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Yr 1 Sem 1 > Molecular > Flashcards

Molecular Flashcards

1
Q

Simple multi gene family

A

All genes same, proteins needed in large amounts
e.g. ribosomal RNA genes

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2
Q

Complex multi gene family

A

Genes not identical but have similar DNA sequences. Great organismal complexity
e.g. human globin genes

arises due to gene duplication over time

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3
Q

Molecular clock

A

measure of rate at which DNA sequence of a gene changes

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4
Q

Pseudogenes

A

genes that have changed so much that they have lost their function
4 in a-globin family, 1 in b-globin family

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5
Q

DNA topoisomerases

A

Remove supercoils
- Type I nicks one strand opening up DNA so replication fork can continue up strand
- Type II cuts double strand, passes other DNA strand through gap created + rejoins relieving tension in DNA

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6
Q

3’ -> 5’ exonuclease activity

A

Polymerase can remove nucleotides it has j inserted, proofreading allows correction of errors
DNA pol I and III (bacteria) and pol delta (eukaryotes) uses it

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7
Q

5’ -> 3’ exonuclease activity

A

Polymerase can remove DNA already attached to template
DNA pol I (bacteria) uses it

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8
Q

Leading strand replication

A

Bacteria - primer made w/ primase enzyme, DNA pol III replicates new strand

Eukaryotes - RNA primer extended by pol alpha, pol delta synthesises strand

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9
Q

Lagging strand

A

Must be done in sections (Okazaki fragments) as synthesis always 5’ -> 3’

Bacteria - pol III stops when reaches primer, pol I w/ 5’->3’ continues synthesis + ligase joins fragments together

Eukaryotes - pol delta + helicase push aside primer, FEN1 (endonuclease) cuts flap/branch, ligase joins fragments

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10
Q

Telomerase

A

RNA protein complex

Eukaryotes - it prevents end of chromosomes being shortened, extends parent strand by adding TTAGGG repeats so last Okazaki frag can now be primed

sequence added in prokaryotes is TTGGGG

most cells don’t have it, only expressed in stem cells + cancer cells

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11
Q

Genome

A

complete set of DNA mols possessed by a organism

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12
Q

Role of PCNA (proliferating cell nuclear antigen)

A

Acts as sliding clamp at eukaryote replication fork,
holds pol delta tightly onto DNA
Forks merge in linear DNA so no need for tight control

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13
Q

Initiation of replication in E.coli

A

2 replication forks (bidirectional) from origin of replication which has specific sequence
DnaA proteins bind close to origin forcing base pairs to break
- Pre-priming complex formed by attachment of DnaB proteins (helicase) so helix unwinds
- primosome formed by attachment of 2 primase enzymes

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14
Q

At replication fork in E.coli

A

gamma complex attaches/detaches pol III from lagging strand, beta complex holds pol III onto template

fork meets at terminator sequences, Tus proteins bind + ensure directionality so replication stopped

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15
Q

Chromatosome

A

Nucleosome + DNA + linker histone (H1)

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16
Q

2 types of heterochromatin

A

Constitutive - always tightly packed in all cells
Facultative - tightly packed only in some cells, can be opened up

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17
Q

Karyogram

A

Staining of metaphase chromosomes to create bands which cane be used for gene mapping + identifying chromosome structure

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18
Q

Telomere

A

Protects ends of chromosomes from exonuclease attack + from being mistaken as broken ends

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19
Q

Lac operon

A

5’ promoter, operator, 3 genes (lacZ, lacY, lacA)
lacZ hydrolyses lactose, lacY -> permease which allows lactose into bacteria
Kept switched off by lac repressor

No lactose - lac operon repressed, repressor binds to O preventing RNA polymerisation

Lactose present - binds to repressor so it detaches from O so pol can transcribe genes, lactose is an inducer + under neg. feedback

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20
Q

Cis acting genes/sequences

A

contain operators + promoters, only regulate DNA it is joined to and is dominant

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21
Q

Trans acting genes/factors

A

regulate genes anywhere, mostly TFs + mostly recessive
trans acting factors bind to cis acting sequences

22
Q

Catabolite repression

A

preferential use of glucose by bacteria, so operons only active when glucose used up

uses CRP (catabolite repressor protein)
- binds to promoter near RNA pol
- cAMP binds to CRP permitting DNA binding

if high glucose, then cAMP used up (low) meaning lac operon off

23
Q

Trp operon

A

5 genes (A,B, C, D, E), code for enzymes that synthesise tryptophan, promoter + operator

Operator binds to repressor protein stopping transcription when tryptophan present
-> Trp Operon repressed by tryptophan

24
Q

Regulatory sequence of Eukaryotic class II genes

A

Promoter, Enhancer (has TF binding sites), intron, UTR (3’ and 5’)

eukaryotic genes large but most is non-coding

coding strand (sense) is 5’ - 3’
template strand (antisense) is 3’ - 5’

25
Q

Transferrin receptor

A

Fe in blood binds to transferrin + enters cell via receptor, if enough intracellular Fe2+ then Tf receptor mRNA degraded

Regulated by RNA secondary structure as IRE-BP bound to 3’-UTR, it then dissociates and binds to Fe2+, RNA degraded so receptor not made

26
Q

Ferritin gene

A

Ferritin binds to Fe2+ within cell
in low iron, IRE-BP loses its Fe2+ and binds to IRE preventing translation initiation of ferritin

27
Q

Roles of RNA

A

rRNA (siting and catalysis) + tRNA - synthesis of proteins
snRNA - processing mRNA (splicing introns)
snoRNA - processes ribosomal RNA
catalytic RNA - self splicing introns + ribozymes

28
Q

mRNA capping

A

Guanosine triphosphate (GTP) joins to mRNA at 5’ end
methylation at 2’ position on first 2 nucleotides + on G
-> increases stability, needed for efficient splicing

29
Q

3’ cleavage + polyadenylation

A

CPSF binds to AAUAA, CstF binds to G/U - recruits cleaving factors + polyA polymerase
polyA tailing functionally linked to transcription

30
Q

pre-mRNA splicing

A

Conserved sequences at 5’ and 3’ sites + branchpoint region act as signals
- cleavage at 5’ splice site, lariat formation at branchpoint
- cleavage at 3’ splice sites, intron region removed + exon ligation

31
Q

Spliceosome

A

complex of small nuclear ribonucleoprotein particles (snRNPs)
U1, U2, U4, U5, U6 are snRNPs involved
U2+U5+U6 make up active site

32
Q

Alternative splicing

A

Exon inclusion/exclusion can lead to altered or truncated protein products if exon has stop codon
-> isoforms can be produced from single gene, different functions

33
Q

Amino acid activation

A

A.acids attach to tRNA 3’ acceptor arm
uses ATP -> AMP

Met codon (AUG) follows Shine-Dalgarno sequence in code (AGGAGG) -> identitifes site of initiation + interacts w/ 30s ribosomal unit

34
Q

Initiation of translation

A

Initiation factors/GTP bind to 30s subunit
Initiator tRNA + mRNA join complex, large 50s subunit joins completing complex

ATP + GTP used to form ADP + GDP, IF3 dissociates

35
Q

Elongation

A

P site where peptide bonds form , tRNA-met only tRNA that can bind to P site
Elongation factors needed -> ternary complex formed
A site (aminoacyl-tRNA) where incoming ternary complexes bind
Association of EF-G-GTP , ejection of empty tRNA from P site
Ribosome translocates, freeing up A site

36
Q

Termination

A

RF-GTP binds to A site where termination codon appears
3 prokaryotic release factors
Hydrolysis of polypeptide chain from tRNA + dissociation of tRNA + RFs

37
Q

tRNA structure + function

A

Anticodon, a. acid acceptor arm on 3’ end
Facilitated by aminoacyl-tRNA synthetases, specific for tRNA-amino acid complex (proofreading)

38
Q

How can tRNAs recognise more than one codon?

A

Wobble - allows unconventional base pairing between 3rd base in codon and 1st base in anticodon
3’ end codon/ 5’ end anticodon loose base pairing
Inosine (altered guanine) can pair w/ A, C and U

39
Q

Mutation

A

Alteration in nucleotide sequence of a DNA molecule (propagated as DNA replicates)

40
Q

Errors in DNA replication

A

Causes spontaneous mutations
Arise due to base tautomerism - tautomers are isomers w/ slightly different chemical structures
keto-guanine -> enol-guanine

41
Q

Mutagens

A

Base analogues - 5bU is analogue of thymine (still pairs w/ A), enol-5bU tautomer very common + pairs w/ G not A

Direct structural change - deaminating agents change nucleotide structure, deamination of adenine give hypoxanthine which pairs w/ C not T
e.g. deamination of cytosine gives uracil
e.g. deamination of guanine gives xanthine which blocks DNA replication

42
Q

Other mutagenic agents that cause structural change

A

Alkylating agents - add alkyl group
Intercalating agents - inserts between base pairs
UV causes base dimerization - not easy to fix
Heat causes detachment of bases - creates AP site

43
Q

Direct repair of mutations

A

Enzyme corrects nucleotide alteration

e.g ADA enzyme in E.coli can remove alkyl groups, MGMT enzyme in humans removes alkyl groups position 6 of G

e.g. Base dimers from UV can be repaired, DNA photolyase in E.coli

44
Q

Excision repair

A

Damaged nucleotide removed + gap filled by DNA synthesis

2 types: base excision, nucleotide excision (longer piece of DNA)

45
Q

Mismatch repair

A

Corrects errors in DNA replication, parents strand has correct nucleotide, daughter strand has mismatch

e.g. in E.coli mismatch in daughter strand recognised by MutH and MutS enzymes, MutH cuts DNA excising error

  • less understood in humans + more complex
46
Q

Non-homologous end joining

A

Corrects double strand DNA break, telomeres mark natural ends so can be distinguished from breaks

In humans, Ku proteins attach to broken ends + attract one another, DNA ligase joins ends together

47
Q

How can you reverse the effect of a mutation?

A

In 2nd site reversion, 2nd mutation restores correct a.acid sequence despite nucleotide sequence still being altered

48
Q

Monogenic disorder

A

Inherited diseases caused by defects in individual genes
6,000 known disorders e.g. cystic fibrosis

49
Q

Effects of mutation on cystic fibrosis gene

A

Mutation in CFTR gene causes dysfunctional salt/water balance
Recessive disorder so needs mutation in both alleles to be affected
- F508del deletion of 3 nucleotides means CFTR protein still made but does not reach cell mem.
- G542X nonsense mutation changes glycine to uracil (stop codon created), CFTR protein not made + mRNA degraded
- G551D non-synonymous point mutation, G to A codes for aspartic acid, CFTR protein made + gets to cell mem. but only works at 4% of normal rate

50
Q

Treatment for cystic fibrosis

A

Orkambi made from lvacaftor and lumacaftor
-> effective in people w/ 2 copies of F508del

  • lumacaftor improve conformational stability of CFTR so can reach cell mem.
  • llvacaftor is a CFTR potentiator which increases Cl- ion transport
51
Q

Haploinsufficiency

A

When not enough gene product formed due to a mutation in just one allele, so chromosome directs synthesis through single functional allele

Yr 1 Sem 1 (3 decks)

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