Gene Expression

Gene expression

The process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead function as RNAs (genotype gives rise to phenotype)

Main phases of gene expression

1. transcription (RNA processing and maturation)
2. translation

Sense dna sequence

sequence is the same as RNA copy transcribed from , 5' to 3'

Where does gene expression take palce?

transcription - nucleus
translation - cytoplasm

Transcription

genetic info encoded in nucleotide sequence of coding dna strand is transferred to mRNA that carries it from nucleus to cytoplasm

What is an asymmetrical synthesis of RNA on a DNA template by polymerization of ribonucleotides?

transcription

Function of RNA polymerase in transcription

binds to promoter region, makes complementary strand of mRNA in 5'-3'

What enzyme, during transcription, allows for binding of RNA polymerase to the dna molecule and the regulation?

transcription factors

Steps of Transcription

1. pre-initiation (dna unzipped)
2. initation, rna polymerase binds
3. elongation (of mRNA on 3')
4. termination (mRNA and RNA polymerase released, template reunites w/ complementary strand)

transcription starts at what region?

Inr (initating) region

how does elongation take place in transcription?

assembly of ribonucleotides and removal of 2 terminal phosphates, until rna polymerase reaches termination site

how is RNA polymerase and mRNA released in transcription?

rho-independent terminator has inverted repeat + 6 nucleotides w/ A
when transcribed, will form H+ bonds creating hairpin loop w/ U string

Why does the result of transcription have to go through rna processing?

it contains non-coding introns that must be spliced and rna is susceptible to nucleases

Process of capping

on 5' end a link bw nucleotides after transcription starts, to make end unrecognized by nucleases + assist transport from nucleus to cytoplasm + bind to ribosomes

poly-A tail

Modified end of the 3' end of an mRNA molecule consisting of the addition of A, protects sequence (it's attacked before sequence)

Splicing in transcription

non-coding introns removed from pre-mRNA and coding exons joined into a mature mRNA

Splicing is carried out by

spliceosome (big protein complex called snurps)

How do ribonucleotides recognize introns

ribonucleotides are made of proteins and U-rich snRNA that is complementary w/ GU and AG dinucleotides on the ends of most introns

snurp role in transcription splicing

attaches to 5' end of intron + makes it into loop

Why does splicing allow for mRNA to leave nucleus thru pores to cytoplasm?

removing introns reduces dimension

What leads to mature mRNA w/ diff nucleotide sequences after splicing in transcription and also production of proteins?

alternative splicing + exon shuffling + trans-splicing

RNA editing

chem modifications of mRNA, changing gene expression w/o changing gene, affects also tRNA

rna editing mechanisms

c becomes u, a becomes i, nucleotide addition

editosome

protein complex that performs rna editing and inserts uridines

Translation

translates info coded by dna sequence transcribed into mRNA strand, in cytoplasm on ribosomes

Ribosome subunits

Large and small subunits, w/ proteins and rRNA, catalyze a-a attachment

large ribosomal subunit contains 3 sites where tRNA can bind:

A (a-a) binding site, tRNA pairs w/ mRNA
P (polypeptide) site, a-a transferred to polypetide chain
E (exit) site, tRNA released in cytoplasm

In translation, when the ribosome reaches the stop codon, it releases

the mRNA and the polypeptide (w/ the a-as)

tRNA

carry a-a to anticodon in ribosome

How does the polypeptide chain grow in translation?

ribosome moves along mRNA and matches codon w/ anticodon, adding a-as

Steps of translation

1. pre-initiation
2. initiation
3. elongation
4. termination

Pre-initiation of translation

attachment of small subunit of ribosome to 5' end of mRNA w/ pre-initiation complex

initiation of translation

@ START AUG cod, both subunits of ribosome, tRNA brings first a-a (met) and protein synthesis begins, w/ initiation complex

elongation of translation

ribosome moves 5'-3' on mRNA, adding a-as to peptide according to codon sequence, free tRNA released on E site so attachment of next a-a, bringing tRNA to A site

untranslated regions in translation

5' end beginning of mRNA bw cap and START codon
3'-UTR bw STOP and poly(A) tail

initiation complex of translation

consists of a charged tRNA (w/ met) and a small ribosomal subunit, both bound to the mRNA

termination of translation

STOP codon reached, protein + mRNA released, ribosome subunits dissociate

How are peptide bonds bw adjacent a-as during translation formed?

by peptidyl transferase activity of rRNA

polysome

A complex formed when multiple ribosomes are translating the same mRNA into proteins.

What is done for the primary polypeptide structure after translation to be functional?

chaperones fold it to attain 3D structure
must attach to other molecules (quaternary structure)

Activation of tRNA by binding of specific a-a during translation is catalyzed by

synthetases

wobble effect

unusual base pairing bw the last nucleotide of codon and first nucleotide of anticodon: 1 tRNA can recognized 2+ codons

Why can only nucleotide triplets (codon) code for the 20 a-as

unequal # bw 4 possible N-bases and nucleotides in DNA and the 20 a-a

Code is _______, so there are no common nucleotides in 2 adjacent codons

non-overlapping

Some _______ have a diff nucleotide sequence but code for the same amino acid

codons (synonymous)

What is the universal START codon in eukaryote coding for Met

AUG

STOP codons

UAA, UAG, UGA

What does regulation of gene expression refer to?

control of protein/RNA production that permits cell to adapt to enviro + act according to cell cycle phases + various dev stages

Benefits of gene regulation

increases versatility + adaptability of an organism, conserves energy

Up vs down regulation

up - within a cell triggered by a signal, increased expression
down - decreased gene and protein expression

Inducible vs repressible systems in gene regulation

inducible - off unless inducer allows expression
repressible - on unless corepressor suppresses expression

Interactome

The complete set of protein complexes/protein-protein interactions present in a cell, tissue, or organism.

What gene expression processes take place in the nucleus

transcription, mRNA processing, transport

What gene expression processes take place in the cytoplasm

translation, post-translational changes

What gene expression process take place in the cytoplasm

protein degradation

the accessibility of dna for factors responsible for transcription depends on what

chromatin structure, its density

DNA demethylation and histone acetylation lead to gene activation by

unwinding chromatin, accessible for transcription factors and rna polymerase

DNA methylation is an epigenetic signaling method used to

inactivate genes

Dna methylation occurs at the level of _____ by enzyme ________

cytosine bases, DNMT

The methylation of promoters correlates with

low or no transcription

Transcriptional control is carried out by

cys - regulating factors
trans - regulating factors (TFs)
bind to dna and controls its fxn

Cys-regulatory dna sequences

regulate initiation and control of transcription by binding TFs

Types of cys-regulatory sequences

promoters, response elements, enhancers, silencers

Promoters

nucleotide sequences located before 5' end of transcription start site, regulatory region involved in gene expression

Promoter sequences serve as

binding sites for TFs

which promoter recruits RNA polymerase II and promotes transcription initation

TATA box

enhancers vs silencers

Enhancers increase transcription

Silencers decrease transcription

- binding or activation TFs

How is transcription initiated

TF binds to promoter, transcription complex is formed and recruits RNA polymerase and transcription

transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.

General TFs

position RNA polymerase at the start of sequence and then release it to transcribe the mRNA

Activator

TF that binds to enhancers and increase transcription

Repressors

TF that binds to silencers and inhibit binding of transcription complex

Coactivator

adapter TFs that assist binding of general TFs with activators and repressors

How is the activity of TFs modulated

intracell signals, nuclear membrane that controls duration of control proteins

Dna-binding vs trans-activating domains of TF

dna-binding - binds to dna sequence in promoter, enhancer or silencer regions
trans-activating - binds to proteins

optional signal sensing domain of TF

sense external signals and transmit them to the rest of the transcription complex, resulting in gene expression

Classes of TFs

leucine zipper, helix turn helix, zinc finger, helix loop helix

Post-transcriptional regulation is modulated by

rna processing, rna editing, sequence-specific nuclear export rates, rna interference and digesting

Rna structure depends on

use of alternative promoters, splicing, editing of bases

mRNA is stable until

translation takes place

importins and exportins

regulate transport thru nuclear pores of RNA for translation

microRNAs

can bind to complementary sequences on mRNA molecules either degrading the target mRNA or blocking its translation