AP bio unit 6 gene expression and regulation

transformation

external DNA is taken up by a cell changing physiology

purines

double ring

Pur As Gold

A, G

pyrimidines

single ring

CUT the pie

C, U, T

griffiths transformation experiments 1928

r strain not deadly, s strain deadly

when heat killed s strain + r strain were placed in mouse, mouse died due to transfer of virulence from s to r

hershey chase experiments 1952

radiolabeled DNA and proteins of bacteriophage

when bacteriophage infected bacterial cells, radioactive DNA was present

determined DNA was genetic material

chargaff 1952

concentration of nucleotide bases varied between species but not between individuals

A=T (2)

G=C (3)

components of nucelotides

pentose sugar, nitrogenous base, phosphate group

pentose sugar

5 carbons

deoxyribose or ribose

ribose has OH at 2C

deoxyribose has OH at 3C(r does too but also has extra)

nitrogenous base

attached to 1 carbon

negatively charged phosphate group

attached to 5 carbon sugar

DNA strands

antiparallel in directionality (3-5) (5-3)

eukaryotic genome

multiple linear chromosomes

prokaryotic genome

circular chromosomes in nucleoid region

plasmids

can be in eukaryotes or prokaryotes

small extrachromosomal

double stranded circular

conservative model of replication

produces entire new strand at a time

semiconservative model of replication

correct

one strand used as template for new strand

dispersive model of replication

parent and new strand spread evenly

meselson & Stahl experiment

cultured bac with heavy isotope of nitrogen

nitrogen took up in nitrogenous bases

found that the heavier isotope switched, supporting semi conservative

steps of replication

1.helicase opens replication fork at origin of replication

2.single strand binding proteins keep it open

3.topiosmerase attaches to opening relaxing pressure

4.rna primase intiates replication by adding short segments of RNA primers to allow DNA to attach

function of RNA primase

synthesizes 5-10 nucleotide long primer complementary to template DNA, required bc DNA polymerase can only add groups to existing strand

DNA polymerase 3

reads 3’-5’ to synthesize nucleotides in 5’-3’

DNA polymerase 1

replaces RNA primers with DNA nucleotides and proofreads as it goes

telomeres

repeating units of short nucleotide sequences that don’t code for enzymes,form cap at the end of DNA to postpone erosion

gets shorter as cells divide

telomerase

adds telomeres to DNA

nuclease

removes segments of nucleotides and DNA polymerase and ligase replace segments

leading strand

can be synthesized continuously

3’-5’ direction

moves towards inner replication fork

lagging strand

cannot be continous

5’-3’ direction strand

forms okazaki fragments

moves away from replication fork

dna ligase

connects okazaki fragments together

origin of replication

eukaryotes have multiple on each chromosome

prokaryotes usually have one

dna polymerase proofreading function

polymerase checks whether the newly added base has paired correctly with base in template strand

mismatch repair

specific repair enzymes recognize the mispaired nucleotide and excise part of the strand that contains it

nucleotide excision repair

removes damaged base pairs

gene expression

process of DNA directing synthesis of proteins

transcription

synthesis of RNA using information from DNA occurs in nucleus

mRNA

messenger rna synthesized during transcription using DNA template, carries info from DNA to cytoplasm

rRNA

ribosomal rna builds ribosomes, catalyzes peptide bonds between amino acids

tRNA

transfer RNA-carries specific amino acid, attaching to mRNA via anticodon

strand being transcribed, complementary to mrna

template, noncoding, antisense, -

strand not being transcribed, same as mRNA but t-u

coding strand, sense, +, nontemplate

transcription intiation

RNA polymerase attaches to promoter region (upstream of gene)

transcription promoter name

TATA eukaryotes

Pribnow prokaryotes

transcription elongation

RNA polymerase opens DNA reading template strand(3’-5’)

moves downstream and only small sections of DNA at a time

single gene transcribed by several RNA polymerase strands

transcription termination

goes through termination sequence and RNA polymerase detaches

3 eukaryotic rna processing events

1. 5’ capping

2. 3’ poly a tail

3. splicing

5’ cap

modified GTP nucleotides added to 5 end to protect mRNA, prevent degradation, and help bind to ribosomes

3’ Poly A Tail

poly-A-polymerase adds adenine to 3’ end, works as flagellum

splicing

introns cut out, exons joined together

translation

protein synthesis, involves decoding mRNA into polypeptide

enzyme involved in transcription

aminoacyl tRNA synthase: attaches amino acids to tRNA

where does translation occur

ribosome

prokaryote ribosome composition

70s

30s small subunit

50s large subnit

eukaryotic ribosome composition

80s

40s small subunit

60s large subunit

intiation

ribosome units assemble upstream from first start codon, initiator tRNA interacts with first start codon

A site

incoming charged tRNAS held

P site

charged tRNA transfers amino acid to growing polypeptide

E site

releases tRNA to get recharged

elongation

mRNA provides tRNA binding specifity, ribosome moves in 3’5 direction

termination

nonsense/stop codon reaches A site signaling for release factor hydrolyzing bond that holds peptide to P site

chaperone proteins

help proteins fold

post transcription modification

phosphorylation- addition of phosphate groups, charges can change protein conformation

proteolysis-breaking down long peptide chain into final products by proteases

glycosylation- addition of carbohydrates to form glycoproteins

cell specialization

caused by gene regulation, turning on or off based on environmental and internal cues

operons

group of genes that can be turned on or off

promoter

region where RNA polymerase can attach

operator

on/off switch

genes

code for related enzymes in pathway

repressible ON TO OFF

transcription can be repressed

inducible OFF TO ON

transcription can be induced

regulatory gene

produces a repressor protein that binds to the operator to block RNAP from transcribing

TRP operon

synthesizes tryptophan

repressible

active until turned off by TRP repressor

more trp binds to repressor, turning off transcription

TRP BINDS TO REPRESSOR

we have enough, dont need more

Lac operon

inducible operon

controls synthesis of lactase, breaking down lactose

inducible, transcription is always off and can be turned on

lac repressor bound to the operator until allolactose turns the repressor off

point mutations

change in single nucleotide pair of gene

subsitutions

replacement of one nucleotide and its partner with another pair of nucleotides

types of substitutions

silent, missense, nonsense

silent mutation

substitutions codes for same amino acid

missense

subsitutions result in different amino acid

nonsense

substitution results in stop codon

conservative vs semiconservative

conservative changes amino acid w/o changing properties, so protein folds same

frameshift mutation

reading frame of genetic info is altered, either insertion or deletion

large scale mutation

nondisjunction, translocation

translocation

inversions:segment reversed

duplications: segment repeated

deletion: segment lost

transformation

uptaking of DNA from nearby cell

transduction

viral transmission of genetic material

conjugation

cell to cell

transposition

movement of DNA segments between DNA molecules

gel electrophoresis

separates DNA fragments by size

DNA loaded into wells on one end of gel and electric current applied, smaller fragments move down towards positive charge quickly

PCR

makes several copies of specific DNA segments amplified results anlzyzed through gel electrophoresis1

histone aceytlation

adds acetyl groups to histones which loosen DNA

DNA methylation

adds methyl groups to DNA causing chromatin condensing

epigenetic inheritance

chromatin modifications dont alter nucleotides can be heritable to future generations

→ modifications can be reversed unlike mutations

cytoplasmic determinants

substances in maternal egg that influences cells

homoeotic genes

map out body structures