Gene Regulation and Protein Synthesis Flashcards by Ciara McGloin

structure of RNA

single stranded

local stretches of intramolecular base-pairing (sums and loops)

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3 main RNA classes

rRNA - combines with proteins to form ribosomes where protein synthesis takes place, stable
tRNA - carries amino acids to be incorporated into protein, stable
mRNA - carries genetic info for protein synthesis

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what is the most common type of RNA in cells

rRNA - 80%
tRNA - 15%
mRNA - 5%

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describe the structure and function of tRNA

adapters between nucleic acid code and amino acid code
anti-codon consists of 3 nucleotides
3D structure

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where is the attachment site for specific amino acid

anticodon sequence codes for specific amino acid

added to free 3’ end OH attachment site

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how is RNA made

use one DNA strand to copy nucleotide sequence

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how many types of RNA polymerase do eukaryotic cells have

3 - Pol I, Pol II, Pol III

Pol II synthesises all mRNA

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5 steps of transcription

RNA polymerase II binding - detection of initiation sites (promotors) on DNA, transcription factors required (NO PRIMER)
DNA chain separation - local unwinding of DNA to gain access to nucleotide sequence
Transcription initiation - selection of first nucleotide of growing RNA
Elongation - addition of further nucleotides to RNA chain
Termination - release of finished RNA

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role of RNA polymerase

bind promotors (DNA sequence), specific to RNA pol II
Transcription starts at nucleotide +1
TATA box is present about 25 nucleotides upstream before transcriptional start

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what is TBP

TATA box binding protein
recognises TATA box
introduces kink into DNA (determines transcriptional start and direction)
Provides platform for further transcription factors & RNA polymerase

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what is TFIID

general transcription after

required for all pol II transcribed genes

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how is transcription initiated

general transcription factors
Pol II & TFIIF extend transcript on their own
TFIID remains at promotor, a new initiation complex can assemble allowing transcription at low basal rate

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what happens during transcription elongation

transcription bubble moves in one direction along DNA

DNA is unwound infant of DNA polymerase then rewound behind it

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in what direction is RNA chain synthesised

in a 5’ to 3’ direction
new RNA is complementary to template strand
identical to the coding strand (U replaces T)

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how Is transcription terminated

new RNA strand makes stem loop structure followed by stretch of Us
A specific enzyme cleaves finished RNA, releasing it

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how is transcription regulated

requires specific transcription factors (DNA binding proteins, DNA binding domain and transcriptional activation which causes other protein/factors to increase rate of transcription)
Bind to specific DNA sequences near promotor enhance/ repress transcription (loop back on itself)

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how are genes expressed

in response to specific stimuli eg hormones, cell stress

transcription factor activated by modification eg by extracellular factors phosphorylation/cleavage

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describe steroid receptors and how they are activated

transcription factors (nucelar hormone receptors)
DNA-binding and ligand-binding domain highly conserved
in cell cytoplasm (inactive)
when ligand (steroid) binds move to nucleus and bind to DNA at steroid response elements

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describe the activation of the glucocorticoid receptor

steroids transported in blood (by albumin binding)
enter large cell by diffusion
bind to inactive steroid receptor in cytoplasm causing receptor activation
translocates to nucleus
binds to response elements (as homodimer)
coordinated regulation of genes

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are all genes expressed

no
some at basal rate
some never expressed DNA will be tightly coiled around histone, packaged away - never transcribed
genes are regulated by transcription factors

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what are coding regions

exons, disturbed by non coding regions - introns

all transcribed into pre-mRNA

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what is splicing

removal of introns before translation forming mRNA, only exons in mature mRNA
works in 5’ to 3’ direction
this is how one gene can make different proteins depending on whats classed as an intron and exon

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how is the end of mRNA processed

addition of poly(A)tail

capping - addition of 5’ cap

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what are codon anti-codon base pairs

during translation anticodons of tRNA molecules form base pairs with codons on mRNA
3 nucleotides
genetic code based on triplets

how many combinations code for 20 amino acids

64 amino acids

what is the start codon

AUG - methionine

what does degenerate mean

many codons make the same amino acid

define unambiguous

each codon codes for only one amino acid - stop

what is the stop codon

UAA UAG UGA

what determines where translation takes place

reading frames 3 different types | coding frame will give longest stretch without a stop codon in between

components of translation

``` amino acids tRNAs Aminoacyl-tRNA synthetases ribosomes mRNA ATP & GTP as sources of energy a specific set of protein factors for each of (initiation of protein synthesis, elongation of polypeptide chain/translocation, termination) ```

what is the role of aminoacyl-tRNA

synthetases bind amino acids to their corresponding tRNA molecule (highly specific) at least one for each amino acid ATP provides energy for formation of covalent bond catalysis ATP to ADP

how many molecules of rRNA are in a ribosome

4 | also hae protein components

what are the 3 binding sites on a ribosome

``` E = exit P = peptidyl A = Aminoacyl ```

how is translation initiated

initiation factors

where does the energy for translation come from

hydrolysis of GTP supplies energy for initiation

what happens when mRNA comes in contact with rRNA

small ribosomal subunit binds to 5' end of mRNA | moves along mRNA until AUG start codon found (ATP dependant)

describe initiation of translation process

special initiator tRNA with UAC anticodon base pairs with start codon (carries methionine) large subunit joins assembly and initiator tRNA is located at site P

role of elongation factor EF-1a

brings next aminoayl-tRNA to A site GTP is hydrolysed EF released from tRNA second EF regenerates EF 1 to pick up next amino-acyl-tRNA

how do peptide bonds form between adjacent amino acids at ribosome

peptidyl transferase catalyses peptide bond formation between amino acid in P and A sites so peptide is in A site

What moves ribosome along mRNA

EF-2

what does the tRNA do once it has dropped its amino acid off at site P

empty tRNA enters E site so can exit and reload tRNA with growing peptide moves from A to P site, A site empty for next amino acid right > left E P A

what bond is between amino acids

peptide

when does termination of translation occur

when A site of ribosome encounters stop codon | no aminoacyl-tRNA base-pairs with stop codon

what happens during termination

release factorRF binds to stop codon GTP hydrolysis finished protein cleaved off tRNA components dislocate

what is the polysome

many ribosomes acting on one mRNA strand to synthesise polypeptide at same time working ribosomes added in 5' to 3' direction

what is a point mutation

change in single base in DNA

what is a missense mutation

results in change of amino acid sequence | can change protein function eg haemoglobin in sickle cell

what are the 3 types of point mutation

missence nonsense silent

what is a nonsense mutation

creates termination codon | changes length of protein due to premature stop of translation

what is a silent mutation

no change of amino acid sequence due to degeneracy of genetic code no effect on protein function

what is a frameshift mutation

addition/deletion of single base | changes reading frame of translation

what are chromosomal mutations

affect larger portions of genome deletion duplication translocation inversion

what happens to finished protein

targeting - moving protein to final cellular destination, many possible locations, depends on amino acids in sequence modification - addition functional groups degradation - unwanted/damaged proteins removed

what do free ribosomes in cystol make proteins destined for

cystol nucleus mitochondria translocated (post-translationally)

what doe bound ribosomes on rough ER make proteins destined for

``` plasma membrane ER Golgi-apparatus secretion translocated (co-translocationally) ```

what is gycosylation

addition and processing of carbohydrates in ER and golgi

what happens during post-translational modifications

formation of disulphide bonds in ER folding/assembly multisubuni proteins in ER specific proteolytic cleavage in ER/gogli/secretory vesicles hereditary for of emphysema - misfiling of protein antitrypsi in ER