Exam 2 Flashcards
1
Q
Synthesis of DNA is a non-spontaneous reaction. Energy is provided by ATP hydrolysis. T or F?
A
False
2
Q
What is the central dogma?
A
DNA replication
RNA synthesis
Protein synthesis
Unity of Life
3
Q
How does genetic info flow through cells?
A
DNA > transcription > RNA > translation > protein
4
Q
What is gene expression?
A
Process by which genetic instruction is used to synthesize gene products
5
Q
Are all genes expressed in at the same level in all cells?
A
No
6
Q
What is the first step in gene expression?
A
Transcription
7
Q
What is the main enzyme that catalyzes transcription? Does it require a primer?
A
RNA polymerase
No
8
Q
What sequences indicate where transcription should start and stop in bacteria?
A
A promoter recognizes the 5’ and 3’ ends
9
Q
How is transcription initiated in eukaryotes?
A
Promoter
10
Q
What are 3 ways that RNA differs from DNA (structurally)?
A
Single stranded
Uracil instead of thymine
One more oxygen
11
Q
What are the 4 major types of DNA and what are their functions?
A
mRNA: code for proteins
rRNA: form structure and catalyze protein synthesis
miRNA: regulate gene expression
tRNA: adaptors between mRNA and amino acids during protein synthesis
12
Q
What are 3 ways that eukaryotic mRNAs must be processed in the nucleus before they are translated in the cytosol?
A
Capping: 7mG cap (add special nucleotide)
Polyadenylation: adding A’s
Splicing: introns releasing
13
Q
Where does translation take place?
A
Cytoplasm
14
Q
What is a codon?
A
Groups of 3 nucleotides
15
Q
How is the genetic code translated into a specific amino acid?
A
Cod of the mRNA is read in groups of 3 nucleotides
16
Q
How many possible codons are there?
A
61 (64)
17
Q
How many possible amino acids are there?
A
20
18
Q
Is one amino acid specified by more than one codon?
A
yes
19
Q
What is tRNA charging and why is it important that it be done correctly?
A
Synthetase connects amino acid with it’s matching tRNA and is hydrolyzed to AMP
20
Q
What is the role of tRNA in protein synthesis?
A
adaptors between mRNA and amino acids
21
Q
How and where is protein synthesis initiated?
A
At the start codon when the amino acid methionine is added in
22
Q
What roles do initiation factors play?
A
They begin translation
23
Q
Compare and contrast initiation of translation in prokaryotes and eukaryotes. What AUG is used in each?
A
Prokaryotes
24
Q
Why can’t the first AUG in the mRNA be used to start translation in prokaryotes?
A
They are polycistronic and encode more than one protein
25
How is translation terminated?
Stop codons
26
What is the catalytic molecule in a ribosome?
23S RNA
27
What is protein degradation and how can it be controlled in the cell?
When proteases break down the proteins inside a cell
28
What are 3 ways that transcription and translation vary between prokaryotes and eukaryotes?
Prokaryotes are polycistronic and eukaryotes are monocistronic
Eukaryotes must be processed
Bacterial RNA pol can initiate transcription but eukaryotic pols need accessor proteins
29
How does each of the two DNA strands act as a template for the synthesis of the other strand?
The two strands separate, allowing for new bases to be added in
30
Where does replication start?
Replication origins
31
What is the template strand of DNA?
Original DNA that is on the outside of the bubble
32
What does 'semi-conservative replication' mean?
Original strands remain intact
| Each new daughter DNA is one old strand and one new strand
33
How many replication forks are formed at each origin of replication?
2 in each bubble
34
How many polymerases are operating at each replication fork?
2
35
In what direction does DNA polymerase synthesize new DNA?
5' > 3' (looks opposite in bubble)
36
What provides the energy for synthesizing DNA?
DNA polymerase
37
What are the leading and lagging strands?
The new, synthesized DNA
38
Why is synthesis of DNA on the lagging strand referred to as discontinuous
It is in small pieces due to the fact in needs a primer
39
What is an Okazaki fragment and how does it tie in with discontinuous synthesis on the lagging strand?
It is the small fragments backstitched into the DNA strand
40
What role does DNA ligase play?
Reforms the phosphodiester backbone using energy from ATP hydrolysis
41
What are the functions of RNA primers?
To backstitch the Okazaki fragments in
42
What is the role of the enzyme primase?
Synthesizes RNA primers
43
What is the proof-reading activity of DNA polymerase?
It checks before adding the next nucleotide and can edit
44
What does it do during replication of DNA?
It joins the nucleotides together
45
How are the very ends of chromosomes replicated on the lagging strands of DNA?
Telomerase attaches to the end and connects to nucleotides
46
Why is DNA repair necessary?
To avoid cancer and uncontrolled cell proliferation
47
How does mismatch repair work?
It repairs errors missed by DNA polymerase by distorting the backbone and identifying by mismatch repair proteins
48
How is the incorrect nucleotide identified?
By mismatch repair proteins
49
Describe thymine dimers.
two adjacent thymines connected together
50
What happens if thymine dimers are not repaired?
Can cause a lesion
51
Describe what happens in depurination and what the consequences are if the mistake is not repaired.
Can result in the loss of a base pair
52
Describe what happens in deamination and what the consequences are if the mistake is not repaired/how they are repaired.
Cytosine is converted to uracil
| C-G base pair can be converted to a U-A base pair
53
Describe the repair process for DNA damage.
1. Excision of segment of damaged strand
2. Repair DNA pol and fill in missing nucleotides in top strand using the bottom strand as a template
3. DNA ligase seals nick
54
What steps do repair of thymine, dimers, depurination, and deamination have in common/are different?
Excision uses different enzymes based on the damage
| Steps 2/3 are common for all repair
55
When does mismatch occur?
When replicating the DNA
56
How does mismatch repair compare to other repair?
Mismatch occurs immediately after synthesis
57
What is a restriction enzyme?
Enzymes that digest foreign DNA
58
What is a restriction site?
Specific sequences where DNA is cut/digested
59
What are palindromes?
Backwards and forwards are the same
60
What is different about a DNA palindrome
Base pairs must correlate
61
What types of bonds are broken by restriction enzymes?
Phosphodiester bonds
62
What is a compatible cohesive end or sticky end?
They must be complimentary (the same)
63
Can sticky ends generated by different restriction enzymes anneal (match/base-pair) to one another?
Yes if they are complimentary
64
What is agarose gel electrophoresis? What are 3 ways that it is different from SDS-PAGE?
Separating DNA fragments according to size
Different:
1. SDS has uniform charge
2. SDS interrupts structure
3. gel electrophoresis is for DNA-negative charge of the sugar-phosphate backbone
65
How are agarose gels visualized and how does the staining process work?
Ethidium bromide slips in between stacked bases
66
Are all regions of the DNA transcribed and translated (and in all cells)?
No
67
The main difference between DNA and RNA is that
DNA lacks a 2' hydroxyl group
68
Which would have more severe consequences, an uncorrected mistake in DNA replication or the same mistake during transcription?
Mistakes in replication are more severe
69
What is true about splicing?
Introns are spliced out of mRNA and exons are kept
70
The RNA/protein machine that performs splicing is called the spliceosome. T or F?
True
71
Will it effect the polypeptide if introns are NOT removed?
Yes, if introns are not removed, then the reading frame will not be correct, altering the sequence of amino acids
72
Which of the following is a function of tRNA?
tRNA transports amino acids
73
Prokaryotic translation starts at the first AUG. T or F?
False, prokaryotes are polycistronic and start at AUGs close to the ribosome binding site
74
The start codon, AUG, does not correspond to an amino acid while the stop codons do correspond to amino acids. T or F?
False, the start codon is methonine
75
Many antibiotics kill bacteria by blocking their ribosomes. T or F?
True
76
In the absence of the enzyme primase, only the leading strand of DNA would be replicated. T or F?
False, DNA polymerase always needs a primer
77
When does mismatch repair take place?
Immediately after DNA is replicated to catch an errors made by DNA polymerase
78
Deamination and depurination events are repaired by mismatch repair systems. T or F?
False, they are repaired by base excision
79
What DNA sequence is likely to be a restriction site?
AAGCTT
| TTCGAA
80
DNA ligase reforms hydrogen bonds between the nitrogenous bases of sticky ends. T or F?
False, DNA ligase reforms phosphodiester bonds of the sugar-phosphate backbones
81
What is the basic flow of steps in a cloning experiment?
Digestion with restriction enzymes, ligation, transformation, selection on antibiotics
82
A single DNA strand has polarity because the nitrogenous bases contain amino groups. T or F?
False, it refers to the order of the sugar-phosphate backbone
83
G-C base pairs are more stable than A-T base pairs. T or F?
True, G-C are held together with 3 hydrogen bonds instead of 2
84
What do centromeres do?
Serve as an attachment point for the spindle fibers during mitosis
85
What do telomeres do?
Protect the ends of chromosomes during DNA replication
86
What are the levels of chromosome organization, in order from lowest to highest?
Nucleosome, 30 nm fiber, supercoiled loops, mitotic chromosomes
87
A motif...
Is a recurring substrate
88
What would happen if a mutation caused the amino acid aspartic acid to be changed to glutamic acid?
The protein would still function as an enzyme
89
What would happen if a mutation caused the amino acid aspartic acid to be changed to lysine (basic amino acid)?
The protein would probably no longer function as an enzyme
90
Protein-ligand (or protein-substate) interactions are mediated by covalent bonds. T or F?
False, covalent bonds are strong but can only be broken by an enzyme which is too strong
91
Phosphorylation of a protein by a kinase will always increase protein activity. T or F?
False, depending on the protein, phosphorylation can turn it on or off
92
How did Griffith's and Avery and MacLeod's experiments demonstrate that DNA was the transforming principle?
Hereditary information can be transferred from one bacterium to another
The molecule that transforms 'R' to S-strain is DNA
93
How is genetic information encoded in DNA?
In the sequences of nitrogenous bases
94
What type of bond connects nucleotides together in DNA and RNA?
Hydrogen bonds
95
What are 3 differences between the structure of DNA and RNA?
Double stranded
Uracil instead of Thymine
One less oxygen in DNA
96
What are the base pairing rules for DNA?
Purine Pyrimidine
A----------T
G----------C
97
What are the base pairing rules for RNA?
A-U
| G-C
98
Do RNA molecules have 3-D structures?
No, they are linear
99
How are the two strands of the DNA double helix held together?
Hydrogen bonds and pairs of bases
100
Why is DNA considered a polar molecule?
Because it has 5' and 3' ends
101
How is DNA stored in eukaryotic cells?
Organized into chromosomes
102
What segments are required for a chromosome to be maintained and replicated?
Telomeres (tips)
103
What two types of molecules together make up chromatin?
A long linear DNA and protein, so that it can be more compact
104
What is a nucleosome and how is it constructed?
DNA + histones (octamer) = nucleosome
105
How does the amino acid composition of histones allow the proteins to interact with DNA?
DNA wraps around the histone octamer and HI links the DNA together
106
What is a 30 nm fiber and how is it constructed?
Supercoiled chromatin
107
How is the 30 nm fiber further packaged?
Packaged in a zig-zag model
108
What are the levels of chromosome packaging?
DNA > nucleosomes > chromatin > chromatin loops > condensed > chromosome
109
How does DNA packaging influence gene expression?
Tight packaging around histones can cause genetic inactivity
110
What is heterochromatin?
Compacted chromatin including centromeres, telomeres, and some genes
111
What is euchromatic?
Diffused state of DNA
112
What is X-inactivation?
Two doses of some proteins on the X-chromosome are lethal so one must be turned off (i.e. calico cats)
113
What are the chromatin remodeling complexes and how do they influence gene expression?
They loosen DNA, making it more accessible
114
How is chromatin structure dynamic?
Chromatin remodeling can loosen DNA to make it more accessible
115
How is chromatin heritable?
Turns into chromosomes and becomes replicated in meiosis
