Exam 3 - Lecture 14 Flashcards
what is a genome?
all of the DNA present in a cell or virus
what is a genotype?
a specific set of genes an organism possesses
what is a phenotype?
collection of observable characteristics
how many sets of DNA do prokaryotes have? what about eukaryotes?
- prokaryotes: haploid (1N)
- eukaryotes: diploid (2N)
who did the first experiments proving DNA is the genetic material?
Fred Griffith
what was the bacteria used in the transformation experiments?
Streptococcus pneumoniae
explain the transformation experiment done with smooth and rough strains.
- 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
what is a nucleoside? what is a nucleotide?
- nucleoside: nitrogenous base + 5 carbon sugar (ribose)
- nucleotide: nucleoside + phosphate
which strand of the DNA does the mRNA resemble?
the plus (+) strand
can RNA be double stranded?
yeap (folded in on itself)
what are the four major types of RNA?
- messenger (mRNA)
- ribosomal (rRNA)
- transfer (tRNA)
- small regulatory (sRNA)
where does replication complete in circular bacterial DNA?
the terminus
DNA synthesis only occurs in what direction?
5’ to 3’
DNA polymerase adds new bases to what end of the DNA?
the 3’ end
what are the three things DNA polymerase requires?
- template
- primer
- dNTPs
how many DNA polymerases does E. coli have?
5
which DNA polymerase plays the major role in replication in E. coli?
DNA polymerase III
which DNA polymerase is involved in lagging strand synthesis in E. coli?
DNA polymerase I
what is the role of helicase?
unwinding DNA strands
what is the role of single-stranded binding proteins?
keeping the DNA strands apart for replication to occur
what is the role of DNA gyrase & topoisomerases?
alter DNA supercoiling to relieve tension from rapid unwinding of double helix
what is the role of primase?
synthesizes short complementary strands of RNA (~10 nucleotides) to serve as primers needed by DNA pol I
what is the role of ligase?
attaching two pieces of single stranded DNA together
which strand of the DNA is synthesized non-continuously? how about continuously?
- lagging strand: non-continuously
- leading strand: continuously
how many primers does the lagging strand need?
a primer is needed for every Okazaki fragment
which DNA polymerase removes and replaces the RNA primers with DNA?
DNA pol I
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
minor mistakes in DNA synthesis can be corrected by __________ activity
exonuclease
which direction does exonuclease work in?
3’ to 5’
do all polymerases have exonuclease activity?
nah
which DNA polymerase(s) has/have exonuclease activity?
DNA pol III
what is catenation?
when two circular chromosomes do not fully separate after replication
how is catenation solved?
topoisomerases temporarily break DNA molecules so that the strands can separate and then are ligated back into circular formation
what is the end replication problem?
shortening of chromosomes after each round of replication
what enzyme solves the end replication problem?
telomerase
what is another name for a cistron?
a gene
what does CDS stand for in a gene?
coding DNA sequence
which strand is the template strand: the sense or the anti-sense?
anti-sense strand
which strand is the coding strand: the sense or the anti-sense?
sense strand
what is the promoter?
the recognition/binding site for RNA polymerase (-35 and -10 regions)
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)
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)
what is the coding start region?
the DNA sequence 5’-ATG-3’ aka RNA sequence 5’-AUG-3’
what does AUG code for in bacteria?
N-formylmethionine, a modified amino acid used to initiate protein synthesis in bacteria
where does translation stop?
stop codon (UAG, UAA, UGA)
what is a “trailer” in protein coding genes?
a 3’ untranslated region which contains a terminator sequence used to stop transcription
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
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’
true or false: there are exons and introns in bacterial genes.
false; there are no introns or exons.
true or false: bacterial transcripts can be polycistronic or monocistronic.
true
operons are present on monocistronic or polycistronic transcripts?
polycistronic
what is a polycistronic mRNA?
an mRNA that has directions for more than 1 polypeptide in it
what enzyme carries out transcription?
RNA polymerase
how many subunits does RNA polymerase have? what are they?
- two
- the core enzyme + the sigma factor = holoenzyme (RNA pol)
what does the core enzyme do and how many proteins is it composed of?
- catalyzes RNA synthesis
- composed of 5 proteins
what is the purpose of the sigma factor?
has no catalytic activity but helps core enzyme recognize the promoter
what are the two nucleotide positions of the promoter?
- 35 and -10 relative to transcription site (+1)
what enzyme unwinds the DNA in transcription?
RNA polymerase
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
match the following:
- RNA stem loop/transcription terminator
- stop codons (TAG, TAA, TGA)
a. transcription stop site
b. translation stop site
1a
2b
what is Rho-independent transcription termination?
- no proteins involved
- DNA sequence alone results in termination of transcription
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
what is translation?
mRNA is translated into an amino acid sequence/polypeptide chain
what is a codon?
a 3 bp long DNA code that specifies an amino acid
what amino acid does AUG code for?
methionine (start codon)
how many possible codons are there?
64
how many sense codons are there? how about nonsense (stop) codons?
- 61 sense codons
- 3 stops codons
up to how many different codons can code for the same amino acid?
six
what is the anticodon sequence for the tRNA that brings Met (give it in 5’ to 3’)?
CAU
are there exceptions to the genetic code?
yes, some protists only have one stop codon (UGA) and the other two code for Gln instead
what are the 21st and 22nd amino acids found in some microbes?
- selenocysteine Sec; U (UGA)
- pyrrolysine; Pyl; O (UAG)
true or false: some bacteria have exceptions to the start codon.
yeah
what is the direction of polypeptide synthesis: C to N terminal or N to C terminal?
N terminal to C terminal
what is the ribosome?
the site of translation
which domain(s) of life has/have coupled transcription and translation?
bacteria and archaea
what is a polyribosome?
mRNA with multiple ribosomes
which end of tRNA carries the amino acid: 5’ or 3’?
3’
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
true or false: tRNA are recycled.
true
what enzyme catalyzes the attachment of amino acids to tRNAs?
aminoacyl-tRNA synthetases
true of false: recharging of tRNA does not cost energy.
false; it costs ATP
what is the size of the bacterial ribosome? what about the subunits?
70S (30S + 50S subunits)
what are the two types of rRNA in the ribosome?
16S and 23S rRNA
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
what is the function of 23S rRNA?
ribozyme that catalyzes peptide bond formation
what amino acid does bacterial translation start with?
N-formylmethionine
what amino acid does archaeal translation start with?
methionine
