Biology 2B: Genetics and Evolution

structure of dna

double helix structure, paired nucleotide based, nucleotides held together by hydrogen bonds, molecule has net negative charge

eukaryotic dna packaged into

chromatin; stabilized by nucleosomes

less dense chromatin; rich in genes; looser

euchromatin

more dense chromatin; non coding; tightly packed

heterochromatin

what are prokaryotes transcribed as

operons

cell position for replication intiation

oric

circular, double stranded DNA molecule; can replicate independently

plasmid

replicates of DNA

intron

functional genes; shorter

exons

intron regions and exon redundancy; different versions of protein encoded by same gene so it takes up less space

alternative splicing

single copy; sex cells

haploid

paired copy

diploid

spindles, tubules attachment, very repetitive, middle position

centromeres

protect ends, shorter with each division

telomeres

complete set of nuclear material; 98% noncoding, 95% repetitive

genome

compare closely related species to see evolutionary divergence

comparative genetics

why is alternative splicing more useful in eukaryotes

good range in diversity; minimize space needed; sub cellular locations and different organelles, proteins, and cell types required for development

dna → rna→protein

central dogma

1 coding sequence → 1 protein

monocistronic RNA

multiple sequences → multiple proteins

polycistronic RNA

transcription on → repressor → transcription off

negative gene regulation

transcription off → activator → transcription on

positive gene regulation

3 genes (promoter |lac Z|lac Y|lac A

lac operon

transfer of genetic material (plasmid) between two bacterial cells

conjugation

structural rna genes

pol I

responsible for protein coding genes

pol II

structural RNA genes

pol III

5’ end capping, 3’ end polyadenylation, splicing

rna trancript processing

recognizes end sequences in introns; based on end similarities, can excise exons as well

spliceosome

quick response to environmental signals, saves transcription and translation time, reversible end energy saving

post translational modification of proteins

regulates protein protein interactions key to cell cycle and express kinases in each stage = addition of phosphate group to an organic molecule; can cascade and amplify at every step

phosphorylation

study of heritable changes in gene expression and gene function that cannot be explained by changes in DNA sequence; can imprint and be passed on

epigenetics

present in both prokaryotes and eukaryotes; transfer of methyl group on nucleotides; established by writer enzymes and reversibly by eraser proteins; inhibits transcription binding in gene promoter regions recognized by reader proteins; only present on old strand

dna methylation

epigenetic marks allow cell to remember cell type

mitotic inheritance

DNA negatively charge and histones positively charged = attraction, acetylation neutralizes histones and is more loose which is more accessible for transcription; 3 protein and lysine acetylated

H3K9ac

recruits readers which condenses chromatin, DNA not accessible to proteins and gene expression silenced; 3 protein, lysine and trimethylated

H3K27me3

molecule built from identical smaller monomers

biopolymers

dna polymerase adds to which end

3’ end

dna replication is

semiconservative (parental strands separate and go with daughter strands)

second catalytic site in enzyme to remove mistakes

exonuclease

remove supercoiling and relieve stress

topoisomerases

AT rich regions = melts; binds and helices unwinds; primes makes primers to start replication in both directions

OriC

DNA region replicated from single origin

replicons

begins process of replication; lots of proteins required to be brought

ORC (origin recognition complex)

each round leaves 50-200 bp DNA unreplicated; slowly shrink and die; extend to compensate for what’s lost in replication

telomeres

adds acetyl group (CH3O) to lysine residues on histone tails; weakens attraction between histones and DNA and opens euchromatin and increase transcription

acetylation

adds 1-3 methyl groups (CH3) to lysine and arginine residues; activates and represses transcription depending on which amino acid is modified and how many groups are added; tighter packing of heterochromatin and gene silencing

methylation

adds negative phosphate group (po3 3-) to serine, threonine and tyrosine residues'; alters electrostatic interactions; condensation of chromosomes in mitosis; DNA damage repair and transcriptional regulation

phosphorylation

double stranded, single stranded, nicked, gapped

4 types circular DNA

unwinds strands (hexametric and monomeric); use ATP hydrolysis source of energy, as strands separate they can reanneal without using energy; directionality only one way

helicase

cleave sugar phosphate backbone

nucleases

string nucleotides into nucleic acids

polymerases

cleave 1 nucleotide at a time; need DNA ends for activity

exonucleases

attack circular DNA

endonucleases

directionality of polymerases

5’ → 3’ directionality

ability of polymerase to extend a DNA strand before dissociating from DNA and needs to bind again; clamps keep DNA and polymerase connected ; slides along a closed ring and clamp loader is enzyme that opens clamp and loads onto DNA

processivity

DNA damage forms lesions caused by

uv light, ionizing radiation, alcohol, oxidative damage, and mechanical stress - increased chance of risk due to replication

structural integrity altered by:

free ends signal backbone breaks, ssDNA accumulates and persists damage, incorrect base pairing, incorrect base/sugar

genetic change in DNA

mutation

organism carrying a mutation

mutant

activates enzyme photolyase to reverse issue, induced by UV light

thymine dimers

most dangerous damage

double strand breaks

large deletions, inversions, insertions; originate from erroneous DSB repair, common in cancer cells

gross chromosomal rearragements

only dangerous in proliferating cells; drugs available that target cancer cells but can also target stem cells

interstrand crosslinks

DNA damage checkpoints in eukaryotes

G1, G2. Intra S

2 steps of mutation process

lesion → (escape correct repair) → mutation