Exam 1
This STUDY GUIDE is for your use in preparing for the exam.
This resource does not reflect the questions or format you will see on the exam.
The questions in this study guide are purposefully broad so that you are able to use your
recall skills to answer. More specific questions and problem solving problems can be found
in your text-book and on the Supplemental Instruction website:
https://apps-dso.sws.iastate.edu/si/course.php?id=751
This resource is to help you identify what you need to work on more. If there is a concept
that you still do not understand, it would be prudent to go back and read that section in the
text-book.
Everything in this resource will not be found on the test, nor will everything on the test be
found in this resource.
The concepts reviewed in this guide are what I estimate to be most important by my own
experience. Saying that, I do not specifically know what will be on the exam and cannot tell
you.
If you have any question feel free to contact your professor by email or myself through the
SI website.
Good Luck!
-Lilli
Exam 1 Review
Supplemental Instruction
Iowa State University
Leader:
Course:
Instructor:
Date:
Lilli Howard
BIOL/GEN 313
Dr. Rodermel/Dr. Tuggle
09/19/14
CHAPTER 1
1. What are some of the implications of all organisms having similar genetic systems?
a. That all life forms are genetically related
b. That research findings on one organism’s gene function can often be applied to
other organisms
c. That genes from one organism can often exist and thrive in another organism
d. All of the above
2. Name and describe the three sub-disciplines of genetics.
1. Molecular genetics: How genetic information is encoded, replicated and expressed
2. Transmission genetics: How traits are passed from one generation to the next
3. Population genetics: How composition of genes in a population changes
geographically and through time
3. Name some characteristics of model genetic organisms. Why are they important?
1. Short generation time
2. Production of numerous progeny
3. The ability to carry out controlled genetic crosses.
4. Controlled conditions of growth (e.g., growth chamber)
5. The availability of numerous genetic variants (mutant collection)
6. An accumulated body of knowledge about their genetic systems (genomes sequenced)
4. Who proposed the concept of cell theory and what is it?
Matthias Jacom Schleiden & Theodor Schwann 1839
--all life is composed of cells
Cells arise only from preexisting cells
The cell is the fundamental unit of structure and function in all organisms
5. Briefly describe pangenesis, pre-formationism, and germplasm theories.
Pangenesis
--(Greeks) 500 BC to 1800’s:
-- body-part specific particles (gemmules) travel to sperm and eggs, form zygote
--compatible with blending inheritance (offspring are a mixture of parental traits):
Parents: Blue + Yellow
Green offspring
--compatible with inheritance of acquired characteristics (acquired traits are hereditary)
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Preformationism
-- Dutch, 1600s; microscope development: oberve little people in sperm and eggs
-- Miniature person was called a homunculus; it simply grows to an adult after birth
-- All traits come from one parent, so NOT compatible with pangenesis concept
Germ Plasm: Cells in reproductive organs contain complete set of genetic information that is
passed on to sperm and eggs
6. Compare and contrast the following terms:
a. Eukaryotic and prokaryotic cells:
i. Both have lipid bilayer membrane, DNA genomes, and machinery for
DNA replication, transcription translation, energy metabolism, response to
stimuli, growth and reproduction.
ii. Eukaryotic cells have a nucleus containing chromosomal DNA and
possess internal membrane-bound organelles.
b. Gene and allele
i. A gene is a basic unit of hereditary information, usually encoding a
functional RNA or polypeptide. Alleles are ariant forms of a gene, arising
through mutation.
c. Genotype and phenotype
i. The genotype is the set of genes or alleles inherited by an organism from
its parents. The expression of the genes of a particular genotype, through
interaction with environmental factors, produces the phenotype, the
observable trait.
d. DNA and RNA
i. Both are nucleic acid polymers. RNA contains a ribose sugar, whereas
DNA contains a deoxyribose sugar. RNA also contains uracil as one of the
four bases, whereas DNA contains thymine. The other three bases are
common to both DNA and RNA. Finally, DNA is usually double stranded,
consisting of two complementary strands, whereas RNA is single
stranded.
e. DNA and chromosome
i. Chromosomes are structures consisting of DNA and associated proteins.
The DNA contains the genetic information.
CHAPTER 10
Extra: What are the key properties of hereditary material?
f. Genetic material must contain complex information
g. Must replicate faithfully
h. Must encode the phenotype
i. Must be able to be variable
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7. What were the major contributions from the following scientists:
a. Meischer: purified nuclei contain a compound that is acidic & rich in phosphorus
(named it nuclein)
b. Kossel: Nucleic acids contain nitrogen-containing bases
DNA: adenine (A), cytosine (C), guanine (G), thymine (T)
RNA: A, C, G, Uracil (U) for RNA
c. Levene: Nucleic acids consist of repeating nucleotides: sugar + phosphate + base
i. Tetranucleotide theory
d. Chargaff: Chargaff’s Rules:
i. The amount of T = amount of A (A/T = 1.0)
ii. The amount of C = amount of G (C/G = 1.0)
e. Watson, Crick, Wilkins, Franklin: W&C correctly interpreted X-ray diffraction
data of Wilkins and Franklin by building models: model must be consistent with
X-ray data and with other known properties of DNA (a major clue, Chargaff’s
Rules)
Describe the experiments that the following scientists performed.
8. Griffith:
Lives
Dies
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9. Avery, McCarty, MacLeod
10. Hershey-Chase
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11. Fraenkel, Conrat, Singer
12. Be familiar with the structure and numbering of the all five bases. Draw an example
including the sugar and phosphate.
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13. Describe the structure of DNA. What are the components? What bonds are included?
-- DNA is a double helix (2 strands wind around each other)
-- 2 strands run in opposite orientations (called antiparallel)
-- Sugar-phosphates are on the outside of helix; bases are on the
inside of the helix
-- Two complementary strands held together by H bonds between
the bases, following Chargaff’s Rules:
A base pairs with T (2 H-bonds)
C base pairs with G (3 H-bonds)
[C-G is stronger than A-T]
A phosphodiester bond forms between the -OH groups of adjacent sugars at 3’-C & 5’-C
B-DNA forms a right-handed helix (clockwise spiral) and there are 10 base pairs per helix turn
(3.4 nm/turn)
Major and minor grooves bind proteins that regulate transcription and replication
--A-DNA: It forms when water is NOT plentiful (also a right-handed helix, but is shorter and
wider than B-DNA (not found in organisms)
--Z-DNA: left-handed helix due to specific sequences (e.g., alternating C and G); it play a role in
transcription
14. Describe the three levels of DNA structure?
•
•
•
Primary: linear sequence of covalently- linked nucleotides (called a polynucleotide
strand)
Secondary: 3-D structure (this is the double helix)
Tertiary: packing arrangements of the double helix in the chromosome
15. What is a hairpin and how is it formed?
RNAs form hairpins (stem/loops): sequences in the hairpin are complementary
CHAPTER 11
16. What is supercoiling? How does it come about? What is its purpose? What else do we
know about bacterial DNA packaging?
- requires closed circular DNA molecules (no free ends)
- refers to over-rotating (positive supercoil) or under-rotating (negative supercoil) the circle
-Topoisomerase - enzyme that adds and removes turns
Negative supercoiling: fosters separation of the two strands
–required during replication and transcription (called breathing)
-circular DNA; no histones, but binds other proteins that anchor the DNA, forming loops that
free rotation; loops are supercoiled (& further compacted)
-compacted into a nucleoid
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17. What are organelle genomes and what is the theory about them?
-Chloroplasts and mitochondria have prokaryotic features: circular DNAs, protein synthesis
machinery (prokaryotic-like enzymes for transcription and translation using 70S ribosomes)
-This is a reflection of their endosymbiotic
18. What are the 6 points of eukaryotic chromosome packing that we talked about in class?
1. Packing is dynamic : DNA can exist in a condensed (compacted) state or decondensed
(extended) state, and can change from one to the other (hence, a continuum of condensation)
- decondensed : provides access to DNA strands (e.g., during DNA replication, transcription)
- very condensed: so chromosomes don’t get tangled up when they are moving (e.g., in Mitosis
and Meiosis; at Metaphase plate)
- moderately condensed: during Interphase (part of cell cycle between Mitoses)
2. Point 2: Chromatin = DNA + associated proteins
a. euchromatin: undergoes dynamic packing; it contains nearly all genes and is where
transcription occurs
b. heterochromatin: very highly condensed; present in centromeres, telomeres; inactivated X
(female mammals); most of Y; very little transcription occurs in heterochromatin
3. Chromatin proteins: two classes
-Class one: Histones (50% of chromosomal proteins)
-- 5 types of histone proteins: HI, H2A, H2B, H3, H4
-- all contain positively- charged amino acids (arg, lys, his)
-- they bind PO4-3 of DNA: histone binding to DNA promotes the condensed state (nucleosome
formation)
Class Two: Nonhistone chromosomal proteins (50% chromosomal proteins). These include:
-- structural proteins at centromere (e.g., spindle attachment proteins) & at telomere (e.g.,
proteins that stabilize the chromosome)
-- enzymes involved in transcription and DNA replication (e.g., DNA & RNA
polymerases)
-- other DNA-binding proteins (e.g., regulatory proteins such as transcription factors)
4. Nucleosomes are the “repeating unit” of chromatin (“beads-on-a-string”)
-A nucleosome “core” contains 145-147 base pairs (bp) of DNA wrapped ~1.6X around a histone
octomer (2 each of H2A, H2B, H3 and H4)
5. Point 5: H1 histone clamps DNA to histone octomer; H1 binding requires 20-22 bp DNA
beyond the 145-147 bp (this is the 167 bp nucleosome)
6. : The nucleosome-containing DNA is further packaged by looping, coiling, and compression
to make fibers that are further looped, coiled and compressed
19. Describe centromeres and telomeres. What are their functions and characteristics?
Centromeres: attachment site for spindle microtubules via the kinetochore; composed of
heterochromatin
Centromere identity: determined by the presence of histone CenH3 in place of the usual H3.
Cen3 causes the chromatin to condense into a structure that is recognized as a “centromere”
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This is an epigenetic change: a stable alteration of chromatin structure that can be passed on to
progeny cells; this is NOT a change in the base sequence of the DNA (is not a mutation).
Telomeres: chromosome ends; composed of heterochromatin
Meta-: middle, Telo-: at very end, Acro-: near the end, Submeta-: anything else
2 functions:
1. “Stabilize” chromosomes
2. Provide a means of replicating chromosome ends
Telomeres bind shelterin (a multisubunit protein complex) that prevents degradation of
chromosome ends (by DNA repair enzymes). Shelterin acts as a protective cap.
Telomere is defined by a consensus sequence, called the telomeric sequence: short repeats of
[A/T] followed by several G
G-rich strand protrudes at end of chromosome, called the 3’ overhang, is important for
replication (Ch. 12, Figure 12.19); its length gets shorter as we get older and this phenomenon
might explain aging, also explains some cancers and other diseases
20. What is the c-value? Describe the c-value paradox.
•
•
C-value = amount of DNA in a cell
C-value paradox: why is C-value so variable in eukaryotes? The amount of DNA does
not correlate with biological complexity
21. Describe unique sequence, moderately repetitive and highly repetitive DNA. Include in
your answer information about euchromatin and heterochromatin.
Unique sequence DNA (can be transcribed into RNA)
A. single copy genes
B. gene families = similar but not identical copies of genes, arose via duplication of a
single ancestral gene (several to a few hundred copies)
Moderately repetitive DNA
- short sequences (150 to 300 bp long), repeated 103 – 105 copies/genome!!!
- can be transcribed into RNA
- are tandemly-repeated or interspersed-repeated (scattered throughout genome)
Highly repetitive DNA
- usually <10 bp long (106 or more copies/genome)
- clustered in long tandem arrays, especially at centromeres and telomeres
(heterochromatin); is usually AT-rich
- does not contain genes; is not transcribed
- function is unknown
22. What are gene families?
---members of gene families code for isoforms of a given protein (they differ from one another in
a few amino acids)
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DNA
23. Be able to interpret a kinetics curve.
50%
0%
% ss
100%
T
m
24. Describe the packaging of eukaryotic DNA. What is the difference between the
nucleosome and the chromatosome?
-see number 17
CHAPTER 12
25. Describe the Meselson-Stahl experiment and how it can be applied to the three models of
DNA replication.
CsCl equilibrium density
gradient centrifugation: DNA
migrates to a position in the
gradient that corresponds to its
own buoyant density
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26. Fill in the following table
27. Be able to identify the following areas on a diagram of any model of replication.
a. Origin
b. Replication fork(s)
c. Leading and lagging strand(s)
d. Primers
e. Okazaki fragments
f. Template strands
g. Polarity of both template and new strands
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28. Bacterial DNA replication takes place in what four stages? For each stage, name the
enzymes associated with it.
1. Initiation: initiator proteins
2. Unwinding: DNA Helicase, SSB Proteins, DNA Gyrase
3. Elongation: Primase, DNA Pol III, DNA Pol I, DNA Ligase
4. Termination: Tus Protein
29. Name the three ways bacterial replication keeps a low error rate.
1. DNA Polymerase III active site is very good at nucleotide selection (1 mistake per
100K nt)
2. Pol III also has proofreading activity: if it adds a wrong nucleotide, it will back up,
remove the wrong one (using its 3’ 5’ exonuclease, or proofreading activity), and
insert the correct one (using its 5’ 3’ polymerization activity)
1 & 2 decrease the error rate to 1 mistake in 10 million nucleotides
3. Mismatch repair (will discuss in Ch 18): occurs after replication is finished; mismatch
repair enzymes recognize that the helix is distorted and they correct the error
30. Memorize the following table
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31. State the 8 Basic Rules of Replication
Replication is always semiconservative
Replication begins at sequences called origins
DNA synthesis is initiated by short segments of RNA called primers
The elongation of DNA strands is always in the 5 > 3 direction
New DNA is synthesized from dNTPs; in the polymerization of DNA, two phosphate
groups are cleaved from a dNTP and the resulting nucleotide is added to the 3’ OH
group of the growing nucleotide strand.
6. Replication is continuous on the leading strand and discontinuous on the lagging
strand
7. New nucleotide strands are complementary and antiparallel to their template strands
8. Replication takes place at very high rates and is astonishingly accurate, thanks to
precise nucleotide selection, proofreading, and repair mechanisms
1.
2.
3.
4.
5.
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