Bio 1A unit 2

Function of DNA helicase during replication?

Unwinds dsDNA helix ahead of the replication fork via breaking H-bonds by hydrolysis

Function of single-stranded binding proteins (SSBs)

Binds to single stranded template DNA to straighten regions and prevent it from reannealing or form hairpins during synthesis

Topoisomerase

Relieves supercoiling and torsional strain ahead of replication fork via a nick allows roation before resealing

RNA Primase

Synthesize short RNA primer to provide 3’ OH group for DNA polymerase to initiate DNA synthesis

DNA polymerase III

synthesizes main leading and lagging strande in 5’-3’

DNA polymerase I

Removes RNA primers and replaces them w/ corresponding nucelotides

DNA Ligase

Seals nicks in sugar phosphate backbone, join Okazaki fragments

Alternative splicing

selectively includes or skips different coding exons when processing pre-mRNA transcripts (allows single gene to encode many protein isoforms)

How does Lacl repressor regulate lac operon

Bind to operator when lactose is absent to block RNA polymerase, while allolactose acts as inducer to inactivate it=transcription

cAMP-CPR complex function

positive activator when glucose is low, elevated cAMP binds to CRP attatching upstream of promoter to recruit RNA polymerase=high transcription

Histone Acetyltransferases (HATs)

Add acetyl groups to lysine residues on histone tails = nuetral= realax into euchromatin= transcription on

Histone deacetylases (HDACs)

Remove acetyl groups to condense chromatin into heterochromatin= transcription off

Maintenance DNA methylation

DNMT1(animals) MET1(plant) recognize hemimethylated CG sites at fork and methylates the cytosine on newly synthesized complementary strand in semi-conservative manner

Maintenence of histone modifications

Parental nucleosomes diassemble and redistribute randomly on daughter strands dispersively where reader-writer proteins recognize old marks and copy them onto the new nucleosomes

Bacteria restriction defense

Restriction endonucleases cleave unmethylated foreign phage DNA, while host methyltransferases methylate bacterial recognition sites to protect itself for cleavage

Prokaryote CRISPR-Cas system

provides immunity be storing phage fragment DNA between genomic repeats, transcribing crRNAs that direct Cas9 endonucleases to cut foreign phage DNA

What defense mechanisms fo prokaryotes have

CRISPER-Cas, methyltransferase, and restriction modification

Eukaryotic defense against virus

RNA interference (RNAi) where foreign dsRNA is processed into siRNAs loaded into RISC which then degrades and blocks translation

Why is BCL11A used for sickle cell

a transcription factor that represses HbF and using CRISPR to knock out an enhancer of BCL11A turns HbF back on to replace defective adult hemoglobin

How DNA methylation and Histone modification are different

DNA methylation modifies the DNA strand and is semiconservative, Histone modification modifies histone proteins and is despersive but both are epigenetic and cause condensing and uncondensing

Difference between eukaryotic and bacteria transcription and translation

Eukaryotic transcription is in nucleus and translation in cytoplasm also has mRNA processing, while bacteria all in one place no processing

Silent Mutations

Single nucleotide mutations that does not change the amino acid product

Missense mutation

Single nucleotide mutation that leads to a amino acid substitution

Nonsense mutation

Singlue nucleotide mutation that creates a premature stop codon

Frameshift mutation

Single nucleotide insertion/deletion shifts the reading frame downstream

RNA processing in eukaryotes

adds 5’cap and poly-A tail are added to the ends=prem-RNA then a spliceosome cuts out introns and splices together exons

Alternative splicing (eukaryotes)

Different splicing patterns can exclude exons to change protein coding sequences = different protein isoforms and be specific for different needs (ex.nerves v skin) (stay in the same order ex:1,2,3 NOT 3,1,2)

What frequency means genes are unliked

1:1:1:1 = >50% unliked

De novo methylation

starts new mathylation patterns on previously unmethylated DNA

Retrotransposons

moves RNA intermediate w/ reverse transcriptase and integrase

RNA direct DNA methylation

siRNAs paired w/ RISC target transcripts from transposable elments recruiting de novo to silence

Exon shuffling

Transposons move via transposase in the DNA

Cut and paste transposons

transposase cuts DNA out of og site and pastes it into new target sequence

Copy and paste transposons

Transposon is duplicated and transposase inserts new copy into target site

Positive sense single stranded RNA virus

in viral genome, there’s an mRNA coding strand then the host ribosomes translate it into proteins including RdRp which uses the mRNA as template to synthesize negative-sense RNA which is then used as a template to make many more virus rna

What viruses do eukaryotes get

RNA viruses (+ssRNA and -ssRNA) and retro viruses

Negative sense single stranded -ssRNA

genome has a noncoding template strand and RdRp which transcribes it into +ssRNA strand to be used for proteins and to make more viral RNA

Retroviruses

has 2 identical ssRNA and reverse transcriptase and converts its RNA to DNA which allows permenant integration into host genome which is then transcribed by host

Bacteriophage cycles prokaryotic

lysogenic and lytic

lysogenic cycle

injects it DNA then puts it into bacteira chromosome=prophage and stays repressed then host devides then when stress or a signal it leaves host chromosome and enters lytic cycle

Lytic cycle

injects host cell w viral DNA and uses host to make viral proteins then reasemble the phage then the cell lyses and phages can infect more

Incomplete dominance

heterozygous intermediate phenotype ex.dom red, recessive white, heterozygous=pink

codominance

both alleles fully expressed in heterozygotes ex AB blood type

Epistasis

gene at 1 locus alters or masks expression of gene at another ex1 gene codes for pigment the other is color but if no pigment=no color no matter what

polygenetic inheritence

phenotypic effect of multiple genes ex skin color

Gene linkage

genes close together often inherited together RF=#recombinant offspring/total offspring x 100

G1 checkpoint

Checks for growth factors, nutrience, DNA integrity

G2 checkpoint

DNA replication was finished and no DNA damage

M checkpoint

checks chromosomes are aligned and microtubules are attatched equally

Ribosomes mRNA→polypeptides

A site accepts tRNA, P site holds growing polypeptide and forms peptide bonds, E site: tRNA is ejected

DNA replication proofreading

DNA polymerase backtracks to take out mismatches, if not caught=bubble where protein MutS&MutL scan and if it finds a bubble chews and removes it, then thymine dimers caused by UC are taken out by nucleases and fized w DNA polymerase and ligase

Chromosome end problem and solution

removing final RNA primer of lagging strand=overhand=reisk of sequence degredation so adds telomeres non coding repetitive DNA sequences

PCR

denature, primer annealing, extension using DNA polymerase to amplify a target sequence

DNA cloning plasmid

Restriction enxyme cuts to make sticky ends and DNA is inserted via transformation w selected markers

Gel electrophoresis

separates DNA fragments by size

Sanger sequencing

uses fluoresent ddNTPs for chain determening sequences

PT-PCR & CDNA

converts RNA to CDNA w reverse transcriptase to measure gene expression

gene pertubation

kockout via CRISPR or homologous recombination or RNAi to know gene function

Forward genetics

start w/ mutant and work back to original to indetify responsible genes