Exam 3 - Lecture 14 Flashcards
1
Q
what is a genome?
A
all of the DNA present in a cell or virus
2
Q
what is a genotype?
A
a specific set of genes an organism possesses
3
Q
what is a phenotype?
A
collection of observable characteristics
4
Q
how many sets of DNA do prokaryotes have? what about eukaryotes?
A
- prokaryotes: haploid (1N)
- eukaryotes: diploid (2N)
5
Q
who did the first experiments proving DNA is the genetic material?
A
Fred Griffith
6
Q
what was the bacteria used in the transformation experiments?
A
Streptococcus pneumoniae
7
Q
explain the transformation experiment done with smooth and rough strains.
A
- smooth cells (S strain) have capsules and kill the host mouse
- rough cells (R strain) have no capsule and do not kill the host
- heat-killed S strains do not kill the host
- live R strain with heat-killed S strain kills the host because the unharmful R strain transformed with the DNA of the lethal S strain
8
Q
what is a nucleoside? what is a nucleotide?
A
- nucleoside: nitrogenous base + 5 carbon sugar (ribose)
- nucleotide: nucleoside + phosphate
9
Q
which strand of the DNA does the mRNA resemble?
A
the plus (+) strand
10
Q
can RNA be double stranded?
A
yeap (folded in on itself)
11
Q
what are the four major types of RNA?
A
- messenger (mRNA)
- ribosomal (rRNA)
- transfer (tRNA)
- small regulatory (sRNA)
12
Q
where does replication complete in circular bacterial DNA?
A
the terminus
13
Q
DNA synthesis only occurs in what direction?
A
5’ to 3’
14
Q
DNA polymerase adds new bases to what end of the DNA?
A
the 3’ end
15
Q
what are the three things DNA polymerase requires?
A
- template
- primer
- dNTPs
16
Q
how many DNA polymerases does E. coli have?
A
5
17
Q
which DNA polymerase plays the major role in replication in E. coli?
A
DNA polymerase III
18
Q
which DNA polymerase is involved in lagging strand synthesis in E. coli?
A
DNA polymerase I
19
Q
what is the role of helicase?
A
unwinding DNA strands
20
Q
what is the role of single-stranded binding proteins?
A
keeping the DNA strands apart for replication to occur
21
Q
what is the role of DNA gyrase & topoisomerases?
A
alter DNA supercoiling to relieve tension from rapid unwinding of double helix
22
Q
what is the role of primase?
A
synthesizes short complementary strands of RNA (~10 nucleotides) to serve as primers needed by DNA pol I
23
Q
what is the role of ligase?
A
attaching two pieces of single stranded DNA together
24
Q
which strand of the DNA is synthesized non-continuously? how about continuously?
A
- lagging strand: non-continuously
- leading strand: continuously
25
how many primers does the lagging strand need?
a primer is needed for every Okazaki fragment
26
which DNA polymerase removes and replaces the RNA primers with DNA?
DNA pol I
27
DNA ligase forms a bond between what in the lagging strand?
between the 3'-hydroxyl of the growing strand and the 5'-phosphate of an Okazaki fragment
28
minor mistakes in DNA synthesis can be corrected by __________ activity
exonuclease
29
which direction does exonuclease work in?
3' to 5'
30
do all polymerases have exonuclease activity?
nah
31
which DNA polymerase(s) has/have exonuclease activity?
DNA pol III
32
what is catenation?
when two circular chromosomes do not fully separate after replication
33
how is catenation solved?
topoisomerases temporarily break DNA molecules so that the strands can separate and then are ligated back into circular formation
34
what is the end replication problem?
shortening of chromosomes after each round of replication
35
what enzyme solves the end replication problem?
telomerase
36
what is another name for a cistron?
a gene
37
what does CDS stand for in a gene?
coding DNA sequence
38
which strand is the template strand: the sense or the anti-sense?
anti-sense strand
39
which strand is the coding strand: the sense or the anti-sense?
sense strand
40
what is the promoter?
the recognition/binding site for RNA polymerase (-35 and -10 regions)
41
what is the leader sequence?
- 5' untranslated region that is transcribed into mRNA but not into amino acids
- region between the +1 transcription start site and translation start site (ATG)
42
what is the Shine-Dalgarno sequence?
- sequence important for initiation of translation
- ribosome binding site located in the 5' UTR (typically 6-10 nucleotides upstream of start codon)
43
what is the coding start region?
the DNA sequence 5'-ATG-3' aka RNA sequence 5'-AUG-3'
44
what does AUG code for in bacteria?
N-formylmethionine, a modified amino acid used to initiate protein synthesis in bacteria
45
where does translation stop?
stop codon (UAG, UAA, UGA)
46
what is a "trailer" in protein coding genes?
a 3' untranslated region which contains a terminator sequence used to stop transcription
47
what does the transcription terminator do? what kind of DNA sequence does it have?
its DNA sequence is a palindrome and as it's transcribed, it forms a hairpin loop that knocks RNA polymerase off the DNA, stopping transcription
48
put these components in order of 5' to 3':
- coding region
- leader
- terminator
- promoter
- trailer
- transcription start
- 5'
- promoter
- leader
- transcription start
- coding region
- trailer
- terminator
- 3'
49
true or false: there are exons and introns in bacterial genes.
false; there are no introns or exons.
50
true or false: bacterial transcripts can be polycistronic or monocistronic.
true
51
operons are present on monocistronic or polycistronic transcripts?
polycistronic
52
what is a polycistronic mRNA?
an mRNA that has directions for more than 1 polypeptide in it
53
what enzyme carries out transcription?
RNA polymerase
54
how many subunits does RNA polymerase have? what are they?
- two
- the core enzyme + the sigma factor = holoenzyme (RNA pol)
55
what does the core enzyme do and how many proteins is it composed of?
- catalyzes RNA synthesis
- composed of 5 proteins
56
what is the purpose of the sigma factor?
has no catalytic activity but helps core enzyme recognize the promoter
57
what are the two nucleotide positions of the promoter?
- 35 and -10 relative to transcription site (+1)
58
what enzyme unwinds the DNA in transcription?
RNA polymerase
59
in what direction does RNA polymerase read the template strand? why?
- 3' to 5'
- so that the RNA is synthesized in the 5' to 3' direction
60
match the following:
1. RNA stem loop/transcription terminator
2. stop codons (TAG, TAA, TGA)
a. transcription stop site
b. translation stop site
1a
2b
61
what is Rho-independent transcription termination?
- no proteins involved
- DNA sequence alone results in termination of transcription
62
what is Rho-dependent termination?
- protein factor rho binds to the mRNA at the rut (rho-utilization) site
- rho moves along the mRNA in same direction as RNA pol
- RNA pol pauses at the rho terminator
- rho catches up and knocks RNA pol off
63
what is translation?
mRNA is translated into an amino acid sequence/polypeptide chain
64
what is a codon?
a 3 bp long DNA code that specifies an amino acid
65
what amino acid does AUG code for?
methionine (start codon)
66
how many possible codons are there?
64
67
how many sense codons are there? how about nonsense (stop) codons?
- 61 sense codons
- 3 stops codons
68
up to how many different codons can code for the same amino acid?
six
69
what is the anticodon sequence for the tRNA that brings Met (give it in 5' to 3')?
CAU
70
are there exceptions to the genetic code?
yes, some protists only have one stop codon (UGA) and the other two code for Gln instead
71
what are the 21st and 22nd amino acids found in some microbes?
- selenocysteine Sec; U (UGA)
- pyrrolysine; Pyl; O (UAG)
72
true or false: some bacteria have exceptions to the start codon.
yeah
73
what is the direction of polypeptide synthesis: C to N terminal or N to C terminal?
N terminal to C terminal
74
what is the ribosome?
the site of translation
75
which domain(s) of life has/have coupled transcription and translation?
bacteria and archaea
76
what is a polyribosome?
mRNA with multiple ribosomes
77
which end of tRNA carries the amino acid: 5' or 3'?
3'
78
a tRNA with an amino acid attached is also known as a __________ tRNA. one without an amino acid is known as an __________ tRNA.
charged; uncharged
79
true or false: tRNA are recycled.
true
80
what enzyme catalyzes the attachment of amino acids to tRNAs?
aminoacyl-tRNA synthetases
81
true of false: recharging of tRNA does not cost energy.
false; it costs ATP
82
what is the size of the bacterial ribosome? what about the subunits?
70S (30S + 50S subunits)
83
what are the two types of rRNA in the ribosome?
16S and 23S rRNA
84
what is the function of 16S rRNA?
- binds to the Shine Dalgarno site to initiate protein synthesis
- binds initiation factor 3 (protein) to the 3' charged end of tRNA
85
what is the function of 23S rRNA?
ribozyme that catalyzes peptide bond formation
86
what amino acid does bacterial translation start with?
N-formylmethionine
87
what amino acid does archaeal translation start with?
methionine
