BIO 1203 > Exam Five > Flashcards

Exam Five Flashcards

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1
Q

DNA is composed of four nucleotides,

A

while proteins contained 20 distinct amino acids.

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2
Q

DNA discovery timeline:

A

1866 - Gregor Mendel
1944 - Oswald Avery
1950 - Erwin Chargaff
1952 - Rosalind Franklin
1953 - Watson & Crick
1962 - Marshall Nirenberg

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3
Q

Chargaff’s Rules:

A

Amount of adenine = Amount of thymine / Amount of cytosine = Amount of guanine

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4
Q

A single strand of DNA extends in what direction?

A

5’ to 3’.

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5
Q

Two strands are arranged as the double helix, forming two grooves. What are these called?

A

Larger major groove + smaller minor groove.

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6
Q

How many hydrogen bonds are created in base pairs?

A

Two between A and T, three between C and G.

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7
Q

Explain the anti-parallel configuration of phosphodiester strands:

A

5’-3’ or 3’-5’, because the two strands of a single DNA molecule have opposite polarity to one another.

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8
Q

How and why are the three models of DNA replication different?

A

The three models of DNA replication are different because of how they are copied.
1. Conservative model - both strands of the parental DNA remain intact, new DNA copies consist of all new molecules.
2. Semiconservative model - daughter strands each consist of one parental strand and one new strand.
3. Dispersive model - new DNA is dispersed throughout each strand of both daughter molecules after replication.

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9
Q

Which model of DNA replication is accurate?

A

Semiconservative model.

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10
Q

What is needed to replicate DNA?

A
  1. Something to copy - Parental DNA molecule.
  2. Something to do the copying - Enzymes.
  3. Building blocks to make copy - Nucleotide triphosphates.
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11
Q

Stages of DNA replication:

A

Initiation - replication begins.
Elongation - new strands of DNA are synthesized by DNA polymerase.
Termination- replication is terminated.

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12
Q

What’s the role/function of DNA polymerase?

A

DNA polymerase matches existing DNA bases with complimentary nucleotides, linking them together, which builds the new DNA strands.

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13
Q

What do all DNA polymerase share?

A

They all add new bases to the 3’ end of strands, they synthesize in the 5’ to 3’ direction, and they all require a primer of RNA.

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14
Q

How are RNA polymerase and DNA polymerase connected to each other?

A

RNA polymerase makes primer, then DNA polymerase extends the primer.

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15
Q

What is the role of helicases in DNA replication?

A

Unwind DNA

Helicases use energy from ATP to separate the DNA strands.

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16
Q

What are Okazaki fragments?

A

DNA fragments on the lagging strand

These fragments are synthesized discontinuously and must be joined together.

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17
Q

What is the function of DNA ligase?

A

Joins Okazaki fragments

DNA ligase is essential for forming complete DNA strands on the lagging strand.

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18
Q

What is a replisome?

A

Macromolecular assembly of enzymes in DNA replication

It includes primase, helicase, and two DNA polymerases.

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19
Q

True or false: DNA replication is bidirectional from a unique origin.

A

TRUE

This means replication proceeds in both directions around the chromosome.

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20
Q

What is the function of topoisomerases during DNA replication?

A

Prevent supercoiling

Topoisomerases relieve torsional strain introduced during DNA unwinding.

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21
Q

What is the first stage of DNA synthesis by the replisome?

A

Access the text alternative for slide images.

This stage involves the initial setup for DNA replication.

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22
Q

What is the second stage of DNA synthesis by the replisome?

A

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This stage continues the preparation for DNA replication.

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23
Q

What is the third stage of DNA synthesis by the replisome?

A

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This stage further develops the replication process.

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24
Q

What is the fourth stage of DNA synthesis by the replisome?

A

Access the text alternative for slide images.

This stage is crucial for completing DNA replication.

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25
What is the **fifth stage** of DNA synthesis by the replisome?
Access the text alternative for slide images. ## Footnote This stage finalizes the DNA replication process.
26
Eukaryotic replication is more complex than in **prokaryotes** due primarily to:
* Larger amount of DNA in multiple chromosomes * Linear structure (versus circular chromosomes) ## Footnote These factors contribute to the complexity of eukaryotic DNA replication.
27
Eukaryotic replication uses **multiple origins**. What are they called?
Multiple replicons ## Footnote Each chromosome has multiple origins of replication.
28
What is the role of **helicases** before the S phase in eukaryotic replication?
Loaded onto possible replication origins, but not activated ## Footnote This prepares the replication sites for activation during the S phase.
29
During the S phase, a subset of helicases is activated, and the rest of the **replisome** is assembled. What is the priming complex composed of?
Both DNA polymerase α and primase ## Footnote This complex is essential for initiating DNA synthesis.
30
Which DNA polymerase synthesizes the **leading strand**?
DNA polymerase epsilon (Pol ε) ## Footnote This enzyme is responsible for continuous DNA synthesis.
31
Which DNA polymerase synthesizes the **lagging strand**?
DNA polymerase delta (Pol δ) ## Footnote This enzyme synthesizes DNA in fragments on the lagging strand.
32
What are **telomeres**?
Specialized structures found on the ends of eukaryotic chromosomes ## Footnote They protect the ends of chromosomes from nucleases and maintain integrity.
33
What problem does the replication of the end of linear DNA present?
The last primer removed from the 3′ end of the lagging strand cannot be replaced ## Footnote This leads to shortening of chromosomes with each round of cell division.
34
What is **telomerase**?
An enzyme that synthesizes the telomere repeat sequences at the ends of strands ## Footnote It uses an internal RNA template for this process.
35
Telomerase activity is developmentally regulated. When is it **high**?
In early development/childhood ## Footnote This regulation is crucial for proper cell division during growth.
36
Telomerase plays a role in **senescence/aging**. What happens to mice that completely lack telomerase activity?
They had nonviable offspring after six generations ## Footnote This indicates the importance of telomerase in reproductive viability.
37
Cancer cells generally show activation of **telomerase** to maintain what?
Telomere length ## Footnote This allows cancer cells to continue dividing indefinitely.
38
What are **mutagens**?
Any agent that increases the number of mutations above background level ## Footnote Examples include radiation and chemicals.
39
What are the two categories of **DNA repair**?
* Specific repair * Nonspecific repair ## Footnote These categories define how DNA damage is addressed.
40
What does **mismatch repair (MMR)** do?
Removes incorrect bases incorporated during DNA replication ## Footnote It replaces them with the correct base by copying the template strand.
41
In E. coli, mismatch repair involves methylation of the A in the sequence **5′ GATC 3′**. What does this allow?
Distinguishing between the template strand and the newly synthesized strand ## Footnote This is crucial for accurate DNA repair.
42
What is an example of a specific repair mechanism?
Photorepair ## Footnote This mechanism addresses thymine dimers caused by UV light.
43
What does the **photolyase enzyme** do?
Absorbs light in the visible range and uses this energy to cleave thymine dimer ## Footnote This is part of the photorepair process.
44
What is **excision repair**?
Nonspecific repair where damaged region is removed and replaced by DNA synthesis ## Footnote It involves recognition of damage, removal of the damaged region, and resynthesis using the undamaged strand as a template.
45
What is the central dogma?
DNA → RNA → Protein
46
What enzyme performs transcription?
RNA polymerase
47
What are the stages of transcription?
Initiation
48
Which DNA strand is used as the template?
Template (antisense) strand
49
What is a promoter?
DNA sequence where RNA polymerase binds
50
What is the start codon?
AUG (methionine)
51
What are the stop codons?
UAA
52
What does mRNA do?
Carries genetic information to ribosomes
53
What does tRNA do?
Brings amino acids to the ribosome
54
What does rRNA do?
Forms the ribosome and catalyzes peptide bonds
55
What is a codon?
Three-base mRNA sequence that specifies an amino acid
56
What is an anticodon?
Three-base tRNA sequence that pairs with a codon
57
What does degenerate genetic code mean?
Multiple codons encode the same amino acid
58
What is wobble pairing?
Flexibility in the 3rd codon position
59
What are the ribosome sites?
A site
60
Where does transcription occur in eukaryotes?
Nucleus
61
Where does translation occur?
Cytoplasm
62
What does RNA polymerase II synthesize?
mRNA
63
What are the processing steps for eukaryotic mRNA?
5’ cap
64
What is alternative splicing?
Different exon combinations create different proteins
65
What is a mutation?
Change in DNA sequence
66
What is a missense mutation?
Mutation that changes one amino acid
67
What is a nonsense mutation?
Mutation that creates a stop codon
68
What is a silent mutation?
Mutation that does not change the amino acid sequence
69
What is a frameshift mutation?
Insertion or deletion that shifts the reading frame
70
Why can’t eukaryotes couple transcription and translation?
Transcription is in the nucleus and translation is in the cytoplasm
71
Why can prokaryotes couple transcription and translation?
Both processes occur in the cytoplasm
72
What are introns?
Noncoding sequences removed during splicing
73
What are exons?
Coding sequences that remain in mRNA
74
What is a sigma factor?
Protein that helps RNA polymerase bind the promoter
75
Why do cells regulate gene expression?
Prokaryotes respond to the environment; eukaryotes specialize and maintain stability
76
What is an operon?
Cluster of genes under one promoter in prokaryotes
77
What is the lac operon?
Inducible operon activated by lactose and low glucose
78
What is the trp operon?
Repressible operon turned off when tryptophan is present
79
What is an inducer?
Molecule that turns on transcription
80
What is a corepressor?
Molecule that helps shut off transcription
81
What molecule induces the lac operon?
Allolactose
82
What is CAP/cAMP?
Activator system that increases lac operon transcription when glucose is low
83
What is positive control?
Activator increases transcription
84
What is negative control?
Repressor decreases transcription
85
What are general transcription factors?
Proteins required for RNA polymerase II initiation
86
What are specific transcription factors?
Proteins that regulate particular genes
87
What is an enhancer?
DNA sequence that increases transcription
88
How do enhancers work from far away?
DNA loops to bring the enhancer close to the promoter
89
What is chromatin?
DNA wrapped around histone proteins
90
What is a nucleosome?
DNA wrapped around a histone octamer
91
What is chromatin remodeling?
Moving or altering nucleosomes to change DNA accessibility
92
What does histone acetylation do?
Loosens chromatin and increases transcription
93
What does histone deacetylation do?
Tightens chromatin and decreases transcription
94
What does DNA methylation do?
Silences genes
95
What is epigenetics?
Heritable changes in gene expression not caused by DNA sequence changes
96
What do miRNA and siRNA do?
Block translation or degrade mRNA
97
What is RNA interference?
Gene silencing by miRNA or siRNA
98
What is ubiquitination?
Tagging proteins for degradation
99
What is the proteasome?
Complex that degrades ubiquitin-tagged proteins
100
Why is eukaryotic gene expression more complex?
Chromatin structure and multiple layers of control
101
What is differential gene expression?
Different cells express different sets of genes
102
What are housekeeping genes?
Genes expressed in all cells at all times
103
What is attenuation in the trp operon?
Early termination of transcription when tryptophan levels are high
104
What is a regulatory gene?
Gene that encodes a repressor or activator
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