1
Q
What are the three components of a nucleotide
A
A pentose sugar (deoxyribose in DNA, ribose in RNA), a phosphate group, and a nitrogenous base
2
Q
What are the Chargaff rules?
A
The amount of Adenine (A) equals Thymine (T). The amount of Guanine (G) equals Cytosine (C)
3
Q
What bond links nucleotides together in a strand of DNA?
A
Phosphodiester bonds
4
Q
What bonds hold base pairs together in DNA?
A
Hydrogen bonds
5
Q
How do RNA and DNA differ?
A
DNA is double stranded, uses Thymine, and lacks a 2’-OH group. RNA is single stranded, uses Uracil, and has a 2’-OH group
6
Q
What are the requirements for DNA replication?
A
Template strand, dNTPs (nucleotides), enzymes/proteins
7
Q
What is the replication fork?
A
The Y-shaped region where DNA strands are unwound
8
Q
What is the replication bubble?
A
The loop formed by unwinding DNA undergoing replication
9
Q
How many origins of replication do bacteria have compared to eukaryotes?
A
Bacteria have one, eukaryotes have many
10
Q
What does helicase do?
A
Unwinds the DNA helix at the replication fork
11
Q
What do single-strand binding proteins do?
A
Stabilize single DNA strands
12
Q
What does topoisomerase do?
A
Relieves tension caused by unwinding DNA
13
Q
What enzyme synthesizes RNA primers?
A
Primase
14
Q
In which direction is DNA synthesized?
A
In the 5’ -> 3’ direction
15
Q
What enzyme adds new DNA nucleotides
A
DNA polymerase
16
Q
What is the leading strand?
A
The strand synthesized continuously towards the replication fork
17
Q
What is the lagging strand?
A
The strand synthesized discontinuously away from the fork in Okazaki fragments
18
Q
Why are leading strands and lagging strands necessary?
A
Because DNA strands are antiparallel
19
Q
What enzyme replaced RNA primers with DNA?
A
DNA polymerase I
20
Q
What enzyme seals nicks in DNA strands?
A
DNA ligase
21
Q
What enzyme proofreads and corrects DNA replication errors?
A
DNA polymerase III
22
Q
What repair mechanism fixes damaged DNA segments?
A
Nucleotide excision repair
23
Q
Why is eukaryotic DNA replication more complex?
A
Larger genome, multiple linear chromosomes, and DNA packaging into chromosomes
24
Q
What is chromatin?
A
DNA-protein complex forming chromosomes
25
What is euchromatin?
Less condensed, transcriptionally active chromatin
26
What is heterochromatin?
Highly condensed, transcriptionally inactive chromatin
27
Where is permanent heterochromatin found?
Centromeres and telomeres
28
What is facultative heterochromatin?
Temporarily inactivated chromatin, like an inactive X chromosome in females
29
What is gene expression?
The process by which DNA directs the synthesis of proteins, including transcription and translation
30
What are the two main stages of gene expression?
Transcription and translation
31
About how many protein-coding genes do humans have?
Around 20,000
32
What does transcription produce?
Messenger RNA (mRNA)
33
What does translation produce?
A polypeptide (protein)
34
What evidence suggests RNA may have been the original genetic material?
RNA can act as a catalyst (ribozyme), cut and join RNA molecules, and form peptide bonds
35
Why can RNA form more varied structures than DNA?
It is single-stranded and can fold into complex shapes
36
What are three key functions of RNA?
Information carrier (mRNA), adapter for translation (tRNA), and structural/catalytic roles (rRNA, ribozymes)
37
What does transcription require?
A DNA template, RNA polymerase, and accessory proteins
38
What is the template strand?
The DNA strand used as a template to make RNA
39
What is the non-template (coding) strand?
The complementary DNA strand not used in transcription
40
What are the three parts of a transcription unit?
Promoter, coding region, terminator
41
What enzyme synthesizes RNA?
RNA polymerase
42
In what direction does RNA synthesis occur?
5′ → 3′
43
How does RNA polymerase differ from DNA polymerase?
It does not need a primer to start synthesis
44
How many RNA polymerases do bacteria have?
One (holoenzyme)
45
How many RNA polymerases do eukaryotes have?
At least three (I, II, III)
46
What do transcription factors do?
Help RNA polymerase bind to the promoter and initiate transcription
47
What are the three stages of transcription?
Initiation, elongation, and termination
48
What signals the start point for transcription?
The promoter
49
What sequence is often found in eukaryotic promoters?
The TATA box
50
What is the transcription initiation complex?
RNA polymerase II plus transcription factors bound to the promoter
51
How many transcription factors are typically involved in eukaryotic initiation?
More than 12
52
How fast does transcription proceed in eukaryotes?
~40 nucleotides per second
53
What is a transcription bubble?
The unwound region of DNA (~18 bases) inside RNA polymerase
54
How does transcription end in bacteria?
RNA polymerase stops at a terminator; RNA is ready for translation
55
How does transcription end in eukaryotes?
RNA polymerase II transcribes the polyadenylation signal (AAUAAA), and the transcript is released 10–35 bases later
56
What three modifications occur during RNA processing?
5′ capping, 3′ poly-A tail addition, and intron splicing
57
What is the function of the 5′ cap?
Protects mRNA from degradation and helps ribosome attachment
58
What is the function of the 3′ poly-A tail?
Protects mRNA and aids in export from the nucleus
59
What are introns?
Noncoding regions removed from pre-mRNA
60
What are exons?
Coding regions that remain and are joined to form mRNA
61
What enzyme complex removes introns and joins exons?
The spliceosome
62
What is alternative RNA splicing?
Process by which one gene can produce multiple mRNA variants and proteins
63
What is the triplet code?
A series of three-nucleotide words (codons) that specify amino acids in a protein
64
How many possible codons exist?
64 (4³) possible combinations (61 code for amino acids, 3 are stop codons)
65
What is the start codon and what amino acid does it code for?
AUG, codes for methionine
66
What does it mean that the genetic code is redundant?
Multiple codons can specify the same amino acid
67
What does it mean that the genetic code is universal?
All organisms use the same code to translate mRNA into proteins
68
What sets the reading frame for translation?
The start codon
69
What is translation?
The process of synthesizing a polypeptide from mRNA
70
Where does translation occur?
At ribosomes in the cytoplasm (or rough ER)
71
What are the requirements for translation?
mRNA, amino acids, energy (ATP & GTP), ribosomes, and tRNA
72
What are the stages of translation?
tRNA charging, initiation, elongation, termination
73
What is the function of tRNA?
Transfers specific amino acids to the ribosome according to the mRNA codon
74
What is an anticodon?
A three-base sequence on tRNA that pairs with a complementary mRNA codon
75
What enzyme attaches an amino acid to it's tRNA
Aminoacyl-tRNA synthetase
76
How many different aminoacyl-tRNA synthetases exist?
20, one for each amino acid
77
What are ribosomes made of?
Ribosomal RNA (rRNA) and proteins
78
What are the two subunits of a ribosome?
Large and small subunits
79
What happens when ribosomal subunits join?
They form a complete ribosome only when attached to mRNA.
80
What are the three tRNA binding sites on a ribosome?
A site: holds tRNA with the next amino acid
P site: holds tRNA with growing peptide chain
E site: exit site for empty tRNA
81
What happens during the initiation stage of translation?
The small ribosomal subunit binds to the 5′ cap of mRNA; initiator tRNA binds to AUG; large subunit completes the complex
82
What are the three stages of elongation during translation?
Codon recognition, peptide bond formation, and translocation
83
What facilitates codon recognition during translation elongation?
A charged tRNA and elongation factor EF-Tu using GTP
84
What catalyzes peptide bond formation during translation elongation?
A ribosomal RNA (rRNA) molecule within the large ribosomal subunit
85
What happens during translocation during translation elongation?
The ribosome moves 5′ → 3′; tRNA shifts from A → P → E site
86
What signals termination of translation?
A stop codon in the A site
87
What protein recognizes stop codons?
A release factor
88
What energy molecule is used during termination?
GTP (for hydrolysis and complex disassembly)
89
What are free ribosomes?
Ribosomes that synthesize proteins used in the cytosol
90
What are bound ribosomes?
Ribosomes attached to the ER that synthesize secreted or membrane proteins
91
What directs proteins to the ER?
A signal peptide
92
What assists in folding of new polypeptides?
Molecular chaperones
93
What are post-translational modifications?
Cleavage from precursor proteins
Addition of carbohydrates
Phosphorylation, acetylation, methylation
Ubiquitination for degradation
Removal of signal sequences
94
What is a mutation?
A change in the DNA sequence
95
What are point mutations?
Changes in a single nucleotide pair
96
What is a substitution mutation?
One base pair is replaced by another
97
What is a silent mutation?
A substitution that doesn’t change the amino acid due to redundancy
98
What is a missense mutation?
A substitution that changes one amino acid to another
99
What is a nonsense mutation?
A substitution that changes an amino acid codon into a stop codon, creating a truncated protein
100
What are insertions and deletions?
Additions or losses of nucleotide pairs that often cause frameshift mutations
101
What is a frameshift mutation?
A mutation that alters the reading frame, drastically changing all downstream amino acids
102
What is differential gene expression and why is it important?
The expression of different sets of genes by cells that have the same genome. In multicellular organisms, it is essential for cell specialization
103
What are the two main chemical modifications to chromatin that regulate gene expression?
Histone actetylation: attaches acetyl groups to histone tails, loosens the chromatin structure, promotes transcription. DNA methylation: adds methyl groups to DNA, leads to more condensed chromatin, inhibits transcription
104
What is the difference between general and specific transcription factors, and where do they bind?
General transcription factors are required for a low level of transcription for all genes, and bind to the promoter region to help RNA polymerase bind. Specific transcription factors are responsible for high level cell specific expression, and bind to control elements grouped into enhancers
Biology 2107
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