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BIO 214 > Exam 2 > Flashcards

Exam 2 Flashcards

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1
Q

Synthesis of DNA is a non-spontaneous reaction. Energy is provided by ATP hydrolysis. T or F?

A

False

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2
Q

What is the central dogma?

A

DNA replication
RNA synthesis
Protein synthesis
Unity of Life

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3
Q

How does genetic info flow through cells?

A

DNA > transcription > RNA > translation > protein

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4
Q

What is gene expression?

A

Process by which genetic instruction is used to synthesize gene products

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5
Q

Are all genes expressed in at the same level in all cells?

A

No

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6
Q

What is the first step in gene expression?

A

Transcription

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7
Q

What is the main enzyme that catalyzes transcription? Does it require a primer?

A

RNA polymerase

No

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8
Q

What sequences indicate where transcription should start and stop in bacteria?

A

A promoter recognizes the 5’ and 3’ ends

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9
Q

How is transcription initiated in eukaryotes?

A

Promoter

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10
Q

What are 3 ways that RNA differs from DNA (structurally)?

A

Single stranded
Uracil instead of thymine
One more oxygen

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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

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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

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13
Q

Where does translation take place?

A

Cytoplasm

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14
Q

What is a codon?

A

Groups of 3 nucleotides

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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

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16
Q

How many possible codons are there?

A

61 (64)

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17
Q

How many possible amino acids are there?

A

20

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18
Q

Is one amino acid specified by more than one codon?

A

yes

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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

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20
Q

What is the role of tRNA in protein synthesis?

A

adaptors between mRNA and amino acids

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21
Q

How and where is protein synthesis initiated?

A

At the start codon when the amino acid methionine is added in

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22
Q

What roles do initiation factors play?

A

They begin translation

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23
Q

Compare and contrast initiation of translation in prokaryotes and eukaryotes. What AUG is used in each?

A

Prokaryotes

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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

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25
Q

How is translation terminated?

A

Stop codons

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26
Q

What is the catalytic molecule in a ribosome?

A

23S RNA

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27
Q

What is protein degradation and how can it be controlled in the cell?

A

When proteases break down the proteins inside a cell

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28
Q

What are 3 ways that transcription and translation vary between prokaryotes and eukaryotes?

A

Prokaryotes are polycistronic and eukaryotes are monocistronic
Eukaryotes must be processed
Bacterial RNA pol can initiate transcription but eukaryotic pols need accessor proteins

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29
Q

How does each of the two DNA strands act as a template for the synthesis of the other strand?

A

The two strands separate, allowing for new bases to be added in

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30
Q

Where does replication start?

A

Replication origins

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31
Q

What is the template strand of DNA?

A

Original DNA that is on the outside of the bubble

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32
Q

What does ‘semi-conservative replication’ mean?

A

Original strands remain intact

Each new daughter DNA is one old strand and one new strand

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33
Q

How many replication forks are formed at each origin of replication?

A

2 in each bubble

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34
Q

How many polymerases are operating at each replication fork?

A

2

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35
Q

In what direction does DNA polymerase synthesize new DNA?

A

5’ > 3’ (looks opposite in bubble)

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36
Q

What provides the energy for synthesizing DNA?

A

DNA polymerase

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37
Q

What are the leading and lagging strands?

A

The new, synthesized DNA

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38
Q

Why is synthesis of DNA on the lagging strand referred to as discontinuous

A

It is in small pieces due to the fact in needs a primer

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39
Q

What is an Okazaki fragment and how does it tie in with discontinuous synthesis on the lagging strand?

A

It is the small fragments backstitched into the DNA strand

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40
Q

What role does DNA ligase play?

A

Reforms the phosphodiester backbone using energy from ATP hydrolysis

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41
Q

What are the functions of RNA primers?

A

To backstitch the Okazaki fragments in

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42
Q

What is the role of the enzyme primase?

A

Synthesizes RNA primers

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43
Q

What is the proof-reading activity of DNA polymerase?

A

It checks before adding the next nucleotide and can edit

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44
Q

What does it do during replication of DNA?

A

It joins the nucleotides together

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45
Q

How are the very ends of chromosomes replicated on the lagging strands of DNA?

A

Telomerase attaches to the end and connects to nucleotides

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46
Q

Why is DNA repair necessary?

A

To avoid cancer and uncontrolled cell proliferation

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47
Q

How does mismatch repair work?

A

It repairs errors missed by DNA polymerase by distorting the backbone and identifying by mismatch repair proteins

48
Q

How is the incorrect nucleotide identified?

A

By mismatch repair proteins

49
Q

Describe thymine dimers.

A

two adjacent thymines connected together

50
Q

What happens if thymine dimers are not repaired?

A

Can cause a lesion

51
Q

Describe what happens in depurination and what the consequences are if the mistake is not repaired.

A

Can result in the loss of a base pair

52
Q

Describe what happens in deamination and what the consequences are if the mistake is not repaired/how they are repaired.

A

Cytosine is converted to uracil

C-G base pair can be converted to a U-A base pair

53
Q

Describe the repair process for DNA damage.

A
  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
Q

What steps do repair of thymine, dimers, depurination, and deamination have in common/are different?

A

Excision uses different enzymes based on the damage

Steps 2/3 are common for all repair

55
Q

When does mismatch occur?

A

When replicating the DNA

56
Q

How does mismatch repair compare to other repair?

A

Mismatch occurs immediately after synthesis

57
Q

What is a restriction enzyme?

A

Enzymes that digest foreign DNA

58
Q

What is a restriction site?

A

Specific sequences where DNA is cut/digested

59
Q

What are palindromes?

A

Backwards and forwards are the same

60
Q

What is different about a DNA palindrome

A

Base pairs must correlate

61
Q

What types of bonds are broken by restriction enzymes?

A

Phosphodiester bonds

62
Q

What is a compatible cohesive end or sticky end?

A

They must be complimentary (the same)

63
Q

Can sticky ends generated by different restriction enzymes anneal (match/base-pair) to one another?

A

Yes if they are complimentary

64
Q

What is agarose gel electrophoresis? What are 3 ways that it is different from SDS-PAGE?

A

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
Q

How are agarose gels visualized and how does the staining process work?

A

Ethidium bromide slips in between stacked bases

66
Q

Are all regions of the DNA transcribed and translated (and in all cells)?

A

No

67
Q

The main difference between DNA and RNA is that

A

DNA lacks a 2’ hydroxyl group

68
Q

Which would have more severe consequences, an uncorrected mistake in DNA replication or the same mistake during transcription?

A

Mistakes in replication are more severe

69
Q

What is true about splicing?

A

Introns are spliced out of mRNA and exons are kept

70
Q

The RNA/protein machine that performs splicing is called the spliceosome. T or F?

A

True

71
Q

Will it effect the polypeptide if introns are NOT removed?

A

Yes, if introns are not removed, then the reading frame will not be correct, altering the sequence of amino acids

72
Q

Which of the following is a function of tRNA?

A

tRNA transports amino acids

73
Q

Prokaryotic translation starts at the first AUG. T or F?

A

False, prokaryotes are polycistronic and start at AUGs close to the ribosome binding site

74
Q

The start codon, AUG, does not correspond to an amino acid while the stop codons do correspond to amino acids. T or F?

A

False, the start codon is methonine

75
Q

Many antibiotics kill bacteria by blocking their ribosomes. T or F?

A

True

76
Q

In the absence of the enzyme primase, only the leading strand of DNA would be replicated. T or F?

A

False, DNA polymerase always needs a primer

77
Q

When does mismatch repair take place?

A

Immediately after DNA is replicated to catch an errors made by DNA polymerase

78
Q

Deamination and depurination events are repaired by mismatch repair systems. T or F?

A

False, they are repaired by base excision

79
Q

What DNA sequence is likely to be a restriction site?

A

AAGCTT

TTCGAA

80
Q

DNA ligase reforms hydrogen bonds between the nitrogenous bases of sticky ends. T or F?

A

False, DNA ligase reforms phosphodiester bonds of the sugar-phosphate backbones

81
Q

What is the basic flow of steps in a cloning experiment?

A

Digestion with restriction enzymes, ligation, transformation, selection on antibiotics

82
Q

A single DNA strand has polarity because the nitrogenous bases contain amino groups. T or F?

A

False, it refers to the order of the sugar-phosphate backbone

83
Q

G-C base pairs are more stable than A-T base pairs. T or F?

A

True, G-C are held together with 3 hydrogen bonds instead of 2

84
Q

What do centromeres do?

A

Serve as an attachment point for the spindle fibers during mitosis

85
Q

What do telomeres do?

A

Protect the ends of chromosomes during DNA replication

86
Q

What are the levels of chromosome organization, in order from lowest to highest?

A

Nucleosome, 30 nm fiber, supercoiled loops, mitotic chromosomes

87
Q

A motif…

A

Is a recurring substrate

88
Q

What would happen if a mutation caused the amino acid aspartic acid to be changed to glutamic acid?

A

The protein would still function as an enzyme

89
Q

What would happen if a mutation caused the amino acid aspartic acid to be changed to lysine (basic amino acid)?

A

The protein would probably no longer function as an enzyme

90
Q

Protein-ligand (or protein-substate) interactions are mediated by covalent bonds. T or F?

A

False, covalent bonds are strong but can only be broken by an enzyme which is too strong

91
Q

Phosphorylation of a protein by a kinase will always increase protein activity. T or F?

A

False, depending on the protein, phosphorylation can turn it on or off

92
Q

How did Griffith’s and Avery and MacLeod’s experiments demonstrate that DNA was the transforming principle?

A

Hereditary information can be transferred from one bacterium to another
The molecule that transforms ‘R’ to S-strain is DNA

93
Q

How is genetic information encoded in DNA?

A

In the sequences of nitrogenous bases

94
Q

What type of bond connects nucleotides together in DNA and RNA?

A

Hydrogen bonds

95
Q

What are 3 differences between the structure of DNA and RNA?

A

Double stranded
Uracil instead of Thymine
One less oxygen in DNA

96
Q

What are the base pairing rules for DNA?

A

Purine Pyrimidine
A———-T
G———-C

97
Q

What are the base pairing rules for RNA?

A

A-U

G-C

98
Q

Do RNA molecules have 3-D structures?

A

No, they are linear

99
Q

How are the two strands of the DNA double helix held together?

A

Hydrogen bonds and pairs of bases

100
Q

Why is DNA considered a polar molecule?

A

Because it has 5’ and 3’ ends

101
Q

How is DNA stored in eukaryotic cells?

A

Organized into chromosomes

102
Q

What segments are required for a chromosome to be maintained and replicated?

A

Telomeres (tips)

103
Q

What two types of molecules together make up chromatin?

A

A long linear DNA and protein, so that it can be more compact

104
Q

What is a nucleosome and how is it constructed?

A

DNA + histones (octamer) = nucleosome

105
Q

How does the amino acid composition of histones allow the proteins to interact with DNA?

A

DNA wraps around the histone octamer and HI links the DNA together

106
Q

What is a 30 nm fiber and how is it constructed?

A

Supercoiled chromatin

107
Q

How is the 30 nm fiber further packaged?

A

Packaged in a zig-zag model

108
Q

What are the levels of chromosome packaging?

A

DNA > nucleosomes > chromatin > chromatin loops > condensed > chromosome

109
Q

How does DNA packaging influence gene expression?

A

Tight packaging around histones can cause genetic inactivity

110
Q

What is heterochromatin?

A

Compacted chromatin including centromeres, telomeres, and some genes

111
Q

What is euchromatic?

A

Diffused state of DNA

112
Q

What is X-inactivation?

A

Two doses of some proteins on the X-chromosome are lethal so one must be turned off (i.e. calico cats)

113
Q

What are the chromatin remodeling complexes and how do they influence gene expression?

A

They loosen DNA, making it more accessible

114
Q

How is chromatin structure dynamic?

A

Chromatin remodeling can loosen DNA to make it more accessible

115
Q

How is chromatin heritable?

A

Turns into chromosomes and becomes replicated in meiosis

BIO 214 (2 decks)

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