molecular genetics hell

DNA structure requirements

• Chargaff’s rule: %A = %T, %C = %G

• uniform width of molecule

• information content in nucleotide sequencing

• mutations in changes of nucleotide sequencing

• replication process in double-helical nature/ability to open

semiconservative replication model

in a DNA molecule, one strand is conserved from the parent, the other is completely new

conservative replication model

one dna molecule is composed of both parent strands, the other is completely new

dispersive replication model

each DNA molecule has alternating segments of parent and new DNA

DNA polymerase

catalyst for chain elongation reaction

leading strand

parent strand synthesizing towards replication fork

lagging strand

parent strand synthesizing away from replication fork, forms okazaki fragments and ligation

primase

DNA polymerase I, removes RNA primer 5’—>3’ exonucleas

ligase

fills gap left by RNA primer in lagging strand, leaves ligation behind

DNA polymerase III

acts as a dimer, coordinately replicates leading & lagging strand

helicase

opens DNA ladder, breaks hydrogen bonds

topoisomerase

keeps DNA from knotting as it denatures

single-strand binding proteins

coats each DNA strand so they don’t come back together

beta clamp

ensures pol III stays on strand, distributive to processive enzyme

proofreading

pol I & pol III have 3’—>5’ exonuclease activity to remove mismatched bases & prevent mutations

CAF-1 histone chaperone

nucleosomes are a physical block in replication machinery, so they disassemble & reassemble in daughter DNA

telomere problems

because of how the lagging strand is synthesized, the terminal gap after an okazaki fragment is not filled and chromosomes get shorter over time

2009 - Blackburn, Grieder & Szostak

telomeres include thousands of short DNA repeats, discovered telomerase and that telomeres are capped so they are not recognized as double stranded breaks

telomerase

enzyme that extends telomere ends, only active in certain cells. no telomerase leads to cell senescence (stop in cell division), but too much can lead to cancer

telomere lengthening

• telomerase undergoes reverse transcription (RNA to DNA), acts as a template for DNA strand

• 3’ overhang is extended, then telomerase translocates to extend more, causing the DNA repears

template strand

strand RNA binds to during transcription

nontemplate/coding strand

strand that looks like RNA during transcription, RNA DOES NOT BIND TO IT

stages of transcription

initiation, elongation, termination

promoter

upstream from coding region, recruits RNA polymerase (consensus sequences)

+1 location

immediately after promoter, transcription initiation site, starts with the 5’ end

coding region

the actually important bit of the gene, downstream from promoter and +1 region, contains the information that will be transcribed and ultimately turned into a protein

termination site

downstream from coding region, location where transcription ends

untranslated region (UTR)

the chunk between the promoter/+1 and coding region (5’ UTR), and the chunk between coding region and termination site (3’ UTR)

consensus sequence

most found base pairs in a region

RNA polymerase holoenzyme

enzyme made by multiple proteins, binds as a unit sigma factor recognizes promoter sequence and is released upon transcription initiation (prokaryotes only)

RNA polymerase elongation bubble

DNA unwinds and rewinds, creating a bubble where transcription occurs for prokaryotes

proterome

totality of the proteins that can be made by an organism

kinase

posttranslational modification, adds a phosphate groupt to protein

phosphatase

posttranslational modification, removes phosphate group

AUG

start codon

open reading frame (ORF)

sequence between start/stop codon that is translated into a protein. single nucleotide substition mutations don’t change ORF, insertion/deletion mutations do

tRNA

transfer RNA molecule, the translator

anticodon

antiparallellaly interacts with mRNA codons

aminoacyl tRNA synthesase

enzyme that attaches amino acid to tRNA

conjugation

bacteria connect to one another through pilus, donor transfers plasmid to recipient through pilus

transformation

bacteria uptakes DNA from the environment, can be from dead bacteria

transduction

phages can uptake DNA from the bacteria they incubate in and deposit it into the bacteria they infect

cis elements

sites on the DNA strand, like the enhancer, promoter and coding regions

trans elements

proteins, elements that are not on DNA strand

positive regulation

seen in eukaryotes, genes are normally off, they need an activator to function

negative regulation

seen in prokaryotes, genes are normally on, they need a repressor to function

lac operon

turns on only if lactose is present, synthesizes lactose so it can be used for energy things, in prokaryotes only

requisome

DNA replication unit