Genetics (core)

• how can chromatin exist?

  euchromatin: less condensed & = transcribed

  heterochromatin: highly condensed & ≠ typically transcribed
• what is a nucleosome?

  fundamental subunit of chromatin

  = DNA wrapped around core of 8 histone proteins == histone octamer

  → each octamer = 2 copies of each histone protein (H2A, H2B, H3, H4)

  → H1 @ nucleosome linker DNA

  → histone core proteins = +ve charge → tightly bind to -ve DNA backbone
• what is the structure of chromatin?

  nucleosomes folded around each other → form fibre

  → requires histone H1 → binds linker DNA between nucleosome cores → form chromatosome

  chromatin fibres = folded → loops
• how can gene expression take place?

  cell's chromatin must open (chromatin remodelling)

  → necessary to provide access to underlying DNA (enable transcription)
• what are the effects of chromatin remodelling & how can it be remodelled?

  
  

  → mediates activation of transcription

  → exposes promotor sequences

  → ↑ freq. of transcription

  1. ATP-dependent chromatin remodelling complexes either move / eject / restructure nucleosome
  2. covalent histone modifications by specific enzymes
• describe the process of covalent histone modification

  1. histones carry +ve charge (DNA = -ve → phosphate groups) from lysine residues
  2. histone acetyl transferase (HAT) + acetyl group to lysine (remove charge → histone = neutral)
  3. histone affinity for DNA ↓ → unpackaged → ready for transcription
  4. DNA repackaging = histone deacetylase (HDAC) → remove acetyl group (+ve charge back on lysine)
• what are histone tails & how can they be modified?

  = lysine rich

  → N-terminal of histone proteins

  → extend out nucleosome between DNA turns

  modified by ...

  • acetylation of lysine
  • methylation of lysine & arginine
  • phosphorylation of serine

  modified tails act as signals / binding sites for other regulatory proteins

  → some promote condensation / decondensation (facilitate access to DNA)
• what is methylation?


  DNA & histones methylated = inactive chromatin

  DNA: occurs @ cytosines of CpG sites → histone tails = more likely methylated
• where is there unlikely to be genes & why?

  centromere & telomere (chromatin = permanently folded into heterochromatin)
• what are epigenetic effects?

  • influence phenotype w/out altering genotype
  • result of modifications after DNA replication (DNA methylation, histone methylation/acetylation/phosphorylation)

  switch genes on / off depending on environmental factors
• describe Mendel's postulates


  UNIT OF GENETIC INHERITANCE: inherits 1 allele from each parent

  DOMINANCE / RECESSIVENESS: if alleles = different → only 1 trait visible; 1 = dominant  (expressed) & 1 = recessive (not expressed)

  SEGREGATION: alleles = segregated randomly during gamete formation; homozygous or heterozygous

  INDEPENDENT ASSORTMENT: segregating pairs of alleles assort independently of each other (2nd law of inheritance)
• what are alleles?


  alternative ver of genes

  account for variations in inherited characters

  differences in alleles of genes = slight differences in DNA sequence @ same locus → different protein products

  → most common allele = major / wildtype; less common = minor
• what happens to alleles that segregate (during gamete formation)?

  end up in different gametes ∴ female/male gamete only gets 1 of the 2 alleles present

  segregation corresponds to distribution of homolgous chromosomes to different gametes in meiosis (germ cells = haploid following meiosis)
• describe genetic recombination during meiosis

  prophase 1: crossing over (recombination) between homologous chromosomes

  alleles further apart on chromosome = more likely separated than alleles close to each other

  after crossing over: homologous chromosomes separated in different combinations in gametes

  after fertilisation: separated chromosomes reform homologous chromosome pairs w/ genetic material in other gamete
• what are the different types of dominance?

  complete dominance: phenotypes of heterozygote & dominant homozygote = identical

  incomplete dominance: phenotype of F1 hybrids = somewhere between phenotypes of 2 parental varieties; intermediate phenotype

  codominance: 2 dominant alleles affect phenotype in separate distinguishable ways
• what is pleiotropy?


  1 gene = multiple phenotypic effects

  unrelated characters caused by same protein by same allele

  (coat colour pattern & cross eyes in siamese = caused by same allele)
• what is epistasis?


  1 gene @ 1 locus influences phenotypic expression of gene @ 2nd locus

  e.g. 1 gene determines pigment colour & other determines whether pigment is deposited in hair
• describe the genes on mammalian sex chromosomes

  X chromosomes = more genes than Y (53 protein-coding)

  Sry = sex-determining region of Y (single gene) → encodes testis-determining factor (TDF)

  → expression = testes → testosterone → masculine brain phenotype

  → ≠ expression = ovaries → relatively low testosterone → feminine brain phenotype
• what are loss-of-function mutations?

  inactivating mutations

  gene product = reduced / no function

  most common in recessive alleles

  1 normal wildtype = sufficient to produce enough gene product to ensure normal / near normal cellular function

  disease only in mutation in both alleles

  disease e.g.: chondrodysplasia → mutation in collagen binding protein
• what are gain-of-function mutations?

  activating mutations

  gene produce = abnormal function

  mutation increases activity of allele / adds new function / makes gene product available in new location (inside / outside cell)

  could be +ve and/or -ve

  → presence of 1 wildtype allele ≠ protect against disease phenotype

  e.g.: ß-defensin causes black coat colour (enables novel membrane protein interaction)
• what is overdominance?


  heteozygotes in certain genes makes them superior to either homozygote

  e.g. sickle cell anaemia:

  → autosomal recessive

  → heterozygotes = affected but to lesser degree & resistant to malaria

  → affected homozygotes = decreased life expectancy
• what is polygenic inheritance?

  quantitive characters = vary in pop. along continuum

  quantitive variation indicates polygenic inheritance

  → additive effect of 2 / more genes on single phenotype
• describe the gene interactions

  genotype & environment interact = phenotype determination (e.g. light, temp., nutrition affect translation of genotype → phenotype)

  penetrance: proportion of individuals w/ given genotype that express corresponding phenotype

  expressivity of genotype: degree to which it’s expressed in given individual
• how do qualitative (mendelian) and quantitive genetics compare?

  qualitive:

  → inheritance of traits of a kind

  → discrete phenotype classes

  → display discontinuous variations

  quantitive:

  → inheritance of traits of degree

  → spectrum of phenotypic classes

  → contain continuous variation due to multipile genes w/ multiple alles & environmental influences
• what are telomeres?


  repetitive regions @ chromosome ends

  G-rich series of repeat bases (TTAGGG)

  act as caps → protect internal chromosome region

  worn down by small amount every DNA replication round
• how is DNA proofread & corrected?

  polymerase adds incorrect nucleotide to new DNA strand

  polymerase detects mispaired bases

  → uses 3’ → 5’ exonuclease activity → remove incorrect nucleotide
• how does exposure to environmental factors damage DNA?

  depurination:

  → no DNA breaks

  → removal of purines (guanine / adenine bases → leave sugar-phosphate group)

  deamination:

  → no DNA breaks

  → results in C to U transition (conversion of cytosine → uracil)
• what are point mutations?

  genome DNA = transcribed to mRNA → translated into amino acid sequence substituting nucleotide alters codon (silent, missense, nonsense)
• what are the consequences of missense mutation?

  conservative substitution: similar aa R group size & charge

  → similar protein shape & function

  radical substitution: new aa R group different charge / size

  → protein altered 2y / 3y structure → affects function
• what are the consequences of a nonsense mutation?

  nonsense mediated decay (NMD) → during translation

  detects transcripts w/ premature stop codons & degrades them
• what are insertion mutations?

  changes no. nucleotides in gene (adds DNA piece)

  → every nucleotide shifted along by 1 downstream from insertion

  → resulting mRNA shifted by 1 nucleotide

  → every codon from insertion point = different

  → different aa = incorporated into protein → may not function properly

  open reading frame (ORF) = moved / frame shifted (frameshift mutation)
• what are deletion mutations?

  removes DNA piece

  nucleotide in gene shifted up by 1 downstream from deletion
• what are the differences between prokaryotic & eukaryotic transcription?

  PROKARYOTE (cytoplasm)

  → coupled transcription & translation

  → ≠ definitive phase of occurance

  → 1 single RNA polymerase

  → ≠ initiation factors

  → polycistronic

  EUKARYOTE (nucleus)

  → ≠ coupling

  → occurs G1 & G2

  → 3 RNA polymerases

  → multiple general transcription factors (GTFs)

  → monocistronic
• what is non-nuclear / extrachromosomal DNA?

  transcribed differently to standard eukaryotic transcription (similar to prokaryotic)

  e.g. mitochondrial DNA
• describe the splicing stage in processing

  → introns removed by spliceosome (complex of RNAs & proteins)

  → formed from snRNAs (U1, 2, 4, 5 ,6), associated protein factors (snRNPs), ‘other’ proteins

  → exon shuffling enables >100k proteins from human proteome

  → 1 gene can encode several different proteins using alternative splicing
• what is the structure of the ribosome?

  large ribosomal subunit (50S) = 3 slots for tRNA

  → move from A(minoacyl-tRNA) → P(eptidyl-tRNA) → E(xit) as ribosome slides from 5' → 3'

  small ribosomal subunit (30S) = mRNA binding site
• what is the tRNA wobble?

  (allows for fewer tRNA mol. to be necessary)

  → allows for same tRNA to recognise mutiple codons for aa it carries

  ensures tRNA ≠ bind to wrong codon

  main wobble base pair: G w/ U instead of C
• how is tRNA loaded w/ correct amino acid?

  aminoacyl-tRNA synthetases = specific for each aa

  → recognise only aa AND appropriate tRNA for aa

  → utilises ATP

  → proofreading ability (if similar aa added to tRNA)