exam 3 Flashcards
nucleic acid
biopolymer made of monomer units called nucleotides
what are nucleotides?
- nitrogenous base derived from purine or pyrimidine
- contain: pentose sugar, ribose or deoxyribose, phosphoric acid
difference between dna and rna?
no U (uracil) in DNA, no T (thymine) in RNA
nucleotides are linked by what?
phosophodiester bond between phosphate group at C-5’ and the OH on the C-3’
T pairs to
A
G pairs to
C
how many h bonds between t and a?
2
how many h bonds between g and c?
3
double helix
two antiparallel strands are coiled in a right handed manner; structure is based on xray crystallography
histone
a protein particularly rich in basic AAs (lys and arg) found in eukaryotic dna
what is chromatin?
dna molecules wound around particles of histones in a beadlike structure
structure of chromatin
each bead is a nucleosome
each nucleosome consists of
DNA wrapped around histone core
RNA
pentose unit is ribose
- single stranded (can have double stranded regions)
- pyrimidine base uracil instead of thymine
prokaryotic replication (summarized)
separation of 2 original strands and synthesis of 2 new daughter strands using originals as templates
why is replication labelled as semiconservative?
b/c each daughter dna contains one template strand and one new one
dna replication steps
- dna unwinds at origin of replication
- new chains are synthesized in both directions from origin of replication (bidirectional)
- there are TWO replication forks
- 1 origin of replication and 2 replication forks in prokaryotes
in dna replication of euks, there are several…
origins of replication and two replication forks at each origin
dna polymerase functions have the following requirements:
dTTP, dATP, dGTP, dCTP (deoxyribonucleoside triphosphates)
- Mg2+ (cofactor)
- RNA primer
dna polymerase iii is responsible for
polymerization
dna polymerase i is responsible for
the removal of primer and replacing it with DNA
dna is synthesized in a
5’ to 3’ direction
leading strand is synthesized
continuously in a 5’ to 3’ direction
lagging strand is synthesized
discontinuously (okazaki fragments) in a 5’ to 3’ direction, AWAY from the replication fork
dna polymerase reaction
- the 3’OH group at the end of the growing DNA chain acts as a nucleophile
- phosphorus adjacent to the sugar is attacked and then added to the growing chain
helicase is
a helix-destabilizing protein, promotes unwinding by binding at the replication fork
SSB protein is responsible for
stabilizing single stranded regions by binding tightly to them
dna primase purpose
- dna polymerase needs an existing 3’OH
- RNA serves as a primer in dna replication
primase catalyzes
copying of a short stretch of dna template to produce rna primer (~10-20 nucleotides long)
which direction does DNA polymerase 3 synthesize in?
5’ to 3’ (thus the reason for the leading and lagging strands)
what are okazaki fragments?
produced from lagging strand that is replicated discontinuously
what are okazaki fragments sealed together by?
ligas
in prokaryotic dna replication, both dna strands are
synthesized concurrently by looping the lagging strand
topoisomerase function
relieves supercoiling
topoisomerase introduces
a nick in supercoiled dna
- a swivel point is created at the site of the nick
- opens and reseals the swivel point in advance of the replication fork
summary of dna replication in prokaryotes
- dna synthesis is bidirectional
- dna synthesis is in 5’ to 3’ direction
- leading strand is formed continuously towards rep fork
- lagging strand is formed as a series of okazaki fragments glued by ligase later
- topoisomerase introduces a swivel point in advance of the rep fork
- helicase binds and promotes unwinding at the rep fork
- SSB protein protects exposed regions of SS dna and keeps DNA single stranded
- primase catalyzes the synthesis of RNA
- synthesis of new DNA strand (catalyzed pol III, RNA primer removed/replaced w/ DNA, DNA ligase seals nicks)
proofreading in dna is
the removal of incorrect nucleotides via exonuclease activity to prevent errors (mutations) that can occur every 10^6 to 10^9 base pairs
dna polymerase iii has (x) exonuclease activity
3’ to 5’
dna polymerase i has (x) exonuclease activity
5’ to 3’ (which is how RNA is removed and replaced with DNA, synthesized simultaneously in same direction)
what do telomeres do?
- at the end of linear chromosomes
- consist of long stretches of short repeating sequences
- preserve integrity/stability of chromosomes
telomeres are in
eukaryotes
in dna rep in eukaryotes, synthesis at the end of the chromosome is a problem bc…
once RNA primer is gone, free 3’-OH group is not available to continue synthesis
telomerase is an
enzyme that synthesizes the telomere to fill the gap
- ribonucleoprotein with an RNA that serves as the template for the synthesis of its DNA complement
- reverse transcriptase
dna replication yields….
two dna molecules, identical to original one
transcription summary
sequences of bases in DNA is recorded as a sequence of complementary bases in a single stranded mRNA molecule
translation summary
- three base codons on the mRNA corresponding to specific AAs direct the sequences of building a protein
- these codons are recognized by tRNAs carrying AAs
- ribosomes are the ‘machinery’ for protein synthesis
tRNA transports
AAs to site of protein synthesis (small in size)
ribosomal RNA combines
with proteins to form ribosomes (site of protein synthesis) - variable in size
mRNA directs
AA sequence of protein (variable in size)
small nuclear RNA processes
initial mRNA to its mature form in eukaryotes (small in size)
small interfering RNA affects
gene expression (small in size)
micro RNA affects
gene expression (important in growth and development) - small in size
what does mRNA do?
- delivers genetic info from DNA to ribosomes for the synthesis of proteins
- present in cells in relatively small amounts and very short-lived
- single stranded
tRNA characteristics
- single stranded
- has double stranded regions
- clover leaf structure
- carries an AA at its 3’ end
rRNA
- ribonucleic acid found in ribosomes
- ribosomes consist of 60-65% rRNA and 35-40% protein
- both proks and euks, ribosomes have 2 subunits
transcription overview
- synthesized on DNA template by RNA polymerase
- DNA template is unchanged
- requires ATP, GTP, CTP, UTP, Mg2+
- synthesized in 5’ to 3’ direction
- DNA base sequence contains signals for initiation and termination of RNA synthesis
DNA strand that serves as the template for RNA synthesis is the…
template strand
transcription steps
intiation, elongation, termination
what does the promoter sequence do in prokaryotes?
promoters are the instructions for the rna polymerase in the form of a dna sequence
RNA polymerase in prokaryotes needs to know…
- which strand is the template strand
- what to transcribe
- where first nucleotide of gene to be transcribed is
first phase of transcription in prokaryotes
is initiation
what happens during initiation in transcription?
rna polymerase binds to a promoter region in the dna
- dna unwinds at promoter to form an open complex (required for chain initiation)
after initiation is…
chain elongation
in chain elongation, after strands separate,
- rna polymerase catalyzes formation of phosphodiester bonds b/w ribonucleotides
- transcription bubble of 17 bp moves down DNA sequence to be transcribed
what does topoisomerase do during chain elongation?
relaxes supercoils in front of and behind transcription bubble
what is chain termination controlled by?
termination sites (characterized by two inverted repeats)
what happens to the size of the rna post transcription?
- initial size of rna transcript is greater than final size
- ONLY occurs in eukaryotes
RNA modification includes
- leader sequences at the 5’ end
- trailer sequences at the 3’ end
mRNA modification includes…
- 5’ cap (guanylate residue) that tells ribosomes which end of mRNA to start translating
- polyadenylate “tail” added to 3’ end to protect mRNA from nucleases and phosphates
eukaryotes genes frequently contain intervening base…
sequences that don’t appear in the final mRNA
exons
expressed dna sequences
introns
intervening dna sequences that aren’t expressed
introns are (x) and exons get (y)
spliced out, ligated together
in the genetic code, a triplet is…
a sequences of 3 bases (codon) is needed to specify one AA
in the genetic code, universal means
the same in viruses, prokaryotes, eukaryotes
all 64 codons have
assigned meanings
how many code for AAs?
61
termination signals
UAA, UAG, UGA
start codon
AUG (also codes for methionine or met)
does transcription occur in prokaryotes?
yes and in the cytosol - is coupled to translation
amino acids must be activated by…
tRNA and aminoacyl-tRNA synthetases
what does ATP do in AA activation?
provides energy for bond formation of adding AA to tRNA
where on the tRNA is the AA added to?
3’ end
carboxyl group of the AA is
linked to the 3’-OH of tRNA
where does the polypeptide chain start?
N-terminus, ending at C-terminus
in prokaryotes, initiation requires
- tRNA fmet anticodon which pairs with AUG in mRNA
- AUG (initiation codon of mRNA)
- small ribosomal subunit
- large ribosomal subunit
- initiation factors (IFs)
- GTP, Mg2+
what is fmet?
modified methionine in which a formaldehyde group has been added to the AA
the components of prokaryotic initiation form….
the initiation complex
how many sites does tRNA use on the ribosome during chain elongation?
P (peptidyl), A (aminoacyl), E (exit) sites
what does chain elongation require?
- elongation factors
- GTP and Mg2+
- enzyme peptidyl trasferase forms peptide bond (e.g. RNA acting as an enzyme)
chain termination requires
stop codons (UAA, UAG, UGA) of mRNA
release factor (RF)
GTP
why is the genetic code redundant?
b/c more than one codon can code for the same AA (e.g. Leu, Ser and Arg are coded for by 6 triplets
61 different sense codons don’t require…
61 diff tRNAs (usually abt ~45)
some tRNAs can recognize more than one codon b/c…
of variations allowed in H bonding
tRNAs contain…
inosine that can pair with U, C, or A
- e.g. tRNA carrying phenylalanine matches codons UUU and UUC
protein degradation can be caused by
subcellular organelles lysosomes, macromolecular structures proteosomes and in euks: ubiquitinylation
what is ubiquitinylation?
ubiquitinylation becomes bonded to ubiquitin, targeting a protein for destruction
what does the 3’-OH at the end of a new DNA chain do?
- acts as a nucleophile
- phosphorus adjacent to the sugar is attacked and then added to the growing chain
dna polymerase iii carries out the…
synthesis and linking of new DNA strands
RNA primer is removed by….
DNA polymerase 1
dna is unwound and opened by (x) at the (y) forming a (z)
enzyme helicase, origin of replication, replication bubble
what enzyme can lay a primer without having a 3’ end present?
rna primase
what is the main replicating enzyme?
dna polymerase iii
new strand of dna must be made in the (x) direction
5’ to 3’
new nucleotides are added to the (x) end?
3’ end
what takes out the rna primer in the lagging strand?
dna polymerase I
what shows that dna replication is complete?
no rna primers + okazaki fragments are sealed by ligase, making covalent bonds
which enzyme carries out transcription?
rna polymerase
where does transcription take place in eukaryotes?
nucleus
where does transcription take place in prokaryotes?
cytoplasm
what does the +1 in the dna strand during transcription mean?
start/initiation site for transcription
which of the two dna strands is transcribed into the mRNA sequence (template or coding strand)?
template strand
what is the coding strand?
strand with the same “code” sequence as mRNA
purpose of the TATA box?
region that rna polymerase knows to bind to and start the process of transcription (~10 nucleotides downstream)
what is a 5’ cap?
methane group added to the 5’ end
what is a poly-A tail?
AAAAAAA added to 3’ end
could translation and transcription occur simultaneously in eukaryotes?
no b/c mRNA has to leave nucleus
purpose of 3’ poly A tail at ends of mRNA in eukaryotes?
not necessary in prokaryotes; prevents the degradation of actual mRNA sequence
why would a eukaryotes need a 5’ cap?
to allow for the ribosome to know which end of the mRNA to start process of translation
which site does the first tRNA bind to first?
P-site
after the p-site, tRNA moves to…
A site
what is translocation?
tRNA shifting from A site back to P site, and when it no longer is holding an AA, moves to E site to Exit
what is an anticodon?
3 nucleotides sequence on tRNA that is complementary to mRNA codon
if mRNA codon is 5’ CGU 3’, what is the tRNA anticodon?
3’ GCA 5’
can tRNA be reused?
yes
can more than one codon code for the same AA?
yes
what are polyribosomes?
many ribosomes attached to 1 mRNA strand
- all of them are making copies of the same protein (making many of the same protein at once)
which enzyme binds to transcribes the template strand?
RNA polymerase
