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41 Cards in this Set

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Genome
all the genes in the organisms DNA
L3
Proteome
all the encoded proteins
L3
peptide
short polypeptide
gene
an unbroken DNA nucleotide sequence that nearly always encodes a polypeptide
L6
transcription
making an RNA copy of a gene, tiny parts of a DNA strand each encoding a polypeptides
L-6
asdf
asdf
translation
directs the synthesis of the polypeptide amino acids sequence from the RNA gene copy (messenger RNA,mRNA) using transfer RNA (tRNA) and ribosomes, particles containing ribosomal RNA (rRNA)
L-7
Reverse transcription
RNA copied to DNA in retroviruses
L-7
The 5' phosphate is attached to the 3' end of the preceding nucleoside by _____
phosphodiester bonds (as in DNA synthesis)
L-8
5 differences b/t RNA and DNA
1. the ribose retains OH at its 2' position

2. the bases have uridine instead of thymidine

3. RNA is always single stranded

4. Complementary regions may fold back on themselves, forming double helical regions.

5. RNA free protein, for example mRNA, is hydrolyzed by alkali
L-9
requirements of DNA dependent RNA polymerase
These are the core polymerase enzymes

double stranded DNA,

one Zn2+ ion for NTP binding

and Mg2+ ions for catalysis

four nucleotide 5'triphosphates (ATP, GTP, CTP, and UTP)

RNA chain extends from 5' to 3'

catalysis is by 3'-OH end attacking 5'-phosphate of incoming NTP
summary of steps in bacterial RNA synthesis

(pg L-15)
1. transcription starts when sigma factors binds to a promoter consensus sequence.

2. RNA core polymerase binds sigma factor and unwinds DNA.

3. Transcription bubble (17bp) forms

4. RNA bases are selected by hybridizing to the DNA template and extend progressively from 3' to 5' end

5. Single RNA strand has same sequence as DNA coding strand complimentary to the template

6. Two termination sequences: hairpin structure (self-complementary) or rho (p) protein binding
RNA Pol I

(pg. L-16)
transcribes ribosomal RNA genes in nucleous

(products are not transcribed)
RNA Pol II

(pg L-16)
transcribes pre-messenger RNA in the nucleoplasm. Pol II attaches more polypeptide cofactors than bacterial RNA polymerase and recognizes promoters that are much more varied in sequence than bacterial promoters
RNA pol III
transcribes tRNA and most small RNAs

(products are not transcribed)
RNA POl IV
transcribes mitochondrial (non-nuclear) DNA. It resembles bacteriophage RNA polymerases.
---- region TATA box: binds _____ subunit factor
-10 region, sigma 70 subunit factor
what are RNA polymerase core enzyme four subunit functions
alpha- assembly

beta- catalysis

beta'- binding of template

omega- chaperone
sigma protein function
binds promotor sequences on DNA to initiate RNA synthesis
Rho protein function
binds terminator RNA sequences adn stops RNA sythesis
mode of action of Actinomycin D
inhibits all RNA transcription b/c it binds to certain (GpC) sequences in DNA, preventing the open transcription complex from forming
Rifampicin mode of action
binds to the active site of bacterial but not eukaryotic RNA polymerase
a-amanitin mode of action
binds strongly to RNA Pol II, inhibiting eukaryotic but not bacterial mRNA transciption
type of RNA not in prokaryotes
-snRNA b/c there processing of bacterial mRNA
types of RNA in eukaryotic cell, from greatest amount to least amounts present
rrRNA > tRNA > mRNA > snRNA > scRNA
Splicesomes are composed of ______.
snRNA particles
splicesomes attach to RNA Pol ____
II
function of cap and tail in eukaryotic mRNAs
CAP- facilates splicing

TAIL- facilitates mRNA transport out of the nucleus

-Both facilatate initiation of translation by attaching to the ribosomal small subunit
Exosome is a
protein exonuclease particle that digests all types of RNA from 3' to 5'
spliceosome
is an snRNA particle that removes introns as eukaryotic mRNA is being synthesized
Proteasome
is a protein particle that digest ubiquitinylated proteins in the cytosol
sizes of ribosomal particles or their compnent RNAs are measured in
Svedbergs, a sedimentation coefficient measurement
what enzymes synthesizes eukaryotic ribosomes?
the DNA gene encoding eukaryotic ribosomal RNA are transcribed by RNA POLYMERASE I
Enzymes required to process mRNA?
a. Phosphohydrolase, Guanosyl transferase, and Methylase (cap)

b. Polyadenylate polymerase complex containing endonuclease and polyA polymerase (tail)

c. Small nuclear RNA particles with consensus binding sequences (splicosomes)
What enzymes are required to process freshly synthesized tRNA and rRNA
SPECIFIC ENDO- AND EXO-NUCLEASES that trim the ends and may also be required to remove an intron
what are the consensus residues taht identify an intron and are mecessary for its removal from freshly synthesized RNA?
the first two residues at the 5' END,

and the last two at the 3' END

and an ADENOSINE RESIDUE about TWO-THIRDS of the way towards the 3' end
One gene can encode two different polypeptides. How?
1. Alternative splicing

2. Limited proteolytic processing
function of the cap in eukaryotic mRNAs
facilitates splicing
function of tail in eukaryotic mRNAs
facilates mRNA transport out of the nuclues
what function does the tail and cap in eukaroytic mRNA have in common
both facilitate the initiation of translation by attaching to the ribosomal small subunits
where are ribosomes and proteins synthesized in Eukaryotic cells
Ribosomes- made in nucleolus of the nucleus

proteins- in the cytosol, often attached to the rough endoplasmic reticulum