Molecular Biology

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  • Created by: Sarah
  • Created on: 06-05-17 14:46
what is faster transcription of translation?
transcription
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how many nucleotides are made per second in transcription?
10-100
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how any amino aciss are made per second in translation?
10 amino acids
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what replaces thymine in mrna?
uracil
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features of the genetic code?
triplet code, non-overlapping, universal, degenerate, start and stop signals, accomodates miscmatches
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what is the ination codon?
AUG-methionine
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what are the stop codons?
UGA, GAG,UAA
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how do stop codons work?
encode no amino acid
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whats another 3 words for the stop codons?
amber, ochre opal
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what do arginine leucine + serine all have in coomon?
all have 6 codons
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what is the only codon for tryphotphan?
UGG
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How many mutations are needed to restore the reading frame? who discorvered this?
3 mutations, francis crick
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why is the code said to be degenerate?
most aa are encoded by more than one codon
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how did they crack the codons for the genetic code?
used in vitro translation using synthetic rna moleucles and synthesised rna with different ratios of bases and examined proteins that were produced
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who cracked the codon code?
nireberg
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what is the relationship between codon number and residue frequency?
more codons (triplets that code) the more observed frequency in proteins
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what direction is the reading frame
5' to 3'
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what is the adaptor?
tRNA
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what is the different types of amino acids?
acidic, basic, polar and non polar
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each codon the mRNA has what on the tRNA?
a corresponding anti-codon on the tRNA
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eacg tRNA binds what?
its own unique amino acid
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what is tRNA?
bifunctional
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what is the amino acid attached to by what?
attached to ribose of last ribnucleotide by carboxyl group
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structures of tRNA molecule?
D loop on left, T loop on right, anticodon loop with anticodon aty botto, acceptor stem, andatached amino acid at top
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what is wobble base pairing?
the first 2 nucleotides are always the same eg for asp aa codons = GAC and GAU so the third aa can be either and get the same aa
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why do you get wobble base pairing?
tRNA anticodon loop permits flexibility at the first base of the anticodon
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what does wobble base pairing work on?
that several codons code for 1 amino acid, theres more than one tRNA per amino acid, a tRNA can recognise more than 1 codon
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what is the advantage to wobble base pairing?
tolerance to mutations
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what sites of the ribosome are part of the large ribosomal subunit?
EPA
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what sites are part of of the small ribsosomal subunit
PA (exit is only part of large subunit)
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what is the A site of the ribosome?
aminoacyl-tRNA
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what is the P site of ribosome?
peptidyl-tRNA
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what do 60s ribosomes do?
peptide bond formation
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what do 40s ribosomes do?
codon matching
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what codes for more proteins 60s or 40s ?
60s
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describe translation?
1) tRNA binding to codon by cmbp 2) peptide bond formation 3) large unit translocation 4) small subunit translocation
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what subunbit of the ribosome transocates first?
large subunit
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what direction does the ribosome move along the mRNA?
5'-3'
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what happens when a stop codon is reahed?
the ribosome falls off
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what terminus of the growing polypeptide chain does the is the peptidyl tRNA attach to?
c-terminus of growing polypepride chain
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what enzyme catalyses the condensation reaction?
peptidyl transferase
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what is peptidyl transferase?
an RNA enzyme or ribozyme) that is a part of the ribosome
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what happens at the end of translation?
release factor binds to the A site, no more trna, ribosome falls off
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what is faster per second making nucleotides or amino acids?
nucleotides (10-100 nucleotides/s) aa (10aa/s)
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how do you get simultaneous transcription of genes?
by many RNA polymerases
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what is transcription?
dna to mRNA by rna polymerase
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what is the structure of an amino acid?
alpha carbon in centre, r side chain group, amino group (left), carboyl group (COOH) right
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how many different R side chains are there?
20
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what Ph is needed to ionise the amino and carboxyl groups of an aa?
PH 7
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what is the same for all proteins?
the peptide backbone structure
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what are the catergories of amino acid sidechains?
basic,acidic, poolar and non polar
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what environemtn do polar amino acids prefer?
aqueous environment
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what is the primary sructure of a protein?
the sequence of amino acids
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how is the priamry structure read?
from left to right , from amino (N) to carboxyl (C) terminus
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what does the condenstation reaction in forming a peptide bond give out
water and enzyme peptidyl transferase (ribozyme/rna enzyme)
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what side chains does the hyrophobic core region of a protein contain?
non-polar side chains
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what can polar side chains on the outside of the molecule form bonds with?
hydrogen bonds with water
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what happens if you expose a purified pro to high conc of urea -> denature it then remove urea?
once urea is removed original conforkmation of protein reforms
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what non covalent interactions are proteins held together by?
electrostatic forces, van der waals and hydrogen bonds
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what is an eletrostatic force?
attraction between -ve and +ve charged ions
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what is van der waals forces?
short range weak electrical attraction and repulsion
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what is shared in hydrogen bonds?
share H between O and N atoms
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what are the 3 secondary structures of proteins
1) alpha helix, b-sheet, random coil
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what is te secondary structure?
the local folding of the primary aa chain
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intra chain hydrogen bonds are present in every what residue of an alpha helix?
every 4th residue
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how many amino acids are there every 2 turns in an alpha helix?
7 amino acids
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what are the different representations you can have of an alpha helix?
backbone, sticks, space filling and ribbon
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where can H bonds be in proteins?
within and between polypetide chains eg between diff beta sheet
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what are the 2 different types of beta sheets?
anti parallel and parallel
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what is anti parallel beta sheets?
beta sheets in different directions, have b turns
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what is tertiary structure?
way in which secondary structure polypeptides (alpha helices, beta sheets and random coil pack together within a protein and between sub domains of a protein
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what is a coiled coil
everything between beta sheets and alpha helices
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what does 2 proteins with a comon structure indicate? example?
common function, elastase and chymotrypisn
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what is a protein domain?
a conserved part of a particular protein seq and structure that can function independently without the rest of the protein, each domain forms a 3d structure thats independently folded and stable
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what domain occurs in many proteins?
SH2 domains
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what does it mean that proteins can be evolutionary related?
some protein domains are consevred in sequences infor pros in teh worm, yeast and human
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what kind of pro is src tyrosine kinase?
a multidomain protein
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structure of src tyrosine kinase?
U, SH3, SH2- linker- kinase domain- R c-src
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what do SH2 domains bind to?
phosphorylated tyrosine residues
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what does SH3 domains bindto?
proline rich regions
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what is quaternary strutcure?
relationship between individual proteins (subunits) in a multimeric complex
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what does space fillig models of proteins allow?
us to visualise in 3d
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what protein modifications are there?
glycosylation, lipid mod,phosphorylation, proteolysisanddisulphide bonds
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what does protein binding sie topology dictae?
higher order structure
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what does pro binding site topology dictates higher order structure mean?
depending on where the bidning site is depends what it can form a helix, ring or dimer influences how the protein fits together
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what structures can tubulin subunits that make MT make?
sheets, rings, tubes and filaments
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what does tobacco mosaic virus assemble around?
an RNA core
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how do viral capsids assemble?
self assemble from identical molecules
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what are the 3 types of complementary surfaces?
a) surface-surface b) surface-string c) helix-helix
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what do protein-protein interaction require?
surfaces that complete each other
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name each interaction for each of the complementary surfaces?
A) surface -string= domain-loop interaction, B) helix-helix = 2 alpha helices form a coiled coil, C) surface-surface = domain-domain interaction
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what kind of packing does hydrophobic interactions drive?
coiled-coil packing as the non polar hydrophobic residues) go in the middle
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where are disulphide bonds typically found?
in proteints with extreme environments, conditions variables
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what kind of molecules are disulphide bonds found in?
hormones, antibodies, enzymes
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why are disulphide bonds found in extreme conditions?
they provide stability
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how do you get a mature function molecule of pros like hormones and enzymes?
proteolytic cleaving of the precursor protein to make it functionally mature
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what is glycosylation?
adding carbohydrates to a protein
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what proteins usually are glycosylated?
extracelular proteins
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what are lipid modifications?
a variety of lipophollic covalent attachments that help bind proteins to membrane
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what is a modification that is used to regulate proteins?
phosphorylation and dephosphorylation
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what is tertiary structure?
folding of secondary structures into domains and proteins
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what does RNA polymerase III transcribe?
tRNA and 5S ribosomes
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what are housekeeping genes
genes expressed in all cells for survival of the cell
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examples of housekeeping genes?
nucleic acid synthesis, metabolic pathways, cell survival and DNA repair
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what technique to see mRNA?
in situ hybridisation
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how is differential gene expression achieved?
cell type specific gene transcription
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what does the Anetennapedia TF promote?
development of anttenae into legs
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what is Antenepedia TF?
a dequence specific DNA binding protiens
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how does Antp reg transcription?
by protein-protein interactions affecting the TIC complex
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what is the TIC (trascription inititiation complex) made up of?
general transcription factors and RNA polymerase on the promoter
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what is the 3 parts to the modular structure of all TFs?
1) seq specific DNA binding domain 2) regulatory domain (things bind to) 3) activaor repressor domain
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what binds to nuclear hormone recs?
steroid hormones
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what do nuclear hormone recs do?
reg expression of different sets of target genes
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what is the conditional reg mechanism of TF activity?
unmasking,ligand binding, phosphorylation, addition of second subunit, sitmulation of nuclear entry, release from M
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3 ways repressors stop activators?
1) masking of activation surface 2) competitive dna binding 3) binding directly with the general TFs
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what is the zinc finger domain?
protein module can recognise 3 bp of double stranded DNA
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whats needed to stabilise zinc finger domain structure?
zinc ion
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where does the activators/repressorsbind?
enhancer
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what is the protein coding RNA polymerase?
RNA polymerase II
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what does the Gli3 TF regulate?
digit number in humans and mice
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what is gli3?
seq specific dna binding protein that component f hh sig pathway regs transcription of hh pathway target genes
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what is gene expression primarly controlled by?
selective gene transcription
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what are steps in which eukaryotic gene expression can be controlled?
transcriptional control, protein mods, translation, mRNA localisation, mRNA degradation
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what does RNA polymerase I transcribe?
ribosomal RNA
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why would levels of housekeeping genes change?
Nutrient avalibility and rates of tissue growth+proliferation
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what are protein coding genes?
differentially expressed protein coding genes- make cells different to each other
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what are examples of differential transcriptional reg?
cell adhesion proteins, secreted extracellular ligands, ions channels, cell surface recs, TFs, contractile protiens
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how does transcription initiation begin
general TFs bind to the TATA box in the promoter DNA sequence
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examples of general TFs?
TBP, TFIID, TFIIB
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what do General TFs do?what does this allow?
distort promoter DNA seqs, allows RNA polymerase II to bind
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the TIC remains inactive till what?
until contatced by activaor proteins bound to cis-acting enhancer sequences
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what dictates when are where a gene will be transcribed?
other trancriiptional activators + auxillary proteins in addition to the TIC as stabilise TIC and activate RNA polymerase
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what do activators binded to enhancers do?
stabilise interactions of TIC with promoter DNA long enough for transcription
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what does the cyclodea TF promote?
bilateral symmetry in the snapdragon flowers
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what is the Cycloidea protein?
seq specific dna bidning proteins
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how does it reg transcription?
binds to dna seq in promoter
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what do trans acting TF bind to?
cis acting seqs in CHROMATIN
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What is the functional unit/building block of chromatin?
nucleosome
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what are eukarytic chromosomes?
organised supercoiled nuceloprotein fibres = CHROMATIN
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how long is the human genome in base pairs?
3 x 10^9 bp DNA
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how many bp DNA per nucleosome?
146 bp per nucleosome
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what is the prob with chromatin?
makes dna inaccesible to TF
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what does chromatin allow?
large amounts of DNA to be packaged in small nucleus volume
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2 solutions to inaccesible chromatin?
1) chromatin remodelling factors 2) covalent modification of DNA and histones
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what do chromatin remodelling factors do?
move histone octamers along (open+close up DNA seqs) displace linker histones H1
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what directs transcription activator or repressor to target DNA seqs?
flags- covalent modifications
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what doeslinker histone H1 do?
fix nucleosomes in position within chromatin
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good and bad thing about linker histones H1?
facilitates chromatin compaction and organisation but limits accesibility
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what do chromatin remodelling factors displace from stable interactionsof DNA?
histones and linker histones H1
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what mod makes transcriptionally active?
acetylation of lysine residues in the N terminal tails of core histones
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what do acetylated lysines act as flags for?
chromatin remodellers to open up chromatin
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what does methylation of DNA on cytosine bases do?
switch genes off
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in what dinucleotides is he methylation on cytosine bases?
CpG dinucleotide
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why does methylation of cytosine residues switch genes off?
methylation recruits methyl-C binding proteins, which recruit repressors
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what are epigenetic changes?
changes to chromatin structure which affect expresuon of genes but dont alter sequence of nucleotides
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what is an example fo epigenetic changes?
tortoiseshell cats, exhibit an epigenetic phenotype caused by random epigenetic silencing of a coat colour gene in skin pigment cells
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what do linker histone H1 limit?
nucleosome mobility and accesibility of genes
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what are the post transcriptional controls on gene expresion?
Splicing, 5capping, polyadenylation and mRNA translation
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what does RNA splicing involve?
removal of introns and the ligaton of consecutive exons
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what can regulate splicing?
binding of proteins to extron-intron boudaries
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what controls sex determination in drosophila?
regulated rna splicing
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what protein do Fs have that males dont in drosophila?
transformer protein
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what does the transformer protein do?
is a splicing activator
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how do you get a male drosophila steps?
no transformer pro -> splice site inactive -> doublesex pro male isoform
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how do you get a female drosophila?
transformer pro transcription activator -> splice site active-> splice -> doublesex pro F isoform
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what is the 5' cap of eukarytoic mRNAs required for?
translation initaition on circularised polyadenylated mRNAs
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when is 5' cap needed for translationinitiation?
when theres a circularised polyadenylated mRNA
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what is the iron storage protein ferritin positively regulated by?
free ion concentration
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what happens at low iron levels?
aconitase binds to ferritin mRNA and inhibits translation -> no ferrtitin made
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what happens at high iron levels?
aconitase disociates from ferritin mRNA and translation occurs
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how does the 5' cap and 3'polyA tail of mRNAs promote translation initiation?
recruits transcrlation initiation factors that bind to ribosome subunits
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examples of biological prrocesses?
1)dev of fert egg 2) physiology and behaviour of cells, tissues,organisms 3) pathobiology of human diseases 4) evolution of new species, env adaptations
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what can we use to identify the components of physical mechanisms of biological processes and their function?
geenetics
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who discovered genes?
Gregor Mendel
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what was Joseph Gottileb Kolreuteur interested in?
producing new varities and how species formed, true breeding palnt variteis, hybridisation (cross breeding) to get blends, looked at pea plants
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what was mendels idea?
genes are dicrete physical entities, that function independently of one another to determine distinct physical characteristics (NOT BLENDED)
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what experiments did Mendel do?
set up breeding programme of pea plants (was relaible and large nums of offspring with different chracteristics could be counted)
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why did mendel choose pea plants?
easy to grow, hermaphroditic, lots of inherited variation, can count, easily identified, simple characters
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what reproductive organs do hermaphroditic pea flowers have?
male: stamen- pollen, Female: pistil- ova
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how do pea plants reproduce?
by self fertilisation
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what is true breeding?
parents will pass down a specific phenotype to their offspring
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what makes pea plants true breeding?
they self fertilise
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whenmendel used different types of self fertilised pea plants thwat were all true breeding what did he find?
from one generation to next all looked the same, smooth poduced smooth, wrinkled produced wrinkled
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how did mendel go further than Kolreuter?
he investigated the effect of cross breeding 2 different true breeding pea varities
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how did he cross breed pea plants?
removed stamen from one plant and used them to fertilise pistiol on another plant that had its stamen removed
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crossing a plant from smooth seed with a wrinled seed yield what?
all smooth in F1! F1 NOT a blend
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when plants frown from F1 were self fertilised, F1 plants did not breed true what happened?
wrinkled trait absence in F1 re-emerged in F2
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how did mendel make sense of smooth versus wrinkled cross?
pea plants contain two copies of a seed coat factor, R and r alleles but each gamete contains only one copy
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what is the gametes in mendels cross for F1?
RR (smooth) x rr (wrinkled) = all Rr
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why was all F1 smooth phenotype?
cos Rr, R = smooth, smooth phenotype is dominant to wrinkled
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what ratio of smooth: wrinkled ovccured in F2?
3:1
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why do you get a 3:1 smooth:wrinkled ratio in F2?
Rr x Rr = RR, Rr, Rr and rr
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what is homozygous?
carry 2 identical alleles
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what is heterozygous?
carry 2 different alleles
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what does the dominat R mask?
the recessive r phenotype in the heterozygote
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what did mendel conclude?
1) seed shape determined by inherited factor (gene) 2) each geen 2 alternative forms-alleles (R+r) 3) each true breeding parent carrier pair of identical allels (diploid RR or rr) 4) each parent 1 allele, gametes haploid 5) dominant allele R
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what was Mendels first law?
the principle fo segregation
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what is the principle of segregation
2 alleles of a gene segregate from each other during gamete formation, half gametes carry one allele,other half carry other allele
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what else did mendel conclude from cross breeding?
some alleles dominant, others recessive- no blending of characters to give mxed phenotype
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what did Mendel miss?
many genes have many alleles not just 2, not all alleles exhibit dominance or recessiveness, many genes fail to exibit independent assortment when they lie on the same chr
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what was Mendels second law?
the principle of indepedent assortment
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what is the principle of independent assortment?
genes of different traits are inherited sepaately, assorted into gametes independently
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what traits did mendel focus on in his dihybrid cross?
pea color and shape
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what cross was the first dihybrid cross?
RRYY (yellow round) x rryy (green wrinkled) = RrYy
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what were all F1 in the dihybrid cross?
yellow smooth
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mendel backcrossed F1 gen to see if R/r and Y/Y move into gametes together what did he find?
all 4 types of progeny in equal proportions
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if they combined randomly what would there be?
4 phenotypic classes of F2 in equal proportions (there was!)
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what is incomplete dominance?
the heterozygote is intermediate between the 2 homozygous phenotypes
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where is incomplete dominance seen?
carnation flower colour, red x white = pink
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what is co-dominance?
simultaneous expression of 2 phenotypes determined by more than 2 alleles, simultaneously exhibits phenotype of both homozygotes
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what is an example of co-dominance?
ABO blood groups
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wha tis an organisms phenotype determined by?
its genotype
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what integral membrane proteins are there?
1) single pass 2) multipass 3) b-barrel (pore) 4) ampipathic helix
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why do youcalculate the hydrophobicity of successive sequences?
to predict hydrophobic TM spanning alpha helices
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hat do you use to predict proteins?
hydropathy plot
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whas an example of a single pass 1 membrane protein?
T-cell surface glycoprotein CD8 beta chain
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what is a type 1 protein?
N terminus on the extracellular side of M (and removal of its signal sequence)
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where N terminus of type 1 pro?
extracellular (as you come in from outside)
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what is the structure of a sodium channel protein?
type 9 subunit alpha integral m pro with 24 TM helices multipass
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what do beta barrels form from?
different numbers of beta strands
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what types of beta strands are there (4)?
1) 8-stranded OmpaA 2) 12 stranded OMPLA 3) 16 stranded porin 4) 22-stranded FepA
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what is the 8-stranded ompA beta channel for?
receptor
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what does the 12-stranded OMPLA do?
hydrolyses lipids
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what protein is tumour necrosis factor?
single pass type 2 membrane protein
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what is a single pass type 1 m pro?
N terminus on cytoplasmic side, the TM domain located close to the N terminus and functions as an anchor
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what does the TM domain function as on single pass type 2 m pro?
as an anchor
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what are properties of peripheral membrane proteins?
do not penetrate lipid bilayer, associate with integral m pros, contain lipid anchord
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what is the way peripheral m proteins are bound?
by lipid anchor or binds TM pro
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what mod helps bind proteins to membranes inside and out?
lipophillic covalent attachments (lipid mods)
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what are examples of intracellular lipid mods?
1) acylation- addition of myristyl or palmitoyl groups 2)prenylation- addition of fanesyl or geanylgeranyl groups
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what are extracellular lipid mods?
GPI anchors- glycosylphosphatidylinositol (simple sugar+phospholipid)
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what lipid anchors can there be?
1) myristoyl 2) palmitoyl 3) farneysyl with thioether linkage between cysteine and prenyl group
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what do lipid mod do to GTPase Ras?
regulate the cycling of it between membranes
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what targets synaptosomal-associated protein 25 to different membranes?
differential palmitoylation
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what regulates membrane association of synaptosomal-associated protein25?
4 palmitoylated cysteines
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what are the 2 types of glycosylation?
N-linked attachment via asparagine 2) O-linked attachment via hydroxyl group of serine, thereonine or hydroxylysine
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what is the 3 functions of glycosylation?
1)cellular protections- mucins in mucous 2) adhesive properties 3) varied and complex set of surfaces for interactions
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what is glycosylation principally a modification of?
extracellular proteins
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what are blood groups based on?
glycosylation pattern- oligosaccharides attached to spinghomyelin
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what is a major regulatory modification?
phosphorylation/dephosphorylation
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phosphorylation (hydroxyl group to phosphate group happens on what amino acids?
serine thereonine and tyrosine
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how does phosphorylation act as a switch?
changing the pro conformation or altering the binding surface
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what removes phosphates?
phosphatase
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what is the kinome?
the complete set of protein kinases in its genome
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what does the SH2 domain of src kinase bind?
phosphate
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what binds to the SH3 region of src kinase?
ligand
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how does a src-type pro kinase turn on? 3 things
1) phosphate removed from sH2 2) binding of SH3 to kinase domain disrupted 3) phosphate added to tyrosine, on kinase domain
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how is SH3 disrupted from binding to the kinase domain?
activating ligand binds to SH3
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When is a G protein active?
when GTP is bound
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what is GTP?
guanine 5'-triphosphate
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what changes conformation on Ras with GTP bound?
switch helix
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difference between pro phosyphorylation and G-protein signalling?
phosphorylation uses APP (ADP/AP) OR GPP (GDP/GTP)
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What is ubiquitination?
addition of a chain of ubiquitin to lysine residues on target proteins
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what is ubiquitination catalysed by (adding ubquitin part)?
ubiquitin ligase
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what does ubiquitination do?
targets protein for destruction
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types of ubiquitination?
mono-ubiquitiylation, multi0ubiquitlation, polyubiquitylation
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what do post translational modifications form?
codes for the cell to read
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what is an example of a transmembrane protein?
cystic fibrosis transmembrane conductance regulator
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what are molecular motors
'proteins as machines' motor proteins
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what are 3 examples of motor pros/molecular motors?
Myosin on actin, kinesin on MT, polymerases on DNA
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what does the bacterial flagellar motor do?
allow the flagellum to swim, has stator, rotor and hook
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scr tyrosine kinase SH2 somain binds to what residues?
tyrosine residues
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what do SH3 domain of scr tyrosine kinase bind to?
proline rich regions
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features of DNA mutations?
mutations are random, relatively rare, mechanisms to repair them, most mutations silent/non-functional, genome is plastic over evolutionary scale
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what is true for most organisms about dna sequence?
there are multispecies conserved sequences
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what are germ line mutations?
mutations that affect the cells of the reproductive tissues (gonads)
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features of germ line muations?
inherited, progeny then have mutations in somatic and germ line cells
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what are somatic mutations?
mutations that affect the cells and tissues of the body, not inherited but may still cause disease
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what are dominant traits usually?
usually gain of fuctions
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what are recessive mutations usually?
loss of function
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what could be a conditional loss of function mutation?
only works at certain temps
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what could cause a loss of function mutation?
pint mutation, truncation
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what is a hypomorphic mutation?
loss of function, reduction of proteins ability to work
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what is a null or amorphic mutation?
complete loss of function protein
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what is the mutation called when you get an increase in the proteins function?
hypermorph
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what is it called when the mutant product inteferes with WT proteins function?
antimorph or dominant negative
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what is it called when a mutation gives a protein a new function?
a neomorph (dominant gain of function)
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what is a transversion mutation?
CG -> GC orientation of pyridimine and purine is reversed
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what is a missense mutation?
change from one amino acid to the other
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what is a nonsense mutation?
changes amino acid to stop codon
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what is a transition mutation?
point mutation that changes the nucleotide
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what is the effect of a nonsense mutation on translation?
incomplete polypeptide formed, truncated protein
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what is a neutral mutation?
change one amino acid to another aa with similar property
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what is a silent mutation?
change in codon but same amino acid is coded for
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what is a frameshift mutation?
addition or deletion of one or a few bps changes reading frame
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what is a reason of spontaneous mutations?
looping out errors during DNA rep causes insertion or deletions
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2 spontaneous chemical changes?
1) depurination 2) deamination
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what is depurination?
adenine or guanine (purines) are lost from the DNA backbone (if not repaired random base inserted in dna rep)
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what is deamination?
cytosine is deaminated to uracil (cytosine --> uracil) causes CG to TA
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how does ionising radiation (Xrays, radioactivity) cause point mutations?
high energy can break covalent bonds
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what kind of energy does UV radiation have?
low energy
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why is UV radiation a problem for DNA?
causes photochemical changes, causes pyridime dimers (within_between strands) and dna rep problems
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what 3 kinds of chemicals can induce mutations?
base analogues, base modifiers, intercalating agents
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what do interkalating agents do?
insert between bases in DNA
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what do base modifiers do?
alter the chemical structure of bases eg alkylating agents (form permeant coalent bonds with nucleophillic substaces in dna) like MMS methylmethane sulfonate alkylating agent, methylguaine pairs thymine
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what can an intercalating agent cause?
addition/deletion mutations
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what do base analogues do?
transition mutations
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example of base analogue?
5-bromouracil normally pairs adenine but can also pair guanine- transition mutations
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what is an intercalating agent commonly used as a stain in the lab?
ethidium bromide
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what is SCA caused by?
point mutation on amino acid 6 changes glutamic acid to valine
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what happens in SCA?
reccessive mutation in haemoglobin affects its ability to bind oxygen, at low oxygen tension the RBC loses its shape and becomes sickle shaped
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glutamate to valine in SCA changes it from a charged residue to what?
a neutral residue
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how can you observe aa change in SCA?
gel electropheresis
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what does sickle haemoglobin confer tolerance to?
plasmodium infection, malarial parasites grow poorly in RBCs from heterozygous carrier
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does the tolerance to malaria occur in people with SCA?
no only to carriers (sickle cell trait)
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what is ploidy?
chromosome number
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what chromosomal mutations can you have?
deletion, inversion, duplication/insertion, translocation
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what is the function of cystic fibrosis transmembrane conductance regulator?
chloride transport in plasma membrane of epithelial cells
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what does cystic fibrosis transmembrane conductance regulator regulate?
ion concentrations in ECF especially lungs
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what patients with a mutated CFTCR are unable to what?
decrease mucous viscosity osmotically, this leads to build up of mucus in the lungs
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how many cucasians are heterozygous for CFTR?
1 in 27
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what kind of disease is cystic fibrosis?
autosomal recessive disease
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what is the scale of CFTR mutations?
I to V, I-no synthesis, V-rediced synthesis
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why does cystic fibrosis still exist in the population?
selective advantage as some resittance to infection of tuberculosis (pandemic)
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what are G protein activating mutations?
missense mutaions resulting in substitutions, whose side chains are critical for catalysing the GTPase reaction
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why is the activating mutation bad?
loss of GTPase means G pro is constantly on/activated,
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where were activating mutations first identified?
in sporadic growth hormone secreting pituitary adneomas in patients
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ras muations found in cancer cells introduce aa substitutions at what positions>
12, 13 and 61
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what percentage of human cancers do activating ras mutations occur in?
30%
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why is the substitutions in ras cause cancer?
leave it in GTP on state, no GTPase activity, has resistance to GAPs,pros accumulate with GTP bound
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what happens in the philadelphia chr?
ABL gene from chr 9 to chr 22, reciprocal translation of genetic material
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what forms in the philadelphia chr?
an oncogenic BCR-ABL fusion protein in leukemia cancer cells
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what activity does the BCR-ABL protein elevate?
tyrosine kinase activity
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good protein designs can be what?
adapted modifie, duplicated, shufled and reused, molecular and genetic re-use and recycling
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what is a genome?
the entire dna sequence of an organisms chromosomes
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what is a transcriptome?
the sum of all the RNA contained by an organism
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different cells have different what?
transcriptomes and proteomes
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what genes are ubiquitously expressed in all cell types?
housekeeping genes
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how many copies of genes does each somatic cell have?
2
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how many protein coding genes in the human genome?
21,000
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where is the chromosomes in the cell?
nucleus
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the genome of a eukaryotic cell consists of what?
a collection of linear chromosomes
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what is the karyotype f the human genome?
22 autosomes and XY chromosomes
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what is the telomere?
a soecialized dna sequence at the end of linear chromosomes to maintain chromosomal integrity
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what is the centromere?
a repetitive dna sequence to facilitate the attachment of the spindle via the kinetochore, complex nested arrays of reoeated dna seq elements- repeats within repeats
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where are origins of replication located (where the replication fork starts)?
located within the DNA molecules
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where do 2 replication forks move?
away from each other
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what are telomeres maintained by?
telomerase
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what does the genome of the unicellular E.coli comprise
a single circular chromosomal DNA molecule
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how many protein coding genes does E.coli have?
4289
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how are circular bacteriazl chromosomes replicated?
in a bidirectional fashion
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what happens to genome size as organisms become more compelx
more complex organisms have larger genomes
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how many times more DNA does the human genome have than E.coli?
700x
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why does gene density decline as organisms become more complex?
have similar exon sizes but larger introns
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why is the human huntingtin gene x7.5 larger than in the pufferfish?
larger introns
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what percent of the genome is made up of protein coding DNA sequences?
1.5%
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what is more than 50% of the human genome made up of?
repeated DNA elementslike copies of retrotransposons
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where do transcriptional control elements lie?
between transcription units and in introns
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what is distibuted over larger tracts of DNA in more complex organisms?
evolutionary conserved non-repetive dna seq elements lying upstream+downstream of pro-coding genes
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as organisms become more complex what happens to gene density?
it decreases
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what happens to genome size as organisms become more complex?
it increases
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what project is working to decipher the function of transcriptional control seqs?
ENCODE
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as organisms get more complex: genome size increases, gene density decreases, intergenic distances increase, intron sizes increase why?
larger genomes more repetitive dna seqs (retrotansposons) and more complex transcriptional control elements distributed over larger regions of dna (ehacer+promoter elements)
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Other cards in this set

Card 2

Front

how many nucleotides are made per second in transcription?

Back

10-100

Card 3

Front

how any amino aciss are made per second in translation?

Back

Preview of the front of card 3

Card 4

Front

what replaces thymine in mrna?

Back

Preview of the front of card 4

Card 5

Front

features of the genetic code?

Back

Preview of the front of card 5
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