DNA, eukaryotes and prokaryotes

how is DNA packaged to fit into cells

Dna is very long so is supercoiled to fit

features of prokaryotes supercoiling

negatively supercoiled in cells which favours unwinding.

eukaryote supercoiling

supercoiled DNA is stabalised by by nucleosomes containing DNA wrapped aound histone proteins. DNA is tightly packaged into chromatin

euchromatin

least condensed region, rich in genes.

heterochromatin

most condensed region, contains non coding DNA and few genes.

chromosomes in prokaryotes

have only one copy of each gene, arranged in clusters and controlled by the same promotor. circular, no membrane bound nucleus - called a nucleoid.

chromosomes in eukaryotes

individual genes with own promotor, contains exons (coding) and introns (noncoding, allow for alternative splicing). linear, present in pairs, two copies of each gene.

concept of central dogma

once information has got into a protein it cant get out again

general overview of transcription

DNA is transcribed into RNA, mRNA is translated into proteins. a promotor is required for transcription (prokaryotes)

what is an operon

multiple genes under the same promotor (only prokaryotes)

two types of reporters

reporter gene encodes an enzyme with easy to measure activity, or encodes a fluroscent protein like GFP

what are alternative sigma factors

activate specific set of genes in response to environmental signals

what is negative gene regulation

transcription on - repressor - transcription off

positive gene regulation

transcription off - activator - transcription on - activators anchor RNA polymerase at the promotor

lac operon example

encodes proteins required for using lactose as energy and carbon source activator. negative regulation of lac operon and is inactivated in the presence of lactose. positive regulation is the production of enzymes required for lactose consumption only when glucose is not available.

main differences in eukaryotes

eukaryotic mRNAS are generally monocistronic - 3 RNA polymerases. longer and more compex promotors. eukaryotic DNA is wrapped around histones forming nucleosomes, this protein complex is called chromatin.

overview of posttranslational regulation

protein degradation - less protein - activation or inactivation = more stable RNA transcripts = more protein + splicing

what is splicing

excision of introns by spliceosome which recognises the 5’ and 3’ end.

what is alternative splicing

based on the the similiarity of the end-specific sequences in all introns - regulated during development. some genes produce different mRNAs in different tissues as part of the cell differentiation programme.

overview of posttranslational modifications of proteins

regulation by PTMs allow a quick response to environmental signals because it saves time. most are reversible

protein kinases

enzymes which transfer a phosphate group to ATP to serine theonine or tyrosine on a protein. phosphates groups bring a strong negative charge to the surface protein and this can affect its ability to interact with other molecules

cell dependant kinases

express activity specific to each stage of cell cycle - activate the proteins required for a specific stage of the cell cycle

ubiquitin dependant regulation

proteosome is a huge protein complex made in the shape of a barrel where ubiquitinated proteins are unfolded and cleaved into short peptides.

epigenetics

study of heritable changes in gene expression and gene function that cannot be explained by changes in DNA sequences

DNA methylation

transfer of a methyl group on C nucleotides, established by writer enzymes - reversible - removed by ereaser proteins. methylation in gene promotor region inhibits binding of transcription factors.

mitotic inheritance

epigenetic marks allow the cell to remember what type of cell they are

Histones

residues(tail regions) can be acetylated, methylated, phosphprylated or ubiquilated by writers. H3K9aC - acetylated. H3K27me3 - methylated.

polymers made from nucleotides

Polymer - a molecule built from smaller identical or similair molecules monomers, connected covalently.

nucleic acids are biopolymers - phosphates and sugars allow polymerisation of nucleotides.

polarity of DNA

adding the second strand (lagging) sugar phosphate backbone is in the anti parallel orientation. every cell adds nucleotides to the 3’ end, both RNA and DNA.

how is DNA replicated

DNA rep is semiconservative - both strands retain 100% of al genetic information when seperated.

polymerase 3

very efficient proofreading, extends new strands

topoisomerases

removes supercoiling

primase

synthesizes RNA primers

okazaki fragments

synthesis of the lagging strand done in short stretches called okasaki fragments

DNA pol 1

degrades primers and elongates the 3’ end of the okazaki fragment leaving a nick, dna ligase seals the nick.

helicase

opens the dna helix by breaking hydrogen bonds.

DNA rep in prokaryotes

bacterial genome consists of circular DNA molecules. replication not coordinated with cell division. DNAa protein binds to DNA making the A-T rich region melt. has a single origin

replicon

DNA region replicated from a single gene origin - bacteria

telomeres

ends of linear eukaryotic chromosomes - consist of non-coding DNA. with every replication cycle, telomeres shorten. human telomeres shorten through life, so it requires telomerase to extend the DNA strands

DNA damage

can come from UV light, ionising radiation, alcohol, oxidative damage, mechanical stress. DNA rep is the biggest source

DNA lesions

can be corrected - if not corrected then leads to mutation which cannot be repaired as they are genetic changes.

mutation

genetic change in DNA

Mutant

organisms carrying a mutation

cut and patch repair

cut a small gap from one to a hundred nucleotides to remove the structural damage, dna pol fills the gap and ligase seals the nick.

double strand breaks

caused by broken replication forks

interstrand cross links

caused by endogenous metabolites, chemicals

dsb repair

ligation of broken ends or homologous recombination

errounous repair

telomere added to a break

ICL repair

in proliferating cells replication through an ICL requires very complex repair and can be lethal, converted to a DSB then repaired as a DSB

sos response in bacteria

based on transcription activation. can be homolougous recombination - accurate repair or - replication continues/ cell division - inhibitor genes activated

DNA damage signalling the eukaryotic cell cycle

G1 checkpoint - if there is a DSB then entry to S phase is blocked.

S checkpoint - problems with replication forks early in s phase then late origins are not fired.

g2 checkpoint - if the is ssDNA then entry to mitosis is blocked

point mutations

alter the genetic code

silent - no amino acid change

neutral - amino acid change but functional

missense - amino acid change non functional

nonsense - amino acid change to stop codon

frameshift mutation

caused by single base insertions or deletions, insertion causes original reading frame to shift to the right.

true revertant

original DNA sequence restored

psuedo revertant

second mutation suppresses the first

condensin

organises loose chromatin into visible and structured individual chromosomes

stages in mitosis

sister chromatids - identical copies produced by DNA replication during interphase.

one kinetochore attached to each

seperated during mitosis

cytokinesis seperates the two daughter cells.

cohesin

protein complex that holds together sister chromatids, progressive removal during mitosis

bacterial replication

done by binary fission

crossover

reciprocal exchanges of chromosomal segments, chiasma is the site of crossover, crossover leads to recombination

recombination

process of breaking and rejoining which often results in DNA molecules with new sequence.

4 types of recombination

homologous - extended homology.

site specific recombination - limited homology

illegitimate - no homology

replicative - mainly transposition no homology.

homologous recombination

always initiated with a DSB and requires unbroken homologous DNA to repair the break. important for genome stability and genetic diversity.

genetic trait

characteristic of an organism

phenotype

observable trait of a organism

pedigrees

family trees that include information regarding disease

autosomal dominant

signs - both sexes affected, affected individual in all generations

autosomal reccessive

signs - most generations unaffected - parents are heterozygous and unaffected

x linked dominant

appears in all generations

x-linked reccessive

appears to jump a generation, only affects males, females ca be carriers

allelic interactions

interaction between alleles at the same locus

haplosufficiency and haploin

reccessive mutations - one gene copy produce sufficient protein

dominant mutations - one gene copy does not produce sufficient protein

epistasis

expression of one gene masked by expression of one or more other gees

duplicate gene action

2 genes encode some biological function (genetic redundancy)

complementary gene action

phenotype determined by combined action of two genes

modifiers and suppressors

modify expression of a different gene, suppressors is a mutation that reverses the effect of another mutations

the term penetrance

proportion of individuals with a given genotype that shows an expected phenotype

expressivity

degree of gene expression (could be influenced by environment)

complex traits

governed by combination of multiple loci and the environment. do not follow simple mendelion

broad sense heratibility

proportion of phenotypic variance due to genetics - trait and environment specific

narrow sense heratibility

variance due to additive genetic componants for breeding

quantitive trait locis

genomic regions that control the genetic variation of a complex trait - each can have different alleles that make small, quantative contribtions to phenotype

linkage disequillibrium

degree to which one genetic variant is inherited with a nearby genetic variant in given population

pleitropy

a single locus affects two or more distinct phenotypic traits

where do new genes come from

horizontal gene transfer - more common in prokaryotes, responsible for antimicrobial and other chemical resistance, virulence and degradation of rare substances.

duplication - most common in eukaryotes. duplication of whole genome, whole chromosome, DNA segment due to replication error, unequal crossover.

what happens to genes

loss - deletion, genetic drift, selection against, loss of function by mutation

examples of genome evolution in adaptation

antibacterial resistance in bacteria, starch digestion in humans, electric organs in fish.

evo-devo

how a phenotype comes about in the individual via genetic processes.

genetic basis of development

cis elements (enhancers) proximal to the gene. trans elements (transcription factors) encoded by distal DNA regions can be activators or repressors.

cis-element evolution

changes in the enhancers sequence (via mutations) can result in the gain of a trait.

trans-element evolution

changing Tf expression or binding element - addition or alteration of amino acids that can then interact with new proteins.

types of genetic variation

single polymorphism

insertions and deletions

copy number variants

large structural variants

hardy weinburgh equation

p2 + 2pq + q2

assumes random mating and no mutation, selection, migration or genetic drift

relative fitness

offspring divided by 100

selection coefficient

1 - relative fitness

genetic drift

leads to unbiased fixation and loss of alleles

sexual selection

a sub-set of natural selection used to describe the processes underlying the evolution of differences in attributes of males and females.

intra-sexual selection

physical size - weaponry

physiological trait - sperm production, behaviour

inter-sexual selection

most common

behaviour - lekking, eye stalks

direct benefits - food, protection, parental care.

why cooperate

collective self-interest, mutual benefit, group selection, kin selection(alleles present in relatives) - limits growth in groups