzyme that makes DNA from a template of mRNA.
(e) It is a protein used for the transport of oxygen.

A ligase would be used in
(a) control of gene transcription.
(b) synthesis of DNA from the hereditary molecule in the HIV (human immunodeficiency virus).
(c) western blotting.
(d) lagging strand replication.
(e) cutting open a plasmid to prepare for cloning a gene.

In the 1940's, Avery and others showed DNA was the important part of smooth bacterial extract that made rough bacteria pathogenic in Griffith's experiment. The phenomenon Griffith demonstrated is called
(a) transformation.
(b) conjugation.
(c) cloning.
(d) hybridization.
(e) operon regulation.

This page was last revised 6/26/09

**The central dogma lecture

Central dogma and proteins

Assignment
Audesirk, Audesirk & Byers Chapter 10

Today's musical selection
Lewis Lee Attack of the killer tomatoes

Central Dogma of cell biology (review)

Figure 10.3
DNA
transcription
RNA
translation
protein
(reverse transctiption, using reverse transcriptase enzyme, in AIDS-causing retrovirus HIV)
As you will eventually see, there is more to it than this, like RNA processing,

Genetic code (partly a review)

Table 10-3
3 letter code for aa's (codons)
Note, with 20 amino acids, and 4 x 4 x 4 = 64 codons, there is redundancy, called "degeneracy."
For instance, (top left) for phenylalanine, code can be UUU or UUC.
(It is interesting to contemplate that if a mutation converted UUU to UUC or vice versa, the amino acid would still be the same.)
There are 3 stop codons
Methionine is the start codon

Study question: Is this code for RNA or DNA?
Answer: RNA (You can tell when you notice that U is one of the four bases specified)

Figure 10-9
combining the information from the last 2 figures, here is a diagram of what nucleotide sequences might be for DNA and RNA and the amino acid sequence would be.
(It is interesting to contemplate that only one of the two DNA strands would work, the "template DNA strand" or the sense strand [the other being "the complementary DNA strand" or the antisense strand])

Example: Hemoglobin

Table 10-4
On the topic of mutations, consider that if CTT changes to CAT, Glu -> Val, the sickle cell anemia mutation.
When one amino acid is changed to another, this is a missense mutation.

Mutations

(1) change base in degenerate 3rd position - no effect
(2) change a base that matters - "missense" - the protein will have a different amino acid
(3) change base so that there is a stop codon - "nonsense" the protein will not be full length
(4) insertion or deletion - many amino acid changes and/or premature stop
To understand this last point, I introduce the expression "open reading frame;" even though you could conceivably start anywhere, only if you start in right place (the right one of 3 nucleotides) for a normal (non-mutant) gene will the reading proceed for a reasonable distance without hitting a stop codon.

Transcription and translation

Figure 10-4a
RNA polymerase makes mRNA
(I'll say more about the "promoter" later)

Figure 10-5
What transcription looks like

Translation
In general, there are 3 RNA's, t (transfer), m (messenger), and r (ribosomal).
(1) Ribosome is the machinery, and it is big.
(2) mRNA codes for the protein.
(3) Many different tRNA's read (by base pairing, using the anticodon) each codon and carry one amino acid to the growing peptide chain.

Figure 10-8 (I will show Fig. 10-8 b, f, and i)
step by step, peptide is elongated, aminoacyl tRNA (tRNA with amino acid hooked to it) brings in amino acid.
eventually, when one of the 3 stop codons is encountered, the protein is released.

Question: What is a gene?

One theoretical answer: The DNA sequence that codes for one protein.
But: In eukaryotes there is way too much DNA.
Explanations:
(1) There are extra stretches of DNA interspersed in the coding sequence.
(That will be one topic we cover here.)
(2) There are places between "genes," some of which regulate the genes because of:

The need for gene regulation

In multicellular eukaryotic organism,
(1) ALL CELLS HAVE SAME GENES
(2) CELLS ARE DIFFERENT BECAUSE OF WHICH GENES ARE EXPRESSED
(but this can be fairly permanent, development gene regulation)

Prokaryote example, the lac operon

Figure 10-10
(relates to fundamental topic of gene regulation) lac operon - genes for enzymes for metabolism of lactose, the disaccharide in milk. When lactose is present, allolactose pulls repressor off of operator so that RNA polymerase can move from promoter to make mRNA for genes (lacZ, lacY and lacA) that code for their respective enzymes (beta-galactosidase, permease and transacetylase, enzymes for lactose metabolism. The bacterium "does not bother" making lactose metabolizing enzymes unless lactose (the sugar in milk) is present. Note that one mRNA is for 3 proteins, never the case in eukaryotes.

The 1965 Nobel Prize was shared by FRANÇOIS JACOB and JACUES MONOD who established the operon model.

Lactose digestion in humans

Box on p. 113
(also reference in digestion chapter
All infants can digest lactose, obviously
There is a racial difference in whether adults have lactase.
Blacks and Asians are likely to be lactose intolerant
Caucasians are usually lactose tolerant
Europeans evolved with dairy husbandry

Eukaryotic gene structure and RNA processing

Figure 10-7
RNA polymerase II makes "pre-mRNA"
methylated G nucleotide - at 5' cap
extra copied after end of gene is not capped, degraded
poly-A tail 100-200 residues of adenylic acid
site shows where end of gene transcription should be.
primary transcript
Exons are spliced together and form the coding sequence, and introns are spliced out.

Question: Is this splicing useful in any way? (other than to get rid of junk DNA)
Answer: Different exons can be spliced together (for instance in different tissues) to make several different proteins from the same gene.

Promoting gene action

Note that there are places "upstream" of the "gene" (coding sequence), the promoter, where transcription factors (proteins) bind to notify RNA polymerase to do its job. Since the 1980's, there has been a lot of interest in "promoter bashing," determining properties of the transcription factors and the DNA sequences they interact with. Here is where many hormones and signaling pathways determine a cell's specifics

Questions used in 2007 and 2008 related to this outline

Ribosomes might be situated (A-where?) and serve (B-what function?).
(a) A in the nucleus; B to store genetic information.
(b) A in the Golgi apparatus; B to deliver energy.
*(c) A in the rough endoplasmic reticulum; B to synthesize proteins.
(d) A in the microsomal fraction; B to mediate transcription.
(e) A in the intercalated disk; B to carry the genetic code for each protein.

A poly-A tail characterizes
(a) the intron.
*(b) mRNA.
(c) the operator.
(d) methionine.
(e) the anticodon.

In eukaryotes, what gets spliced to what?
(a) The promoter to the coding sequence.
(b) The lacZ, LacY and LacA genes.
(c) The template and complementary DNA strands.
(d) Jacob to Monod.
*(e) One exon to another.

An amino acid can be coded for by more than one codon. What is this called?
(a) Heterozygosity
*(b) Degeneracy
(c) Nondisjunction
(d) Translation
(e) Nonsense mutations

The tRNA molecule for which amino acid binds to the start codon during translation?
(a) Tyrosine
(b) Glucose
(c) Arginine
(d) Glycine
*(e) Methionine

Humans only have a fraction of their DNA that codes for proteins. Where is this? (a) in ribosomes
(b) in operators
(c) in promoters
(d) in introns
*(e) in exons

What factor accounts for the variety of cell types in different tissues?
(a) Some cells are homozygous, others are heterozygous.
(b) Different cells have different subsets of genes.
*(c) Different genes are expressed.
(d) Different cells contain different sets of chromosomes.
(e) Some mRNAs are translated; others are not.

The codons on the table for the genetic code are triplets from
(a) the template DNA strand.
(b) the sense DNA strand.
(c) the complementary DNA strand.
*(d) mRNA.
(e) the RNA sequence of ribosomal RNA (rRNA)

What would happen if a codon for an amino acid were mutated into a stop codon?
(a) Lactose intolerance would result.
(b) There would be a missense mutation.
*(c) The growing peptide would be ejected from the ribosome prematurely.
(d) Not much since the change would be in the third base.
(e) People would suffer from sickle cell anemia.

In the lac operon, RNA polymerase would be blocked if (what) were present?
*(a) The repressor.
(b) Introns.
(c) The operator.
(d) The promoter.
(e) Lactose.

DNA polymerase had already duplicated the DNA to make two identical copies of all the genetic material. Where are these two copies?
(a) in the two kinetochores
(b) in the two centrioles
*(c) in the two sister chromatids
(d) in the two homologues
(e) one in the autosome, the other in the sex chromosome
Which of the following is TRUE of the genetic information in the cells of your body?
A) Different kinds of cells contain different genetic information.
B) Each type of cell contains only the genetic information it needs to be that type of cell.
*C) The genetic information in all somatic cells (this excludes gametes) is identical.
D) Growth, development, and differentiation result from mutations in DNA.
E) Meiosis ensures that each somatic cell will be different.

The number of consecutive mRNA bases needed to specify one amino acid is
*A) 3.
B) 4.
C) 20.
D) 64.
E) many more than any of the above numbers .

"Val is substituted in place of Glu in the sixth position of the beta chain of hemoglobin."
A) This a nonsense mutation.
B) This could only happen if the deletion of one base pair offset the open reading frame.
C) This is because of regulation of the lac operon.
*D) This is a result of a mutation in DNA that causes sickle cell anemia.
E) This is because of degeneracy in the genetic code.

The number of different possible codons is
A) 3.
B) 4.
C) 20.
*D) 64.
E) way higher than any of the above numbers.

"Splicing" is a term applied to
A) the polycistronic (multi-gene) mRNA of bacteria.
*B) putting together exons to make mRNA from pre-mRNA.
C) the release of mRNA from DNA when the RNA polymerase reaches the end of the gene.
D) what happens at the ribosome when a stop codon is encountered.
E) regulating which genes are expressed in different cells.

What would happen if the complementary DNA strand were transcribed into mRNA instead of the template strand?
A) It seems to me it ought to work if RNA polymerase just went the other way along the DNA double helix.
B) That is precisely what happens in the checkpoint letting cells in G0 go on into prophase.
C) That is precisely what the cause of missense mutations is.
D) Lactose would be bound to the repressor.
*E) A ridiculous mRNA would be made and the translation machinery would encounter stop codons.

All of the following occur during DNA replication EXCEPT
A) separation of parental DNA strands.
B) use of parental DNA as a template.
*C) translation into RNA.
D) synthesis of a new strand to make double-stranded DNA.
E) use of DNA polymerase.

When comparing DNA and RNA, we find
A) RNA has the sugar deoxyribose while DNA has no sugar.
B) DNA is a chain of nucleotides while RNA is a chain of amino acids.
C) DNA is used for translation while RNA is used for transformation.
*D) adenine pairs with different bases in DNA and RNA.
E) cytosine pairs with different bases in DNA and RNA.

Questions used in 2002 relating to this outline (and other outlines)

The central dogma of cell biology
(a) postulates that protein is transcribed directly from DNA.
*(b) runs in reverse with the virus that causes AIDS.
(c) applies to how one DNA strand has the information to synthesize the other strand.
(d) states that amino acid sequences are translated into nucleotide sequences.
(e) explains the plasmid.

Introns
(a) are "jumping genes" with inverted repeats at their ends.
(b) are the type of virus that "eat" bacteria.
(c) are only found in prokaryotes.
*(d) are the parts of eukaryotic pre-mRNA that are spliced out to make mRNA.
(e) cause mad cow disease.

In prokaryotes, transcription
(a) makes a molecule with introns and exons.
(b) makes proteins.
(c) makes transcription factors.
*(d) makes mRNA.
(e) takes place in the nucleus.

Anticodon is a term applied to
(a) ribosomal subunits.
(b) the DNA template.
*(c) aminoacyl-tRNA.
(d) the exon.
(e) the poly-A tail.

Reverse transcriptase would work on [A] to form [B].
(a) [A] bacteria; [B] bacteriophage
(b) [A] pre-mRNA; [B] mRNA
(c) [A] mRNA; [B] protein
(d) [A] DNA; [B] PCR reaction products
*(e) [A] RNA; [B] DNA

If the sequences of bases along the template strand of DNA is A-G-A-T, what is the sequence along the mRNA strand?
(a) A-G-A-T
*(b) U-C-U-A
(c) A-T-C-T
(d) A-G-A-U
(e) U-A-G-A

Sickle cell anemia is a
*(a) missense mutation.
(b) nonsense mutation.
(c) frameshift.
(d) thymine dimer.
(e) result of telomerase.

The codes for leucine include CUU, CUC, CUA, and CUG. A nucleotide substitution in the third position of the codon would
*(a) have no effect on the final protein.
(b) have no effect on the exact mRNA sequence.
(c) cause the protein synthesis to stop prematurely.
(d) not even change which tRNA molecule recognizes the codon.
(e) result in an amino acid substitution.

Which enzyme is the hallmark of HIV (human immunodeficiency virus) that causes AIDS (acquired immunodeficiency virus)?
(a) primase.
(b) nuclease.
(c) telomerase.
(d) hemoglobin.
*(e) reverse transcriptase.

Codons such as CUG would be found
*(a) on the mRNA.
(b) on an antibody.
(c) in the restriction endonuclease.
(d) on the ribosome.
(e) on the template DNA.

Nonsense mutations are
(a) codons changed to start.
*(b) codons changed to stop.
(c) codons changed to codons for another amino acid.
(d) mutations in the position that defines degeneracy of DNA.
(e) jumping genes.

One thing that is unique to gene transcription in bacteria is
*(a) several enzymes might be coded for by one mRNA.
(b) introns are spliced out.
(c) there is processing of a pre-mRNA to mRNA before mRNA leaves the nucleus.
(d) genetic information is carried by RNA that is transcribed to DNA.
(e) the hereditary information is carried by proteins.

The genetic code for Met (the amino acid methionine), AUG, is unique because
(a) it is a DNA sequence.
(b) it is the sort of palindrome that is cut by a restriction enzyme.
(c) it is also the binding site for a helix turn helix molecule.
*(d) it is also the start codon.
(e) it is also the stop codon.

This page was last revised 6/30/08

**The mitosis lecture

cell division

Assignment
Audesirk, Audesirk & Byers part of Chapter 11

Reflection
In second grade, my health teacher read us the book "Mickey the microbe," and I learned that bacteria could "multiply and divide;" I was envious since I was not going to learn how to multiply and divide until 4th grade.

Figure 4-10
Mitosis
Chromosome = colored body.

Figure 11-3
cell-cycle
Understand: concepts of 2n is diploid, prophase, metaphase, anaphase.
interphase is when the cell actually functions -
unwound chromatin vs. condensed chromosomes
cell cycle:interphase G1, S, G2, mitosis
G = gap, S = synthesis
arrest in G1 if postmitotic these are the cells which age

Some cells do not divide, others do

In many cell types, for instance brain (CNS Neurons) and heart (myocardial cells) - not divide, which is why stroke and heart attack are so damaging (no new cells replaced by mitosis) vs. in intestines, cells are constantly replaced by mitoses from stem cells since, in that milieu, cells digest themselves.
Centromere (on chromosome) = kinetochore (where microtubules attach)

Figure 11-10
(This figure shows a lot and we will spend some time on it.)
homologues do not line up (contrast with meiosis, next lecture),
DNA had already doubled (S=synthesis)
prophase, centrioles, spindle
Centromere (on chromosome) = kinetochore (where microtubules attach)
later (metaphase) chromosomes line up at metaphase plate, centromeres divide
anaphase, chromosomes separate
telophase when cells separate followed by cytokinesis.

Cell division in eukaryotes to make genetically identical daughter cells
FUNDAMENTAL: multicellular, all cells have same genes (except germ cells)


Human chromosomes

Figure 11-6
observe at metaphase block w drug colchicine
(they are duplicated - sister chromatids.)

Figure 11-9
Karyotype
look different, i.e. where centromere is and size
bands
46 chromosomes (23 pairs [since we are diploid, 2n] one from father and one from mother)
22 pairs of autosomes and 2 sex chromosomes, XX female, XY male
there are two homologues in a pair

Figure 11-13
Progress through cell cycle is controlled

Figure 11-14
Very specific molecules control progress through cell cycle.

Figure 11-15
Many of the signal transduction cascades control this cell cycle.

Figure E11-3
When things go wrong with these controls, cancer occurs.

Questions used in 2007 and 2008 related to this outline

If p53, the tumor suppressor, is mutated,
(a) chromosomes are not divided equally to the two daughter cells.
(b) the homologues never line up next to each other.
(c) chromosomes get stuck at the metaphase plate.
*(d) damaged DNA gets replicated.
(e) cyclin never gets made.

DNA polymerase had already duplicated the DNA to make two identical copies of all the genetic material. Where are these two copies?
(a) in the two kinetochores
(b) in the two centrioles
*(c) in the two sister chromatids
(d) in the two homologues
(e) one in the autosome, the other in the sex chromosome

If a cell exits from the cell cycle to function as a non-dividing cell, from which step does it exit?
*(a) G1, the first gap
(b) S, the synthesis phase
(c) metaphase
(d) cytokinesis
(e) mitosis

Retinoblastoma (Rb) informs us about normal vs abnormal regulation of cell division. When it was stated that cyclin dependent kinase phosphorylates Rb, what is Rb?
(a) some DNA
*(b) a protein
(c) an extracellular growth factor that signals the cell
(d) the centriole
(e) the sister chromatin

The centriole pair organizes a structure for chromosome motility called
(a) interphase.
(b) the metaphase plate.
(c) the karyotype.
(d) colchicine.
*(e) the spindle.

Where did the two homologues come from?
(a) one from the template strand, one from the complementary strand
(b) one from cyclin, one from cyclin dependent kinase
(c) one from the autosome, one from the XY pair
*(d) one from the mother, one from the father
(e) one from p53, one from retinoblastoma

What about mitosis in myocardial (heart muscle) cells?
(a) They undergo mitosis after DNA synthesis is complete.
(b) The p53 molecule cannot block cyclin phosphorylation.
(c) Growth factors present after stroke regulate mitosis in these cells.
*(d) They are in G0.
(e) Colchicine locks them in metaphase.

Why might you want to block mitosis with colchicine?
*A) to prepare a karyotype
B) because of all the DNA damage done by cyclin
C) in situations where p53 does not bind to the membrane growth factor receptor
D) to prevent eye cancer (retinoblastoma)
E) to give the homologues a chance to line up

When does the DNA replicate itself in a eukaryotic cell?
A) prophase
B) metaphase
C) anaphase
D) telophase
*E) interphase

When a eukaryotic cell undergoes mitosis
A) each daughter cell receives exactly half the genetic information in the parent cell.
*B) each daughter cell receives a nearly perfect copy of the parent cell's genetic information.
C) a haploid chromosomal number is passed on to each daughter cell.
D) genetic information is randomly parceled out to the daughter cells.
E) one of each of the two homologues goes to each daughter cell.

The cells of the intestinal epithelium are continually dividing
A) because they are in G0.
B) because p53 is mutated.
*C) to replace dead cells lost from the surface of the intestinal lining.
D) because they do not have autosomes, but they do have sister chromatids.
E) because that is where gametes are made.

If there are 12 chromosomes in an animal cell in the G1 stage of the cell cycle, what is the diploid number of chromosomes for this organism?
A) 6
*B) 12
C) 24
D) 36
E) 48

The microtubules of the mitotic spindle attach to a specialized structure in the centromere region of each chromosome, called the
*A) kinetochore.
B) nucleolus.
C) metaphase plate.
D) chiasma.
E) centriole.

In the human karyotype, you see X-shaped bodies.
A) Each side of the X is one of the strands (template or complementary) of the DNA double helix.
B) This appearance applies to the X chromosome only.
C) This is only the case for XXY (Klinefelter's syndrome) males.
D) At this stage, the genetic material is called "chromatin."
*E) Two copies of one chromosome are still connected at the centromere.

A homologous pair of chromosomes
*A) consists of two chromosomes, one from each parent, with the same genes.
B) consists of two chromosomes having identical alleles.
C) would be one chromosome after it has duplicated before mitosis.
D) might be found in one sperm cell.
E) is found only in haploid cells

Sister chromatids are
A) X chromosomes.
B) specialized gamete-forming cells.
C) inactivated chromosomes (Barr bodies).
D) the same as homologous chromosomes.
*E) duplicated chromosomes held together by a common centromere.

Questions used in 2002 relating to this outline (and other outlines)

Most people have two copies of chromosome 21. These two copies would be called
(a) alleles.
(b) tetrads.
*(c) homologues.
(d) spindles.
(e) centromeres.

A pair of sister chromatids might be X-shaped in the microscope
(a) only for the X chromosome.
(b) during the G2 of interphase.
(c) because of the centriole pair.
(d) in anaphase.
*(e) when they are joined at the centromere.

Karyotypes are produced from
(a) gametes.
*(b) cells arrested in metaphase.
(c) nuclei of myocardial dells.
(d) haploid cells.
(e) cells in meiosis.

A person has 44 autosomes plus one X chromosome plus one Y chromosome. Which statement is true for this person?
*(a) The Y chromosome came from the father.
(b) The X chromosome becomes a Barr body.
(c) The X chromosome could have come from either the father or the mother.
(d) The Y chromosome's inactivation is described by the Mary Lyon hypothesis.
(e) This person has Klinefelter's syndrome.

The kinetochore is most closely associated with
(a) interphase chromatin.
(b) the stamen.
(c) the G protein linked signal transduction cascade.
(d) the part of the gene to which steroid hormone receptors bind.
(e) the centromere.

What is cytokinesis?
(a) the way useful energy is obtained after light excites an electron
(b) the arrest of neurons in adult human central nervous system in G1
(c) the final processes of cell division
(d) how cAMP becomes inactivated
(e) a way to test for genetic or chromosomal abnormalities

A protein called p53 is
(a) coded by the C. elegans gene that promotes cell death.
(b) deficient in sickle cell anemia.
(c) the G protein coupled receptor.
(d) obtained from bacteria that live in hot springs.
(e) a tumor suppressor.


This page was last updated 6/30/09

**The meiosis lecture

Sex, meiosis and biological variability

Assignment
Audesirk, Audesirk & Byers part of Chapter 11


Today's musical selection
Let me tell you about the birds and the bees

Eukaryotes, diploidy, and sexual reproduction

1-1.5 billion years ago, eukaryotic cells originated. Perhaps diploidy soon evolved because lethal and detrimental mutations would be over-ridden by dominant wild-type genes. Sexual reproduction and meiosis arose and gave rise to a powerful mechanism to insure biological variability, shuffling the genetic deck. Variability is very fundamental in evolution since new varieties may be more adapted and hence survive (to reproduction) better as selection pressures change.

Figure 11-20
Humans are diploid
Our gametes (sperm and eggs) are haploid
When sperm fertilizes egg, a diploid zygote is formed

With two homologous chromosomes...

Figure 11-16
...one is from the father and one is from the mother.
Both copies (alleles) of a gene might be the same (homozygous)...
...or they may be different

human and other life cycles

Figure 11-27
haploid (n), diploid (2n), gametes, ova, sperm, fertilization, zygote.

Figure 11-25
Note that while meiosis creates haploid gametes in humans, there are many organisms where meiosis creates a gamete-forming organism (alternation of generations, haploid life cycles).

(Previously, I described how mitosis creates two identical diploid "daughter" cells; here, you can see that mitosis can also create haploid cells from haploid cells in protists, fungi and plants.)

(An anthropocentric view is that meiosis only makes haploid gametes, but here you can see that it can make haploid organisms, again in protists, fungi and plants.)

Meiosis

Figure 11-21
(We will spend a long time with this figure.)
Meiosis. Note that there are two homologous chromosomes, 23 pairs for the human diploid number, 46. Theoretically, one could go to each gamete with one meiotic division. Instead, they align, duplicate, and divide twice.
Homologous chromosomes separate in first division
Sister chromatids separate in second division

Awesome variability

for 2 pairs of chromosomes, there are 4 possible combinations of chromosomes (centromeres) in the zygote. For 46 chromosomes, there are 2 to 23 power = 8.4 million.

The story goes that the king offered to pay the inventor of chess who wanted one grain of wheat for one square on the chess board, 2 for the second and so on. The king readily agreed but then found out that that was more wheat than the country would produce for decades, so he had the inventor beheaded instead. Behold the power of 2 to the power of (whatever).

Figure 11-22
Tetrad (bivalent), homologues have duplicated and are aligned next to eachother
Crossing-over (recombination) increases this beyond measure(shown for one pair of chromosomes)

Coming attractions

Unequal crossing over and gene duplication as major means of protein family evolution

Figure 12.33
Errors in meiosis (nondisjunction) can lead to offspring with aneuploidy (the wrong number of chromosomes) such as trisomy 21

Questions used in 2007 and 2008 relating to this outline

In the bivalent there is/are [A] sister chromatids and [B] homologues
(a) [A] 1; [B] 1
(b) [A] 1; [B] 2
(c) [A] 2; [B] 1
*(d) [A] 2; [B] 2
(e) none of the above

What is the end result of spermatogenesis in the human male?
(a) Four diploid daughter cells
*(b) Four haploid gametes
(c) Four identical chromosomes lined up next to each other
(d) Two haploid spores
(e) Two haploid zygotes

"Meiosis creates haploid gametes." Why is this not the whole truth?
*(a) Meiosis creates haploid organisms when there is alternation of generations.
(b) Heterozygous gametes are not haploid.
(c) Many gametes are diploid.
(d) In plants, meiosis creates zygotes.
(e) In Protista, it is alleles that are made, not gametes.

Two different but closely related proteins may have arisen, over evolutionary time, by a process of
(a) trisomy.
(b) mitosis.
(c) fertilization.
(d) nondisjunction.
*(e) unequal crossing over.

A pair of sister chromatids might be X-shaped in the microscope
*(a) when they are joined at the centromere.
(b) during the G2 of interphase.
(c) because of the centriole pair.
(d) in anaphase.
(e) only for the X chromosome.

The tetrad would form
(a) during the preparation of the karyotype.
(b) in the G1 portion of the cell cycle.
*(c) during meiosis.
(d) only during interphase.
(e) after gametes are haploid.

Two to the twenty-third power = 8.4 million. Why are there even more possible gametes than that in the human?
(a) Diploidy adds to variability.
*(b) Crossing over adds to variability.
(c) Homozygosity adds to variability.
(d) That's how it would be if there were just one meiotic division, but there are two.
(e) That's how it would be in interphase, but gametes are in prophase.

If a human does not possess 46 chromosomes, what is the term for the abnormal chromosome number?
(a) loci
*(b) aneuploidy
(c) hybrids
(d) recessives
(e) bivalents

What processes take place during Anaphase II?
*(a) Centromeres divide and sister chromatids move to opposite poles.
(b) Centromeres do not divide and sister homologues move to opposite poles.
(c) Centromeres divide and bivalents move to opposite poles.
(d) Sister homologues attach to spindle fibers from opposite poles.
(e) Tetrads attach to spindle fibers from opposite poles.

What constitutes a tetrad (bivalent)?
(a) Sister chromatids aligned next to each other.
*(b) Duplicated homologous chromosomes aligned next to each other.
(c) Homologous chromosomes aligning at the center of the cell during anaphase I.
(d) The karyotype when mitosis is blocked with colchicine.
(e) Homologous chromosomes that are connected during telophase I.

"Mitosis creates genetically identical diploid daughter cells." Why is this statement not the whole truth?
(a) In the retrovirus, it makes identical RNA strands.
(b) It's not true at all; mitosis makes haploid gametes.
*(c) When there is alternation of generations, there can be mitosis of haploid cells.
(d) In the central dogma of cell biology, it makes proteins.
(e) It's not true at all; it is meiosis that makes identical diploid cells.

Children with Down syndrome
(a) are heterozygous.
*(b) have 47 chromosomes.
(c) accumulate glycolipids from an enzymatic deficiency.
(d) have a mutation of a gene on chromosome 21.
(e) are born when older men decide to have children.

Name a cell that could have 22 autosomes and one Y chromosome.
(a) a human egg
*(b) a human sperm
(c) a human diploid cell
(d) a body cell from a Klinefelter's syndrome individual
(e) a cell from a Turner's syndrome individual

What is a major source of genetic variation in sexual reproduction?
A) mitosis
B) alternate splicing
*C) crossing over
D) nondisjunction
E) DNA replication

Drosophila have 4 pairs of chromosomes. How many possible arrangements of chromosomes are possible in the gametes owing only to independent assortment (i.e. discounting recombination)?
A) 2
B) 4
C) 8
*D) 16
E) 32

Which of the following statements is FALSE?
A) Meiosis separates homologous chromosomes during anaphase I.
B) Meiosis separates sister chromatids during anaphase II.
C) In plants, meiosis produces spores rather than gametes.
*D) The karyotype is produced from gametes.
E) In animals, it is meiosis that produces sperm and eggs.

If there are 12 chromosomes in a cell that has just completed meiosis II, what is the number of chromosomes in the zygote?
A) 6
B) 12
*C) 24
D) 24 pairs
E) There is no answer because it would be different if there were alternation of generations.

Where does recombination occur?
A) at centromeres
B) at kinetochores
C) at Barr bodies
D) in zygotes
*E) at chiasmata

Name a cell that could have 22 autosomes and one Y chromosome.
A) a human egg cell
*B) a human sperm cell
C) a human diploid cell
D) a body cell from a Klinefelter's syndrome individual
E) a cell from a Turner's syndrome individual

When sperm and egg form the zygote, this is called
A) nondisjunction.
B) meiosis.
C) mitosis.
*D) fertilization.
E) crossing over.

In flowering plants, meiosis
A) makes gametes just as it does in animals.
B) makes sperm and eggs.
*C) gives rise to a separate gamete-forming organism.
D) makes zygotes, in contrast with the situation for animals.
E) makes all the cells of the plants.

Nondisjunction of chromosome #21 in humans leads to
A) Tay-Sachs disease.
B) Crossing over.
C) Klinefelter's syndrome.
D) Turner's syndrome.
*E) Down's syndrome.

Questions used in 2002 relating to this outline (and other outlines)

Disregarding crossing over, in meiosis, [A] separate in the first division, while [B] separate in the second division.
(a) A-single DNA strands, B-centrioles.
(b) A-alleles, B-genes.
(c) A-homozygotes, B-heterozygotes.
(d) A-chromatin, B-tetrads.
*(e) A-homologous chromosomes, B-sister chromatids.

Most people have two copies of chromosome 21. These two copies would be called
(a) alleles.
(b) tetrads.
*(c) homologues.
(d) spindles.
(e) centromeres.

Name a cell that could have 22 autosomes and one Y chromosome.
*(a) a human sperm cell
(b) a human ovum
(c) a human diploid cell
(d) a body cell from a Klinefelter's syndrome individual
(e) a cell from a Turner's syndrome individual

When sperm and egg form the zygote, this is called
(a) nondisjunction.
(b) meiosis.
(c) mitosis.
(d) crossing over.
*(e) fertilization.

The tetrad would form
(a) during the preparation of the karyotype.
(b) in the G1 portion of the cell cycle.
*(c) during meiosis.
(d) only during interphase.
(e) after gametes are haploid.

Haploid is a term that would apply to
(a) interphase.
(b) chromosomes viewed for the karyotype.
(c) daughter cells of a mitotic division
*(d) gametes.
(e) zygotes.

In flowering plants, meiosis
(a) makes gametes just as it does in animals.
(b) makes sperm and eggs.
(c) makes zygotes, in contrast with the situation for animals.
*(d) gives rise to a separate gamete-forming organism.
(e) makes all the cells of the plants.

When does crossing over occur?
(a) during G2
(b) during fertilization
(c) during mitosis
*(d) when the tetrad is present
(e) during interphase

Crossing over occurs
(a) during the preparation of the karyotype.
(b) in the G1 portion of the cell cycle.
*(c) during meiosis.
(d) only during interphase.
(e) after gametes are haploid.

Making haploid cells from diploid cells is called
(a) nondisjunction.
*(b) meiosis.
(c) mitosis.
(d) mapping.
(e) fertilization.

Nondisjunction of chromosome #21 in humans leads to
(a) Tay-Sachs disease.
(b) Crossing over.
(c) Klinefelter's syndrome.
(d) Turner's syndrome.
*(e) Down's syndrome.

A person has 44 autosomes plus one X chromosome plus one Y chromosome. Which statement is true for this person?
*(a) The Y chromosome came from the father.
(b) The X chromosome becomes a Barr body.
(c) The X chromosome could have come from either the father or the mother.
(d) The Y chromosome's inactivation is described by the Mary Lyon hypothesis.
(e) This person has Klinefelter's syndrome.

This page was last updated 6/30/09

**the genetics lecture

This land is your land
and this land is my land
from California to the New York Island
from the redwood forest to the Gulf Stream waters
This land was made for you and me.
-Woody Guthrie

Genetics

Many people may think of "genetics" as one type of biotechnology. Actually, genetisists studied progeny of crosses of living organisms (fruit flies or pea plants), or, alternatively pedigrees (family trees say of humans). Also, the outcomes of the genetic crosses told us more about meiosis than anything else.

Assignment
Audesirk, Audesirk & Byers part of Chapter 12

Today's musical selection
Nervous Norvus - Transfusion

Mendel's work

Figure 12-2
1865 Mendel

Figure 12-3
pea flowers
(might seem strange to think about sexual reproduction in plants)
presumably genes are lined up along chromosomes, each at its own place
thus "locus" is a word for a gene

Figure 12-4
- purple vs. white flowers (phenotype)
P=parental, F1 first generation (filial)

Since cells are diploid, there are two copies (alleles) at each locus, and they can be the same or different.

Figure 12-6
true-breeding = homozygous PP or pp (genotype)

Figure 12-7
hybrids = heterozygous (Pp)
purple (P) is dominant, white (p) is recessive
Thus Pp genotype has purple phenotype

Figure 12-5
F2 has 3/1 ratio
units = gene separate Mendel's first law (segregation)

Figure 12-11
Punnett square
shows haploid gametes (ova and sperm) and genotypes and phenotypes

Mutations - variation and evolution (many are bad also recessive, many are neutral, some might be good under the right environmental circumstances. They can be caused by ionizing radiation or chemicals (mutagens which are also carcinogens).

Taboos against insest-
People carry several detrimental or lethal alleles (such as those discussed later in this outline). They are usually not expressed because they are recessive and heterozygous. Inbreeding is a problem because related people would have mutations in the same genes, resulting in a homozygous recessive expression. "Hybrid vigor" refers to a stronger genetic constitution in organisms with more heterozygosity (and hence more genetic variability

Mendel (knew about Darwin but Darwin did not know about Mendel)
"...this seems to be the one correct way of finally reaching the solution to a question whose significance for the evolutionary history of organic forms must not be underestimated."

Figure 12-14
Mendel's Second Law
The law of independent assortment
green-yellow, round-wrinkled
dihybrid cross (two genes each on a separate chromosome, two alleles each) fill in "Punnett square"
Independent assortment does not apply to linked genes. i.e. genes that are on the same chromosome.

A few human examples

Figure 12-24
Here is a picture showing incomplete dominance (hair texture)

Table 12-1
Blood groups
A=B (co-dominant), O is recessive -- 3 alleles

genotypes...............phenotype.........antigens..........antibodies
IA IA or IA i...........A......................A.....................anti-B
IB IB or IB i...........B......................B.....................anti-A
IA IB......................AB....................A and B..........anti neither
ii ............................O......................none................anti both

O universal donor, AB universal recipient

Question: What is unusual about this situation? Answer: There are already antibodies even though there was no previous exposure to antigens.

Genetic disorders in people

Figure 12-29
Sickle cell anemia
If homozygous, red blood cells have abnormal shape
hgb clumps in low O2, heterozygotes (trait) largely normal
2 alpha, 2 beta. Beta 146 aa, 6th valine instead of
glutamic acid, GUG instead of GAG
blacks, heterozygous gives resistance to malaria

Figure 12-31
Hemophelia
pedigree
Victoria, Nicholas II & Alexandra - Alexis, Rasputin
on X
problem with AIDS for clotting factor

Lethals detrimentals
- everyone carries several recessives, but different
become homozygous if inbreeding

Huntington's - chorea - age 40's or 50's death in 10-20 years
By that age, person has probably already reproduced
autosomal dominant - 50:50 chance to pass on mapped to chromosome #4
Woody Guthrie died of it

Figure E12-1
Cystic fibrosis
lungs fill up with thick mucus
cloned as CFTR, mutation in Cl- transport, children have salty sweat
Life is short, chest must be thumped to clear lungs

Some others we will not take the time to cover
Tay-Sachs disease
Phenylketonuria (PKU)

Mild disorders

Figure 12-30
color blindness
X-linked

Figure 12-28
Albinism
Melanin formed from polymerization of dopa quinones derived from the amino acid tyrosine

Figure 12-26
Himalayan rabbit (like Siamese cat)
"temperature sensitive" presumably missense mutation, enzyme works if cool but body heat denatures it

Questions used in 2007 and 2008 related to this outline

A dihybrid cross was presented to explain
*(a) the 9:3:3:1 ratio.
(b) genetics of blood groups.
(c) sex-linked (X-linked) diseases.
(d) the Hardy-Weinberg ratio.
(e) cephalization.

What blood type is known as the universal donor?
(a) AB
(b) A
(c) B
(d) C
*(e) O

Why is a Siamese cat's nose black?
*(a) There is a temperature sensitive missense mutation.
(b) Cats are mosaic for whether there is a mutation on of the X chromosomes.
(c) Because of convergent evolution.
(d) There was an evolutionary bottleneck.
(e) Because of homeostasis.

Why are some people from African descent resistant to malaria?
(a) They use banked umbilical blood in Africa.
(b) Hemophelia heterozygotes are immune.
(c) They have Down's syndrome.
(d) They are carriers of PTC insensitivity.
*(e) They are heterozygous for sickle cell anemia.

Why does Huntington's disease create such a dilemma?
(a) If they knew how antisocial they were expected to be, they would consider it the self-fulfilling prophesy.
(b) Much of what we know was presented by a nineteenth century British physician with an unsavory attitude toward non-European races.
*(c) Most people did not show symptoms until they already had children.
(d) Though retarded, children with Huntington's disease are pleasant and happy.
(e) Richard Speck, accused murderer of 8 student nurses in Chicago in 1966, had Huntington's disease.

In genetics, if there are two or more different copies of a gene possible, they are referred to as
(a) pedigrees.
(b) homologues.
*(c) alleles.
(d) kinetochores.
(e) filials.

A pea that is heterozygous for purple colored flowers is crossed with a plant having white flowers. What is the makeup the F1 generation?
*(a) 1/2 purple, 1/2 white
(b) 1/4 purple, 3/4 white
(c) all purple
(d) 1/2 pink, 1/2 purple
(e) 1/3 white, 2/3 purple

What genetic disorder relates the history of Europe's royal families and a unique evolutionary selection pressure in the first years of the AIDS epidemic?
(a) Down syndrome
(b) albinism
(c) Huntington's disease
*(d) hemophelia
(e) green-wrinkled syndrome

What is true about people with type AB blood?
(a) They are universal donors.
(b) On the surface of their red blood cells, they do not have A or B glycoproteins (antigens).
(c) They are homozygous dominant.
(d) They are homozygous recessive.
*(e) They don't have antibodies against A or B glycoproteins.

Which statement is false?
(a) Meiosis leads to segregation of two alleles at one locus in plants.
(b) Separate male and female structures in pea flowers allowed Mendel to cross-fertilize.
(c) Mendel knew about Darwin and thought his own genetic studies could help to explain evolution.
(d) The F2 ratio of 3:1 describes phenotypes, not genotypes.
*(e) Plants do not reproduce sexually.

Most people are not born with fatal genetic diseases. Why not?
*(a) Detrimental mutations are usually heterozygous recessive.
(b) The only mutations that can possibly be detrimental are autosomal dominant.
(c) Mutations only occur on extra chromosomes produced by nondisjunction.
(d) Mutations only occur on the Y chromosome.
(e) Most parents do not have detrimental mutations.

Cystic fibrosis
(a) causes spastic movements referred to as "chorea."
*(b) results in thick mucus in the lungs.
(c) is the cause of red-green color blindness.
(d) only begins to appear in people in their 50's.
(e) probably first appeared in Queen Victoria.

What would have happened if Mendel had done his dihybrid cross using two traits that were near each other on the same chromosome?
(a) That is what he did and how he got the 3/1 ratio.
(b) That is what he did and how he got the 9/3/3/1 ratio.
*(c) His ratio would not have been 9/3/3/1 and he might have discovered linkage.
(d) That is what he did and how he obtained the ratio of ABO blood groups.
(e) He would have discovered Klinefelter syndrome.

In the US, sickle cell anemia is most common among Afro-Americans because
(a) it is a mutation in the enzymes that form melanin.
(b) it is an example of convergent evolution.
(c) the antibodies are already present in the blood, even before exposure to the antigen.
(d) it is on the X chromosome, and Afro-Americans are mosaics for which X is active.
*(e) it confers resistance to malaria.

Cystic fibrosis is a genetic disease that leads to the production of excessive thick mucous in the respiratory tract, leading to frequent and serious respiratory infections. The defect is due to
*A) faulty transport of chloride (Cl-) ions.
B) antibodies attacking antigens on red blood cells.
C) bleeding into the mucous because of a mutation that originated in Queen Victoria.
D) a dominant gene defect that is not expressed until about age 50.
E) faulty melanin synthesis.

Which is NOT a difference between the examples of Mendel's dihybrid cross (YyRr) and the ABO blood groups?
A) There are two alleles per gene only for the Mendel example.
B) There are two alleles in one gene that are equally dominant only for the blood groups.
C) There are two genes (loci) only for the Mendel example.
D) ABO blood groups cannot be used to demonstrate independent assortment while Mendel's work on peas can.
*E) Antibodies and antigens apply only for peas.

Gregor Mendel concluded that two units determined pea flower color, and each sperm cell or egg cell contains only one unit. Each individual unit is a(n) ________.
A) chromosome.
*B) allele.
C) trait.
D) homozygote.
E) gamete.

According to the Law of Segregation, in an organism with the genotype Aa,
A) A and a will blend and never be passed on to progeny intact.
B) the organism can have a as its genotype
C) the gametes can be AA, Aa or aa.
*D) half the gametes will have A and half will have a.
E) the phenotype of the gametes can be either A or a.

Red-green colorblindness
A) explains the black extremities on the otherwise white Himalayan rabbit.
B) is dominant.
C) results from nondisjunction.
*D) is on the X chromosome.
E) would be lethal if hemizygous.

Sickle-cell anemia
A) is expressed only after the age of 50.
B) explains the appearance of the calico cat.
C) was the blood disorder in the Russian royal family.
*D) confers resistance to malaria.
E) is caused by a stop codon.

In flowering plants, meiosis
A) makes gametes just as it does in animals.
B) makes sperm and eggs.
*C) gives rise to a separate gamete-forming organism.
D) makes zygotes, in contrast with the situation for animals.
E) makes all the cells of the plants.

Which of the following statements is FALSE?
A) Individuals with the same phenotype might have different genotypes.
*B) Matings between individuals with dominant phenotypes cannot produce offspring with recessive phenotypes.
C) Matings between individuals with recessive phenotypes do not produce offspring with dominant phenotypes.
D) Mating between heterozygotes produce a 3:1 ratio of dominant:recessive phenotypes.
E) Mating between heterozygotes produce a 1:2:1 ratio of genotypes.

Blood typing is often used as evidence in paternity cases in court. In one case, the mother had blood type B and the child had blood type O. Which of the following blood types could the father NOT have?
A) A
B) B
*C) AB
D) O
E) Both choices C and D are correct.


Questions used in 2002 relating to this outline (and other outlines)

What is one reason that type O individuals would be especially useful in a blood drive?
*(a) They are universal donors.
(b) They are universal recipients.
(c) They have A and B antigens as well as antibodies against A and B.
(d) They are homozygous dominant.
(e) They are the only people that are not mutant.

A pea plant with purple flowers is referred to as Pp. Pp
(a) is the plant's phenotype.
(b) indicates that the plant is homozygous.
(c) are only seen in the F2 of a cross of purple- and white-flowered pea plants.
*(d) is the plant's genotype.
(e) is a gamete.

Which is a dominant lethal mutation which probably would not be expressed until after affected men and women have had children?
(a) Down's syndrome
(b) PKU
*(c) Huntington's chorea
(d) Tay Sachs disease
(e) Sickle cell anemia

What made the example of the ABO blood groups an interesting contrast with the pea crosses used to exemplify Mendel's first and second laws?
(a) There were more than two loci.
(b) There are no homozygotes.
(c) There are no genotypes, only phenotypes.
(d) The genes are sex-linked.
*(e) There were three alleles.

Mendel's second law
(a) explains how both yellow or green pea bearing plants would be seen in subsequent generations if homozygous yellow or green pea bearing plants are crossed.
*(b) applies to two alleles of two genes on two different chromosomes.
(c) is the law of segregation.
(d) was used by Darwin to explain some aspects of evolution.
(e) is how linked genes are mapped on one chromosome.

Mendel's laws of segregation and independent assortment apply to
(a) mitosis.
(b) non-disjunction.
*(c) meiosis.
(d) linkage.
(e) mapping.

Which is a mutation?
(a) Klinefelter's syndrome
*(b) Tay Sach's disease.
(c) Down's syndrome
(d) XYY
(e) Turner's syndrome

Hemophelia is a sex-linked recessive allele. If a mother and father have a daughter with hemophelia, which of the following statements is the only one which MUST be correct on the basis of this information?
*(a) The father has hemophelia.
(b) The mother has hemophelia.
(c) Both father and mother have hemophelia.
(d) The daughter inherited all hemophelia alleles from the mother.
(e) Half of the mother's sons would have hemophelia.

Most people are not born with fatal genetic diseases. Why not?
(a) Most parents do not have detrimental mutations.
(b) The only mutations that can possibly be detrimental are autosomal dominant.
(c) Mutations only occur on extra chromosomes produced by nondisjunction.
(d) Mutations only occur on the Y chromosome.
*(e) Detrimental mutations are usually heterozygous recessive.

Which statement applies to the Siamese cat having white fur with black extremities?
*(a) A mutation makes an enzyme for melanin synthesis temperature-sensitive.
(b) Black vs. white depends on which X chromosome is active.
(c) There is incomplete dominance like for snapdragon flower color.
(d) The cat is heterozygous for the body color gene.
(e) Sons of such a female cat will be either black or white.

To analyze a situation like hemophelia in Queen Victoria's family, you use
(a) a Punnett square.
(b) a dihybrid cross.
(c) a pedigree.
(d) PCR.
(e) a northern blot.

Human evolution takes place in a changing environment of medical intervention (allowing survival of some people with genetic disorders). After treatment that helped this condition were established, the early years of the AIDS pandemic created a particularly harsh selection pressure against people with
(a) Tay-Sachs disease.
(b) Turner's syndrome.
(c) anthrax.
(d) hemophelia.
(e) PKU.

The famous American folk singer Woody Guthrie, as well as a large population from Venezuela, had this genetic disorder:
(a) Tay Sach's disease.
(b) PKU.
(c) Klinefelter's syndrome
(d) Huntington's disease.
(e) sickle cell anemia.


This page was last updated 7/9/09

**The chromosome lecture

The gingham dog and the calico cat
Side by side on the table sat;
'T was half-past twelve and (what do you think!)
Nor one nor t'other had slept a wink!
The old Dutch clock and the Chinese plate
Appeared to know as sure as fate
There was going to be a terrible spat.
(I wasn't there; I simply state
What was told to me by the Chinese plate!)

The gingham dog went "bow-wow-wow!"
And the calico cat replied "mee-ow!"
The air was littered, an hour or so,
With bits of gingham and calico,
While the old Dutch clock in the chimney-place
Up with its hands before its face
For it always dreaded a family row!
(Now mind: I'm only telling you
What the old Dutch clock declares is true!)

The Chinese plate looked very blue,
And wailed, "Oh, dear! What shall we do!"
But the gingham dog and the calico cat
Wallowed this way and tumbled that,
Employing every tooth and claw
In the awfullest way you ever saw-
And, oh! How the gingham and calico flew!
(Don't fancy I exaggerate-
I got my news from the Chinese plate!)

Next morning, where the two had sat
They found no trace of dog or cat;
And some folks think unto this day
That burglars stole that pair away!
But the truth about the cat and pup
Is this: They ate each other up!
Now what do you really think of that!
(The old Dutch clock it told me so,
And that is how I came to know.)

The Duel
by Eugene Field (1850-1895)
(Poems of Childhood)

Chromosomes

Assignment
Audesirk, Audesirk & Byers part of Chapter 12, and several other figures

Today's musical selection
Beatles Ob la di
A cover of this song was the theme for the TV situation comedy Life goes on where Corky has Down syndrome

Of course, genes come on chromosomes.
There are autosomes and sex chromosomes.

Sex linkage

Figure 12-21
XY

Figure 12-22
sex determination

Figure (Chapter 10 opener)
Case study - Vive la difference Chapter 10, p. 167
Case study revisited Chapter 10, p. 186
Different organisms have different chromosomal means of sex determination (dimorphism).
Sry gene on Y codes for TDF (testicular determining factor)
In female, Wolffian ducts degenerate and Mullerian ducts develop into oviducts, uterus, and cervix (default pathway).
In male, testes make testosterone and MIH (Mullerian inhibiting factor), Mullerian ducts degenerate, Wolffian ducts become epididymus, vas deferens and seminal vesicles (active, not default)
urogenital groove becomes external genitals

Cartoon
In humans, Y determines male-ness and there are virtually no genes on Y except to differentiate testes in male.
Why map the Y? Science 261, 1993, p. 679
A guy bashing joke with genes like "inability to say 'I love you'" over the phone called "ME-2"
However, I am showing this picture to also make a serious point -- genes eventually get assigned to locations on the chromosome, but first, genetic linkage must be established
Linkage:
Independent assortment (Mendel's 2nd law) does not apply to genes (near enough to each other) on the same chromosome.
map location is based on cross-over probability (determined with a genetic cross)

Figure 12-23
Sex linked inheritance in Drosophila, white x red eye cross. Note that there is no corresponding gene on the Y, hence the term hemizygous.
males are XY, but tissues that are XO are male (though if fly or germ cells are X0, fly is sterile) and XX tissues are female, thus sex is based on number of X chromosomes. grasshopper XO male

Figure 10-13
X inactivation in calico cat

Figure 10-12
XX Barr body, X inactivation Mary Lyon
dosage compensation

Chromosomal abnormalities

Figure 12-32
Chromosomal Abnormalities
Nondisjunction e.g. trisomy
lethal, spontaneous abortions

Table 12-2
X abnormalities survive
Klinefelter's XXY
Supermale XYY
1968 prison if taller than 71 inches 1/11 XXY or XYY
population XXY - .08-.092%
XYY - .069-.095%
Research to find if people have X or Y abnormalities is controversial, for instance because of self-fulfiling prophesy.
It was widely rumored that Richard Speck, known for his mass murder of 8 student nurses in Chicago in 1966, was XYY.
Turner X0 1/2000 females
spatial sense abnormal

Figure 12-33
Autosomal aneuploidies are often lethal
Trisomy 21 = Down's syndrome
(the term "Mongulism" is used less in this era of political correctness, especially in light of Down's unsavory attitude toward non-European races in his writings)
retarded but nice, increases with increasing maternal age and is in percents for women over 40
age 40 almost 1% age 50 almost 10%

Figure 12-34
Here is a graph of that increase with age

Figure E13-5
Many couples choose to test the chromosomes of the fetus using amniocentesis of chorionic villus sampling

All human "eggs" are already made around the time of birth (while sperm are made throughout life). It seems likely that either "eggs" suffer from aging (alternatively the good ones are used in the earlier reproductive years).

Questions used in 2007 & 2008 related to this outline

What would have happened if Mendel had done his dihybrid cross using two traits that were near each other on the same chromosome?
(a) That is what he did and how he got the 3/1 ratio.
(b) That is what he did and how he got the 9/3/3/1 ratio.
*(c) His ratio would not have been 9/3/3/1 and he might have discovered linkage.
(d) That is what he did and how he obtained the ratio of ABO blood groups.
(e) He would have discovered Klinefelter syndrome.

Why is there a relatively high frequency of X chromosomal aneuploidies?
(a) The X chromosome is not subject to amniocentesis.
(b) The X chromosome is even smaller than chromosome 21.
(c) There are many nondisjunctions when mitosis involves the X chromosome.
*(d) All but one X chromosome is inactivated.
(e) X chromosomal abnormalities are not detected in chorionic villus sampling.

The human Y chromosome
(a) has most of the genes that are on the X.
*(b) is important for sex determination.
(c) is not as important for sex determination as the number of X chromosomes.
(d) is seen histologically as the Barr body
(e) is the cause of coat color mosaicism in the Siamese cat

A female fruit fly homozygous for red eyes is mated to a white eyed male.
*(a) Male and female offspring are red eyed.
(b) Female offspring have red eyes but males have white eyes.
(c) Female offspring have white eyes but males have red eyes.
(d) Female and male offspring have white eyes.
(e) Female and male offspring have pink eyes, halfway between red and white.

Amniotic fluid
(a) is used for chorionic villus sampling.
*(b) should contain no maternal cells.
(c) is used for cloning.
(d) is the source of prions.
(e) would be present only if nondisjunction had occurred during mitosis.

Which is a way to test for chromosomal abnormalities in the embryo?
(a) gel electrophoresis
(b) administering dopamine
(c) using rubella
(d) testing for chorionic gonadotroin
*(e) chorionic villus sampling

Children with Down syndrome
(a) are heterozygous.
*(b) have 47 chromosomes.
(c) accumulate glycolipids from an enzymatic deficiency.
(d) have a mutation of a gene on chromosome 21.
(e) are born when older men decide to have children.

Name a cell that could have 22 autosomes and one Y chromosome.
(a) a human egg
*(b) a human sperm
(c) a human diploid cell
(d) a body cell from a Klinefelter's syndrome individual
(e) a cell from a Turner's syndrome individual

A human female has one X chromosome with the normal gene and the other with the recessive mutated gene.
(a) She passes the normal gene to her daughters and the mutated gene to her sons.
(b) She is called "hemizygous."
(c) All her daughters are carriers since she passes both X chromosomes to daughters.
*(d) She is a mosaic of cells expressing one or the other X.
(e) Her sons would have Klinefelter's syndrome

The testicular determining factor is found in what chromosome in humans?
(a) X
(b) #21
*(c) Y
(d) No single chromosome; it is explained by polygenic inheritance.
(e) The chromosome has not been identified yet.

"Early female sexual development is the default." Meaning?
(a) Like with fruit flies, two X chromosomes specify female development.
*(b) Ducts become female genitals in the absence of factors present in the male.
(c) Many genes specifying male characteristics are mapped to the Y chromosome.
(d) Since females have two X chromosomes and males have one, it is no wonder males and females are different.
(e) That is the statement that got Lawrence Summers fired as president of Harvard.

'Dosage compensation explains the high prevalence of abnormalities like Turner's syndrome and Klinefelter's syndrome.' Dosage of
*A) genes on the X chromosome
B) p53
C) colchicine
D) polar bodies
E) antibodies

Chromosome map position
A) was first determined in Darwin's classic genetic experiments.
*B) is based on the cross-over frequency for linked genes.
C) is determined by the normal distribution.
D) was 9:3:3:1 when Mendel figured it out.
E) is calculated using the Punnett square.

Amniotic fluid
A) causes mutations.
B) is hybrid in the F1 generation.
C) is the universal donor in blood transfusions.
D) is produced by the Sry gene on the Y chromosome.
*E) can be used to screen for chromosomal and genetic abnormalities in the fetus.

The failure of chromosomes to distribute equally to gametes is called
*A) nondisjunction.
B) conjugation.
C) segregation.
D) inversion.
E) independent assortment.

Which disorder is more common among the babies of older mothers?
A) Turner syndrome
B) XYY
C) hemophelia
D) Huntington's disease
*E) Down syndrome

Klinefelter syndrome
A) results when detrimental alleles become homozygous because of incest.
B) is an autosominal dominant disorder.
C) females would lack a Barr body.
*D) results from sex chromosomal nondisjunction.
E) is because of crossing-over.



Questions used in 2002 relating to this outline (and other outlines) [some overlap particularly with genetics questions]

In your genetics coverage, you were introduced to the term "locus." Of the following, which would be the best term to substitute for "locus?"
(a) true-breeding
(b) hybrid
(c) chromosome
*(d) gene
(e) allele

Most people have two copies of chromosome 21. These two copies would be called
(a) alleles.
(b) tetrads.
*(c) homologues.
(d) spindles.
(e) centromeres.

Name a cell that could have 22 autosomes and one Y chromosome.
*(a) a human sperm cell
(b) a human ovum
(c) a human diploid cell
(d) a body cell from a Klinefelter's syndrome individual
(e) a cell from a Turner's syndrome individual

Which is a dominant lethal mutation which probably would not be expressed until after affected men and women have had children?
(a) Down's syndrome
(b) PKU
*(c) Huntington's chorea
(d) Tay Sachs disease
(e) Sickle cell anemia

Which is a mutation?
(a) Klinefelter's syndrome
*(b) Tay Sach's disease.
(c) Down's syndrome
(d) XYY
(e) Turner's syndrome

A person has 44 autosomes plus one X chromosome plus one Y chromosome. Which statement is true for this person?
*(a) The Y chromosome came from the father.
(b) The X chromosome becomes a Barr body.
(c) The X chromosome could have come from either the father or the mother.
(d) The Y chromosome's inactivation is described by the Mary Lyon hypothesis.
(e) This person has Klinefelter's syndrome.

Which statement applies to the Siamese cat having white fur with black extremities?
*(a) A mutation makes an enzyme for melanin synthesis temperature-sensitive.
(b) Black vs. white depends on which X chromosome is active.
(c) There is incomplete dominance like for snapdragon flower color.
(d) The cat is heterozygous for the body color gene.
(e) Sons of such a female cat will be either black or white.

To see whether your baby would be born with trisomy-21, you could use
(a) recombinant DNA.
(b) a microarray.
*(c) chorionic villus sampling.
(d) autoradiography.
(e) reverse transcriptase.

Which is the best statement about human chromosomes?
(a) Presence of two X chromosomes causes development of the female.
*(b) Dosage compensation in females works by X chromosome inactivation.
(c) Male development begins under the control of the one X chromosome.
(d) The male genome is haploid while the female genome is diploid.
(e) The Y chromosome has all the same loci as the X chromosome.

This page was last updated 7/13/09

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