DNA Repair, RNA modifications, Transcription, some translation

3 types of DNA repair

Direct repair, base excision repair, nucleotide excision repair

Direct repair

covalent modifications of nucleotides can be reversed by specific enzymes

Enzymes used in direct repair

photolyases and alkyltransferases

Photolyase

can repair thymine dimers, splits the dimers, uses engery of visible light for photoreactivation

Alkyltransferase

repairs alkylated bases, transfers the methyl/ethyl group from base to a cysteine side chain within alkyltransferase, permanently inactivates the enzyme after repair.

Base excision repair

involves a category of enzymes known as DNA N-glycosylases

DNA N-glycosylases

enzymes recognize an abnormal base and cleaves the bond between the sugar in the DNA

Nucleotide excision repair

repairs thymine dimers, chemically modified bases, missing bases, some cross links. 4 key proteins UvrA, UvrB, UvrC, UvrD. They recognize and remove short segment of damaged DNA while DNA pol. and ligase finish the repair

RNA Modifications

4 kinds. RNA splicing, RNA processing, Add 5’ cap, add 3’ poly A tail

RNA splicing

coding sequences called exons are interrrupted by introns. Transcription produces a pre-mRNA corresponding to the entire gene sequence. Introns are removed and exonds are connected (spliced)

Alternative splicing

Exons are in different combinations are RNA splicing. This creates more variations in proteins that are formed from one specific gene

Processing of ribosomal RNA

Creates multiple different rRNA from rRNA encoding genes

How many kinds of rRNA

3 main types, never get translated

Attachment of a 7-methylguanosine cap

to the 5’ end it helps with nuclear transport

Polyadenylation signal sequence

Adding a poly A tail to the 3’ end

Transcription 3 stages

Initiation, elongation, termination

Initiation

sigma factor of RNA pol recognizes -35 and -10 seq of the promoter. The whole enzyme is called RNA pol. holoenzyme

Transciption starts at ___site

+1 site

Promoter specifices direction of transcription

3’ end is adjacent to the promoter

Elongation

sigma factor is relased, carried out by RNA pol.

Termination

Two kinds; Rho-dependent, rho-independentR

Rho-dependent

Requires protein rho, stemp-loop, rho-binding site in RNA

Rho-independent

stem-loop, follwed by a U/A rich sequences, causes the RNA pol to pause and fall off

Transciption in Eukaryotes

core promoter is relatively short, and has a TATA box which is the transcription start site

Core promoter itself prodouces a low level of trasncription

basal transcription

Regulatory elements

DNA sequences that affect the binding of RNA pol. to the promoter

2 kinds of regulatory elements

enhancers and silencers

Enchancers

stimulate transcription and help RNA pol bind

Silencers

inhibit transcription and prevent RNA pol from bindng`

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kinds of RNA pol. for Euk.

3 types

Transcription factors (proteins)

bind to these elements and influence the rate of transcription

__ many kinds of transceiption factors

5 kinds

Translation

start codon sets the reading frame for all remaining codons, anticodons on tRNA are complementary to codons

Codon types

sense codons (encoding AA), initiation codons (AUG), stop codons (UAA, UAG, UGA)

Recognition between tRNA and mRNA

the anit-codon in tRNA vinds to the complementary codon in mRNA

enzymes attach the specific AA to the tRNA are known as

aminoacyltRNAsynthetases

Anticodon is __ to codon

antiparllel

Function Sites of ribosomes

peptidyl site (p), aminoacyl site (a), exit site (e)