Exam 3 Study Guide

Chapter 9 Molecular Structure of DNA and RNA

1. Characteristics of the Genetic Material
a. To fulfill its role, genetic material must meet these four criteria:
i. Information: It needs to carry all the information to make an entire
organism.
ii. Transmission: It must be passed from parents to offspring.
iii. Replication: It must be copied accurately to pass it on during
reproduction.
iv. Variation: It must have the ability to change to explain the differences
between species.
2. Experimental Evidence for DNA as the Genetic Material
a. Griffith and Transformation
i. What Griffith did: He worked with a bacterium called Streptococcus
pneumoniae, which had two types of bacteria: smooth (S) bacteria
that caused disease and rough (R) bacteria that didn't. When he
mixed dead S bacteria with live R bacteria, the harmless R bacteria
turned into disease-causing bacteria.
1. Type S (smooth): It has a polysaccharide capsule.
2. Type R (rough): It has no capsule.
ii. What he found: He concluded that something from the dead type S
bacteria was transforming the live type R bacteria into the harmful
type S. He called this process transformation, but he didn’t know
what caused the transformation (transforming principle).
b. Avery, MacLeod, and McCarty and Identification of the Transforming
Principle
i. What they did: They used Griffith's idea to figure out what the
"transforming principle" was. They purified different macromolecules
(DNA, RNA, protein) from type S cells.
ii. What they found: Only DNA could transform type R into type S. They
treated the samples with RNase (which destroys RNA) and protease
(which destroys proteins), but the transformation still occurred. When
they used DNase (which destroys DNA), the transformation stopped,
meaning it was responsible for passing genetic information, not
protein or RNA.
 c. Hershey Chase Blender Experiment on Bacteriophage
i. What they did: They used a virus (called a bacteriophage) that infects
bacteria. They labeled DNA with radioactive phosphorus (32P) and
proteins with radioactive sulfur (35S). After the virus infected the
bacteria, they used a blender to separate the virus from the bacteria.
ii. What they found: The radioactive DNA (32P) was inside the bacteria,
but the protein (35S) stayed outside, proving that DNA, not protein,
was the genetic material passed into the bacteria.
3. Structure of DNA
a. Structure of Nucleotides
i. Nucleotides are the building blocks of DNA and RNA. They consist of:
1. Phosphate group
2. Pentose Sugar (deoxyribose in DNA, ribose in RNA)
3. Nitrogenous base (A, T, C, G for DNA; A, U, C, G for RNA)
b. Features of a DNA Strand and Double Helix
i. In a DNA strand, nucleotides are linked together by phosphodiester
bonds (which connect the phosphate of one nucleotide to the sugar
of the next).
ii. DNA strands are antiparallel, meaning they run in opposite directions
(one 5’ to 3’, the other 3’ to 5’).
iii. DNA has 5’ to 3’ directionality.
iv. The helix is right-handed.
v. The DNA forms a double helix, where:
1. A pairs with T, and C pairs with G through hydrogen bonds
(complementary bases).
a. A bonded to T = 2 hydrogen bonds.
b. C bonded to G = 3 hydrogen bonds.
2. The bases are stacked on the inside, and the sugar-phosphate
backbone is on the outside.
3. About 10.0 nucleotides in each strand per complete 360 turn
of the helix.
c. Solving the Structure of DNA by Franklin, Wilkins, Watson, and Crick
i. Rosalind Franklin and Maurice Wilkins: Franklin used X-ray
diffraction to study DNA and found that it had a helical structure with
more than one strand and 10 base pairs per turn.
ii. James Watson and Francis Crick: They used Franklin’s data, along
with Chargaff’s Rule (A = T, C = G), to propose the double helix
structure of DNA. They built ball-and-stick models and figured out
 that A pairs with T and C pairs with G because the hydrogen bonding
between them was structurally similar.
d. Major vs. Minor Grooves
i. DNA has two types of asymmetrical grooves on the outside of the
helix: a major groove (larger) and a minor groove (smaller). Certain
proteins bind to these grooves to interact with specific sequences of
DNA.
4. RNA Structure
a. Features of RNA
i. RNA is single-stranded and uses uracil (U) instead of thymine (T).
ii. It uses ribose with 2’ OH as its sugar instead of deoxyribose.
iii. RNA strands are typically shorter than DNA strands, with several
hundred to a few thousand nucleotides.
iv. In RNA synthesis, 1 out of 2 strands of DNA is used as a template.
b. RNA Secondary Structures
i. Although RNA is single-stranded, it allows short regions to form a
double helix by complementary base pairing (A pairs with U, C pairs
with G).
ii. RNA can form different secondary structures like:
1. Bulge loops
2. Internal loops
3. Multibranched loops
4. Stem-loops
iii. RNA double helices are usually right-handed, with 11 to 12 base pairs
per turn.

Chapter 11. DNA Replication

1. General Concepts in Replicating DNA Strands
a. DNA replication is the process by which DNA is copied. The original strands
(called parental strands) act as templates for new strands (called daughter
strands).
b. DNA replication happens quickly, accurately, and at the right time during a
cell’s life.
c. The two DNA strands separate, and each becomes a template for a new
complementary strand, following the A-T and C-G base-pairing rules.
2. Semin-conservative Mode of DNA Replication
a. Three models of replication were proposed:
 i. Conservative model: Both original (parental) DNA strands stay
together.
ii. Semiconservative model: Each new DNA double helix contains one
parental strand and one newly made strand. This is the correct
model.
iii. Dispersive model: Parental and daughter DNA are mixed together in
both strands.
b. Meselson and Stahl (Heavy and Light Nitrogen Isotope-labeling) Experiment
i. What they did: They labeled DNA with heavy and light nitrogen
isotopes and centrifuged the DNA after replication to see if it was
semi-conservative.
ii. What they found: After one replication cycle, DNA was "half-heavy,"
and after two cycles, there were two bands—one light and one half-
heavy. This result fit the semiconservative model.
3. Bacterial DNA Replication
a. Origin of Replication
i. DNA replication in bacteria starts at a specific spot called the origin
of replication (oriC in E. coli).
ii. Proteins like DnaA bind to the origin, causing the DNA strands to
separate.
iii. Helicase further unwinds the DNA using energy from ATP.
iv. Replication occurs in both directions from the origin, forming two
replication forks.
b. Directionality of DNA Synthesis (5’-3’)
i. DNA strands are antiparallel (run in opposite directions), and DNA is
always synthesized in the 5’ to 3’ direction.
ii. DNA synthesis begins with the help of RNA primers made by the
enzyme primase.
iii. DNA polymerase III then adds new nucleotides to the 3’ end of the
primer.
c. Components of the Replisome (Helicase, Gyrase, Primase, and Polymerase)
i. Helicase: Unwinds the DNA helix.
ii. Gyrase (Topoisomerase II): Relieves supercoiling caused by
helicase.
iii. Primase: Synthesizes RNA primers to start DNA synthesis.
iv. DNA Polymerase: The enzyme that adds new nucleotides to form the
new DNA strand.
d. Characteristics of DNA Polymerase
 i. DNA polymerase cannot start synthesizing DNA on its own—it needs
an RNA primer.
ii. It can only synthesize DNA in the 5’ to 3’ direction, but since the two
DNA strands are antiparallel, they are synthesized differently.
e. Leading vs. Lagging Strand (Okazaki Fragments and DNA Ligase)
i. Leading Strand:
1. DNA is made continuously in one smooth direction, 5’ to 3’, as
the replication fork opens.
2. This strand is easier to make because DNA polymerase moves
in the same direction as the opening fork.
ii. Lagging Strand:
1. DNA on this strand is made in short pieces called Okazaki
fragments because it moves in the opposite direction of the
replication fork.
2. DNA ligase connects these fragments, gluing them together to
make the strand whole.
iii. The Looping (Trombone) Model of Synthesis by Replisome on the
Lagging Strand
1. The lagging strand loops out to let DNA polymerase work
smoothly on both strands.
2. When an Okazaki fragment is finished, the loop releases and
reforms to start the next fragment, just like pulling on a
trombone.
4. Eukaryotic DNA Replication
a. Differences Compared to Bacteria
i. Eukaryotic DNA is more complicated because:
1. It has many starting points for replication (bacteria usually
have just one).
2. Eukaryotic DNA is tightly packed with proteins called
nucleosomes.
3. It’s linked with the cell cycle, so it’s more controlled
compared to bacteria.
b. The Problem at the End of Chromosomes
i. DNA polymerase can’t fully copy the ends of chromosomes (the
telomeres), so they would get shorter after every replication.
ii. Telomeres and Telomerase
 1. Telomeres are the protective caps at the ends of
chromosomes. They stop important DNA from getting lost
during replication.
2. Telomerase is an enzyme that adds extra sequences to the
telomeres, keeping them from shortening too much.
a. This helps prevent the chromosome from shrinking,
especially in cells that divide a lot.
b. Telomerase is important in aging (shorter telomeres are
linked to aging) and cancer (cancer cells often keep
telomerase active so they can keep dividing).

Chapter 12 Gene Transcription and RNA Modification

1. What is a gene?
a. A gene is a segment of DNA that makes a functional product, like RNA or a
polypeptide (a chain of amino acids that forms proteins).
b. Transcription is the process where DNA is copied into RNA, which is the first
step in making proteins (this is part of the Central Dogma: DNA → RNA →
Protein).
2. General Concepts and Principles
a. DNA-Protein Interactions Central to Transcription
i. DNA sequences tell the cell where to start and stop making RNA.
ii. Proteins recognize and bind to DNA sequences to start the
transcription process.
b. Regulatory Proteins and Sequences
i. Regulatory sequences are parts of DNA where proteins bind to
control the rate of transcription (e.g., promoters for starting
transcription, terminators for stopping it).
ii. Regulatory proteins can either increase or decrease transcription
by binding to these sequences.
3. Transcription in Bacteria
a. Stages of Transcription
i. Initiation: RNA polymerase binds to the promoter and unwinds the
DNA to start transcription.
ii. Elongation: RNA polymerase moves along the DNA, making an RNA
copy.
iii. Termination: RNA polymerase stops and releases the newly made
RNA when it reaches a terminator sequence.
b. Promoter Sequences (-35 and -10 Consensus)
 i. Promoters are sequences on DNA that tell RNA polymerase where to
start.
ii. In bacteria, promoters have two important regions:
1. -35 and -10 regions, which are called consensus sequences
because they are the most common promoter sequences.
RNA polymerase recognizes these sequences to begin
transcription.
c. RNA Polymerase Holoenzyme (Core Enzyme and Sigma Factor)
i. RNA polymerase is the enzyme that makes RNA from the DNA
template.
ii. It has different parts, including:
1. The core enzyme (which does the copying).
2. The sigma factor, which helps RNA polymerase find the right
promoter by recognizing the -35 and -10 sequences.
d. Rho-dependent and -independent Transcriptional Termination
i. Rho-dependent termination: Uses a protein called rho to stop
transcription.
ii. Rho-independent termination: Doesn’t need rho; instead, it relies on
specific RNA sequences that form a hairpin structure and a uracil-rich
area to stop transcription.
4. Transcription in Eukaryotes
a. General Differences Compared to Bacteria
i. Eukaryotic transcription is more complex because:
1. Eukaryotes have larger genomes with more genes.
2. Eukaryotes have three types of RNA polymerases (RNA pol I,
II, and III) to transcribe different types of RNA.
3. Transcription is regulated to ensure that genes are expressed
at the right time and in the right cells.
5. RNA Modifications
a. Introns and Exons
i. In eukaryotes, exons are the coding sequences, and introns are non-
coding sequences. After transcription, introns are removed, and
exons are spliced together to make the final RNA (this process is
called splicing).
b. RNA Splicing (Group I, Group II, and Spliceosome Introns)
i. Group I and II introns: These introns self-splice, meaning they can
remove themselves from the RNA without the help of proteins.
 ii. Spliceosome: A complex made of snRNPs (small nuclear RNAs +
proteins) that helps remove introns from pre-mRNA in eukaryotic
cells. It cuts out introns and joins the exons together.
c. Additional RNA Modifications
i. 5’ Capping: A 7-methylguanosine cap is added to the 5’ end of the
RNA to help with RNA stability, translation, and exit from the nucleus.
ii. 3’ Poly-A Tail: A string of adenines (A’s) is added to the 3’ end to help
protect the RNA and assist in translation.

Chapter 13. Translation of mRNA

1. The Genetic Code
a. Features of the Code
i. The genetic code is read in groups of three nucleotides called
codons.
ii. Start codon: AUG (methionine) marks where translation starts.
iii. Stop codons: UAA, UAG, and UGA signal the end of translation.
iv. The code is degenerate, meaning multiple codons can code for the
same amino acid (e.g., GGU, GGC, GGA, GGG all code for glycine).
b. Relationship between Gene Sequence, Codons, and Protein Product
i. mRNA is translated into a sequence of amino acids (the building
blocks of proteins) using the genetic code.
2. Protein Structure
a. Polypeptide Directionality (N- and C-terminus)
i. Proteins are made from a chain of amino acids called a polypeptide.
ii. The first amino acid has a free amino group (N-terminus), and the
last has a free carboxyl group (C-terminus).
b. General Characteristics of Amino Acids
i. Amino acids are classified as:
1. Nonpolar (hydrophobic, buried inside proteins)
2. Polar (hydrophilic, often on the surface of proteins)
3. Acidic or basic (charged)
ii. Amino acids determine how proteins fold and function.
3. Solving the Genetic Code
a. Nirenberg and Protein Synthesis in a Test Tube
i. Nirenberg used synthetic RNA and cell-free translation systems to
figure out which codons correspond to which amino acids.
b. Khorana and Synthesis of Specific Messages
 i. Khorana developed a method to make specific RNA sequences (e.g.,
UCU, CUC) and used them to determine which codons code for
which amino acids.
c. Triplet Nucleotide Binding Assays
i. Nirenberg and Leder discovered that specific RNA triplets can bind
tRNAs, helping to decode the genetic code.
4. Transfer RNA (tRNA)
a. Aminoacyl tRNA Synthetase
i. Aminoacyl-tRNA synthetase is an enzyme that attaches the correct
amino acid to its corresponding tRNA. There’s one for each of the 20
amino acids.
b. Anticodons and Wobble Hypothesis
i. The anticodon on tRNA binds to the complementary codon on mRNA.
ii. The Wobble Hypothesis explains that the third base of a codon can
be flexible (wobble), allowing tRNAs to recognize multiple codons for
the same amino acid.
5. The Bacterial Ribosome
a. Subunits and A-, P-, and E-sites
i. Ribosomes have two subunits:
1. Small subunit (30S in bacteria)
2. Large subunit (50S in bacteria)
ii. Ribosomes have three sites:
1. A site: Where new tRNAs carrying amino acids enter.
2. P site: Where the growing polypeptide chain is held.
3. E site: Where empty tRNAs exit.
b. Three Stages of Translation
i. Initiation: The small ribosomal subunit binds mRNA at the Shine-
Dalgarno sequence (in bacteria). The start codon (AUG) is
recognized by the initiator tRNA, which carries methionine.
ii. Elongation: The ribosome moves along mRNA, adding amino acids
one by one to the growing polypeptide chain.
iii. Termination: When the ribosome reaches a stop codon (UAA, UAG,
or UGA), a release factor binds, ending translation and releasing the
polypeptide.

Chapter 14. Gene Regulation in Bacteria

1. General Concepts of Gene Regulation from Transcription to Protein Modification
 a. Gene regulation means that the level of gene expression changes under
different conditions.
b. Constitutive genes are always active and have constant expression levels
because they are needed for survival.
c. Regulated genes help bacteria respond to:
i. Metabolism
ii. Environmental stress
iii. Cell division
d. Gene regulation can happen at many points in gene expression:
i. During transcription: Proteins can bind to DNA and increase or
decrease how much RNA is made.
ii. During translation: Proteins can bind to RNA and stop it from being
translated into protein.
iii. After translation: Changes to the protein itself can affect its function.
2. Inducible and Repressible Gene Regulation
a. Activators, Repressors
i. Activators: These proteins bind to DNA and increase transcription
(positive control).
ii. Repressors: These proteins bind to DNA and stop transcription
(negative control).
b. Inducers, Corepressors/Inhibitors
i. Inducers: These are small molecules that turn on gene expression by:
1. Binding to activators and helping them bind to DNA.
2. Binding to repressors and preventing them from binding to
DNA.
3. Genes regulated by inducers are called inducible genes.
ii. Corepressors/Inhibitors: These small molecules turn off gene
expression by:
1. Corepressors help repressors bind to DNA and block
transcription.
2. Inhibitors stop activators from binding to DNA.
3. Genes regulated by corepressors and inhibitors are called
repressible genes.
3. The lac Operon
a. The lac operon is a set of genes in E. coli that helps the bacteria use lactose
as food.
b. It includes:
i. Promoter: Where RNA polymerase binds to start transcription.
 ii. Operator: Where the lac repressor binds to stop transcription.
iii. CAP site: Where an activator (CAP) binds to increase transcription.
c. Negative Regulation by the lac Repressor and Operator
i. When lactose is absent:
1. The lac repressor binds to the operator, stopping RNA
polymerase from transcribing the lac genes.
ii. When lactose is present:
1. Allolactose (a form of lactose) binds to the lac repressor,
causing it to fall off the operator. This allows transcription to
happen, and the genes for lactose metabolism are expressed.
d. Positive Regulation by Glucose, cAMP, CAP, and the CAP Site
i. When glucose is low, cAMP levels increase. cAMP binds to the CAP
protein, helping it bind to the CAP site.
ii. CAP then helps RNA polymerase bind to the promoter, increasing
transcription of the lac operon.
iii. If glucose is present, cAMP levels are low, so CAP doesn't bind, and
the lac operon is less active.

Chapter 15. Gene Regulation in Eukaryotes

1. General Concepts of Gene Regulation from Transcription to Protein Modification
a. Gene regulation is how cells control when, where, and how much a gene is
expressed (turned on/off).
b. Regulation ensures that the right genes are active at the correct stages (e.g.,
during development or in different cell types like muscle or nerve cells).
c. Gene regulation happens at multiple points: during transcription,
translation, or even after a protein is made (post-translational modification).
2. General and Regulatory Transcription Factors
a. General Transcription Factors:
i. These are needed for basic transcription to happen by helping RNA
polymerase bind to the promoter of the gene. This is called basal
transcription (basic level of gene expression).
b. Regulatory Transcription Factors:
i. These proteins control the rate of transcription. They bind to specific
DNA sequences called regulatory elements near the promoter.
c. Activators and Enhancers
i. Activators: Increase the rate of transcription by binding to
enhancers.
d. Repressors and Silencers
 i. Repressors: Decrease the rate of transcription by binding to
silencers.
3. Transcription Factor Protein Domains and Motifs
a. Domains: Sections of transcription factors that have specific roles, like
binding to DNA or interacting with other proteins.
b. Motifs: Structural patterns within domains that are commonly found in many
transcription factors.
c. Examples of motifs:
i. Helix-turn-helix
ii. Zinc finger
iii. Leucine zipper
4. Modulation of Regulatory Transcription Factors
a. Small Molecule Effectors, Protein-Protein Interactions, Chemical
Modifications
i. How transcription factors are controlled:
1. Small molecule effectors: Molecules like hormones can bind
to transcription factors and change their activity (e.g., steroids
like glucocorticoids).
2. Protein-protein interactions: Transcription factors may need
to interact with other proteins to work.
3. Chemical modifications: Phosphorylation (adding a
phosphate group) can change how a transcription factor
behaves.
b. Glucocorticoid Receptor Example
i. Glucocorticoids are hormones that regulate metabolism. When
glucocorticoids enter the cell, they bind to the glucocorticoid
receptor, which then moves to the nucleus and activates genes by
binding to Glucocorticoid Response Elements (GREs).
5. Chromatin Remodeling and Histone Modifications
a. Nucleosome Positioning and Composition
i. Chromatin remodeling is how the structure of DNA wrapped around
histones (nucleosomes) changes. This can make genes more or less
accessible for transcription.
ii. Remodeling can move nucleosomes or replace histones with
different variants to allow or block access to DNA.
b. The Histone Code – Consequences of Histone Acetylation
 i. Histones can be chemically modified (e.g., acetylation, methylation,
phosphorylation), and these modifications can either open up
chromatin for transcription or compact it to block transcription.
ii. Histone acetylation typically loosens the chromatin structure,
allowing for active transcription.