-
context: RNA
structure
- largely single stranded
- particular shapes: nonconventional vs conventional basepairs due to reactive hydroxyl in 2'C
-
- notice:
- Uracil vs Thymine
- shapes vs histones
- nucleus to cytoplasm vs just nucleus
-
Central dogma of molecular biology
- replication (DNA to DNA), transcription (DNA to RNA), translation (RNA to PROTEINS)
- genes can be turned on or off to make different proteins
-
T/F
Different genes are made in different amounts
TRUE
-
NO PROOFREADING in RNA polymerase, NO PRIMER.
-
context: Gene structure
Promotor region
- 5' untranslated region (5' UTR)
- initiation site for transcription
- RNA polymerase BINDING SITE
- binding site for transcription factors (regulation cis or trans strand)
-
context: gene structure
genes
intron (more: waste) + exons (less: for proteins)
-
context: transcription
what polymerase
- RNA polymerase 2
- using rNTPs
-
context: transcription
Template strand
strand used as template for mRNA synthesis
-
context: transcription
coding strand
- specifies the sequence of a.a.
- (genetic code) in future polypeptide
-
context: types of RNA
mRNA
- messenger RNA
- template for amino acids
- 3-5% total RNA in cell (really small amounts!!)
-
context: types of RNA
t RNA
- transfer RNA
- recognize the mRNA with it's anticodon complementary to mRNA codon.
- to put on corresponding amino acids.
-
context: types of RNA
rRNA
- ribosomal RNA
- portion of ribosomes
- hold mRNA to put on tRNA
-
4 stages of transcription
- 1. Initiation (open up helix, needs PROMOTOR to know where to start)
- 2. elongation (mRNA synthesis 5' to 3', phosphodiester bond)
- 3. termination (stop signal)
- 4. post-transcriptional modification (capping, poly A tail, splicing)
-
context: transcription
Promotors
- varying sequences
- different promotors
- ex: common ones: -35 and TATA box at -10 based on consensus sequences across a lot of studied subjects.
-
context: transcription
bacteria vs eukaryotes
- 1. 1 RNA polymerase vs 3 RNA polymerase
- 2. 1 transcription factor vs many general transcription factors (GTFs)
- 3. no packaging vs packaging (nucleosomes, chromatin)
-
context: eukaryotic transcription
promotor region
upstream TATA box or CAAT box
-
context: eukaryotic transcription
enhancer region
typically upstream of promotor
-
context: eukaryotic transcription
transcription factors jobs and kinds
- 1. transcription factors bind to promotor and recruit RNA polymerase
- 2. must bind to all promotors to get RNA polymerase = basal transcription factors
-
context: eukaryotic transcription
names of transcription factors
-
context: eukaryotic transcription
TFIID
- has a TBP (TATA binding protein)
- that bends the site to get other transcription factors to bind
-
context: eukaryotic transcription
other transcription factors not including TFIID
positive regulation transcription factors
- bind enhancer or DNA response elements
- INCREASE rate of transcription
-
context: eukaryotic transcription
other transcription factors not including TFIID
negative regulation transcription factors
- bind enhancer or DNA response elements
- DECREASE rate of transcription
-
context: eukaryotic transcription
regulating gene expression
- Transcriptional activator protein- activate
- Transcriptional repressor protein -inhibit polymerase activity
-
BOTTOMLINE:
gene regulatory proteins
responsible for controlling gene expression
-
context: Transcription ELONGATION
what polymerase?
RNA polymerase 2
-
context: transcription Termination
in Prokaryotes (cause hard to know eukaryotes)
process to stop sequence
- 1. Hairpin loop with extensive basepairs formed
- 2. ADD UUUUU for polymerase comes off
- 3. RHO protein breaks DNA and RNA apart
-
context: POST-transcriptional
3 steps
- 1) 5' Methylguanosine cap (once 5' is made)
- 2) 3' poly A tail (protect from endonucleases)
- 3) splicing out introns (introns removed, exons join, alternative splicing)
-
context: post-transcriptional modification
splicing with help
- with: snRNA, splicesomes (name of splicers in nucleus)
- 1. 2'OH adenosine forms lariet
- 2. cleave at exon and intron junction
- 3. joined exons
- 4. degrade lariat (introns)
-
context: post-transcriptional modification
splicing without help
- ex: Tetrahymena
- use ribozymes - RNA catalyze self-splicing
-
context: post-transcriptional modification
Bacteria vs Eukaryotes
- no modification vs modification
- many proteins vs one protein
-
context: transcription and translation
Bacteria vs eukaryotes
coupled (no nucleus) vs separate (in nucleus then in cytoplasm)
-
context: translation
3 components
- 1. ribosomes
- 2. mRNA
- 3. tRNA
-
Context: translation
mRNA is translated in what direction?
protein is synthesized in what direction?
- 5' to 3' on BOTH!!!
- amino terminus to carboxy terminus (remember A before C)
-
context: translation
peptide bonds synthesize how many NUCLEOTIDES per second
hint: really fast
45
15 amino acids per second. each amino acid has 3 nucleotides in one codon(amino acid)
-
context: translation
T/F
translation is hard and complicated
- TRUE
- it takes over 100 proteins to process
- plus amazing coordination required
-
4 steps to TRANSLATION
- 1. initiation (start- AUG= A Unique Girl -she's one of a kind)
- 2. elongation (amino acids, peptide bonds)
- 3. termination (stop codon: UAG- Ur A Girl?, UAA- Ur An Ahole, UGA- U Got Ahole)
- 4. post-translational modification (cleaving, folding = folded structure) = use RELEASE FACTORS to end everything. REGULATED by the poly A tail.
-
GENETIC CODE properties (4)
- 1. one codon = read in triplets (letters)
- 2. no commas!
- 3. do not overlap
- 4. redundant/degenerate - many codons for one amino acid
-
HOW come 64 codons = only 61 amino acids
redundancy!
-
Genetic code
Alterations (3)
- 1. silent - no change
- 2. missense - change amino acid
- 3. nonsense - stop codon
-
context: tRNA and translation
How do you get the amino acid on to the correct tRNA?
synthetases- enzymes, SPECIFIC for each amino acid
-
Ribosome binding sites
- E (exit), P (peptidyl site), A (aminoacyl site)
- AND mRNA binding site.
-
context: translation elongation
polysomes
MULTIPLE ribosomes translating one mRNA strand
-
context: post-TRANSLATIONAL modification
5 types of modification
- 1. glycosylation
- 2. phosphorylation
- 3. cleavage to active form (proproteins, specific signal needed)
- 4. folding of polypeptide
- 5. proteins can form 2-4 structures
- BOTTOMLINE: don't need to know this BUT know that MANY modifications occur
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