Unit 6 APBIO

DNA vs RNA- DNA

-located in nucleus of euk

-cytoplasm pro

double stranded molecule in the form of a double helix

DNA vs RNA-RNA

single stranded- can be different shapes and lengths

nucleus or cytoplasm depending on the type

-Transfer RNA- cytoplasm

-RIbosomal RNA- cytoplasm

Messenger RNA

carries information from DNA to ribosomes (nucleus and cytoplasm)

TRNA

carries amino acids to the ribosomes (cytoplasm)

Ribosomal RNA (rRNA)

building blocks of ribosomes (cytoplasm)

nucleotide structure

monomer of DNA and RNA

-3 parts:

• pentose sugar (gives name)

• Phosphate group

• Nitrogenous base (makes monomers different: AT(DNA only) CGU (RNA only)

Purines vs Pyrimidines

Purines- double ringed structure (A G)

Pyrimidines- single ringed structure (T C U)

Erwin Chargaff

-discovered how bases pair tg

-A T 2

-C G 3

-purine + pyr = establish equal distance

Strands

-run antiparallel- allows hydrogen bonds to form btwn base pairs

-ends of the strands by carbon in sugar (3’)

-carbons started by counting top by oxygen

-phosphate on the 5’ end

Nucleotides structure

backbones are made of alternating deoxy and phosphate molecules connected by PHOSPHODIESTRER BONDS

pentose+nucleotide= glycosidic

DNA structure eu vs pro

eu- multiple, linerar DNA in nucleus, larger

pro- single circular DNA in nucleoid region, smaller, may contain plasmids

DNA replication

S phase of interphase

-semiconservative process- each parent strand serves as a template for the duaghter strands, duaghter strands have old and new strand

Enzymes involved

5

Topiosomerase

-prevents DNA from overwinding

DNA helicase

unwinds and breaks hydrogen bonds to seperate the 2 strands

RNA primase

adds 8-10 RNA nucleotides called a RNA primer to template strands (guide DNA polymerase on where to start)

DNA polymearse

adds new DNA nucleotides to 3’ end

proofreading ability (DP3 builds strands DP1 replaces RNA primers w DNA nucleotides)

DNA ligase

links any DNA fragments tg by creating phosphodiester bond to backbone

Initiation

ORi of replication, eu many, pro 1

-topiosomerase relax strands

-helicase unwinds and unzips the DNA by breaking hydrogen bonds to create replication fork

-Single stranded binding proteins (ssb) bind to keep strands from reattaching

-RNA primase lays down RNA primer

Elongation

DP3 attatches to template strand-starts at 3’ end

-primer replaces with DNA nucletides by DP1 once DP3 starts

Leading strand- built continously towards replication fork (follows direction of replication)

Lagging strand- build discontinous away from replication fork forming okazaki fragments

Proofreading

mismatch repair mechanisms also ID and correct any errors that escape proofreading

Termination

DNA ligase bond fragments tg to create 2 completed daughter strands

Telomeres

non coded repetitive nucleotides at the end of chromosomes help portect information

• Telomearse-enzymes that extend telomeres counteracting the shortening in some cells (human gamete cells)

chromosomes get shorter each round of replication which limits number of cell divisions so aging tkes place

gene expression

process that allows information encoded in a gene is used to make a protein molecule

Transcription

nucleus in eu and cytoplasm pro

RNA poly 2 uses single strand of DNA to convert gene to a complementary mRNA works in 5 prime to 3 prime

-template runs 3 prime to 5 prime (noncoding, minus, antisense)

Steps of transcription

transcription factors attach to promoter region called TATA box

-help RNA polymearse 2 bind to strands

-transcription initiation complex created

-RNA polymearse unwinds and open strands to begin copying

-continues until termination sequence (polydenylation (poly A degrades otw out of the nucleus) signal is reached)) -forms hairpin loop by binding to itself

Translation

occurs at the ribsomes in cytoplasm

producing a protein by reading the mRNA gene sequence

all 3 RNA used

requires ATP

Ribosomes

2 subunits- large and small

-large subunit 3 groove sites

• A- binding site for trna molecule

• P- contains growing peptide chain

• E- trnas exits once amino acid delivered

TRNA

carries specfic amino acid

-has anticodon that binds to complementary mRNA

• ensures that correct AA delivered

Translation Initiation

-small unit binds to 5’ end of mRNA to find start codon

-first tRNA bind

large subunit will attach first tRNA into P site

Codon

3 nucleotide on mRNA- 64/61 for AA

Translation- Elongation

-Codon recognition- charged tRNA w complementary anticodon complementary to next codon enteres A site

-Peptide bond formation- ribosome catylzes peptide bond formation btwn P and A site

-Translocation- shifts mRNA moving tRNA from one site to the next so new things can enter and used up can leave

old trna will

be uncharged after leaving and go into the cytoplasm to pick the same amino acid with the help of AMNIACYL-TRNA synthease that charges the tRNA by binding it w right AA

Translation Termination

continues until stop codon found

-release factor blocks A site and causes the polypeptide bond to be release and everything is recycled

After?

-folded into new structure

-conbined w others

-golgi to be repackaged

gene expression eu vs pro

eu- transcription nucleus, translation in cytoplasm

pro- transcrip and translation happen same time no MRNA processing

Mutations

perm change in DNA

-caused by mutogens- external factors

errors in DNA replication or transcription

Errors in cell division

mustations are random, MOST have no effect

point mutations

substitution- base changed but total amount doesn’t

-nonsense- earlier stop codon, protein becomes shortened and not functional

-missense- codes for a different amino acid (single nucleotide changes)

-silent- codes for the same amino acid even tho nucleotide changes

Frameshift mutation

insertion or deletion

-causes shift in reading frame

-changes all codons after mutation

-Negative effect always

Mutations on genetic variation

-mutations can increase genetic variation in population (only if phenotype is changed)

-allele frequency changed, evolution occursed

prokar gv

horizontal gene transfer up genetic variationco

conjugation

direct cell to cell contactt

transfomation

absorption of free DNA from enviorment

Transduction

virus transfer DNa btwn bacteriaTr

Transposition

transposons (jumping genes) can move from one loc to another

cells turns on and off parts of DNA

cell differentiation

pro and eu use ____ to accomplish gene regulation

regulatory sequences

Regulatory sequence

do not code for protein

interact w regulatory proteins to control transcription

do not need to be close to regulate

Reg of gene expression in pro

operon- clusters of genes under control of single promoter

-operator- on and off switch

-promoter- where RNA P bonds

-genes

Inducible Operon

usually off (ex. Lac Operon) unless inducer molecule is present

-produces enzymes when nutrients are avaliable

Lac operon

controls metabolism of lactose (allalatose acts as an inducer)

-no lactose= repressor protein binds to operator no transcription

-lactose= binds to lac respressor protein changining shape so it cant bind to operator sequence

Repressible

usually on unless a product is abundant in the cell (TRP)

TRP

makes AA tryptophan

-if lvls re low, operon is active and enzymes produced

-if high, trypotphan acts a corepressor by binding to repressor protein (allows bind to shut down)

-synthesized only when needed

Activator

help promote enhance transcription (ex. CAP in Lac operon) cAMP helps activate it so it can push transcription along

Reg of gene expression in eu

4

Chromatin structure

adjust how tightly DNA is wound around histones

histone acetylation

acetyl group is added to histone- prevents them from binding too tight o proteins can transcript

DNA methylation

methyl groups added to tighten chromatins to prevent transcription