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Biochemistry Year 1 > Part Bs (Proteins, Enzymes, DNA replication and RNA transcription) > Flashcards

Part Bs (Proteins, Enzymes, DNA replication and RNA transcription) Flashcards

1
Q

Primary proteins structure

A

Sequence of AAs, chirality, psi and phi torsion angles of 50/60 degrees

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2
Q

Positively charged side chain

A

Arginine

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3
Q

Negatively charged side chains

A

Aspartic acid

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4
Q

Polar uncharged side chains

A

Serine

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5
Q

Special amino acids

A

Cysteine, glycine and proline

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6
Q

Hydrophobic side chains

A

Alanine and Valine

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7
Q

Secondary protein structure

A

Alpha helix, 3.6 AAs per turn H bonding between 4th above and below residues - Beta sheets - similar H bonding but between antiparallel chains

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8
Q

Tertiary structure

A

Defined by side group interactions and the formation of hydrophobic, hydrophilic, hydrogen, ionic and disulphide bridge forming, Globular - Myoglobin has 157 AAs with side chain interactions to create motifs and domains (variability and specificity) Fibrous - Keratin (2 helices), Collagen (3 helices that supercoil to form stable structure (H-bonding mainly) - misread into Osteogenesis imperfecta.

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9
Q

Domain crevices that are important for PMs

A

TIM barrel, Rossman fold and Horseshoe fold

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10
Q

Quaternary structure

A

Number of AAs joined together - eg Haemoglobin made of 4 (Alpha has 141 AAs, while beta have 146 AAs)

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11
Q

Ornithine

A

Unusual - non DNA synthesised AA - abnormally accumulated in ornithine transcarboxylase deficiency - accumulation of excess toxic ammonia

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12
Q

Osteogenesis imperfecta

A

Collagen T1 disorder - that has the Hyp - Gly - Pro sequence disturbed - and replaced glycine with cystine or arginine - mis formed and brittle bones are the result

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13
Q

Ehlers Danlos syndrome

A

Collagen T3

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14
Q

Scurvy

A

Vit C deficiency - Hyp -OH group malformation so no sharp coiling and weaker bones

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15
Q

Protein experiment

A

Afinsen 1962 - Urea and 2ME

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16
Q

Enzyme kinetics

A

Michaelis Menten equation - Catalysed vs uncatalysed graphs, lineweaver burke plot and normal 1/2Vmax graph, definitions for Kcat and Vmax, and definitions for Gibbs

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17
Q

Specificity of active site

A

1894 Fischer lock and key
1958 - Koshland induced fit (Cdks)

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18
Q

Reusable enzymes

A

Anfinsen 1962 and conformational changes undone in absence of substrate

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19
Q

Competitive

A

Higher Km, HIV inadivir, binds directly to AS

20
Q

Uncompetitive

A

Lower Km, binds to substrate

21
Q

Non-competitive

A

Same Km binds not to substrate or AS - Allosteric inhibition

22
Q

Competitive permanent

A

Penicillin binding to beta lactam ring of bacteria

23
Q

Organophosphate poisoning

A

Pesticides can act as non-competitive inhibitors of AChE - cholinergic crisis and death

23
Q

Allosteric control

A

Inhibitory subunit to PFK, Activating O2 to Haemoglobin

24
Q

Assistance of catalytic activity

A

Metal and vitamin cofactors - and coenzymes eg Thiamine Pyrophosphate in carbohydrate metabolism

25
Q

What do enzymes do?

A

Covalent (phosphorylation) or non covalent (allosteric control)

26
Q

Big/ small Km

A

Small - tight binding and slow unbinding
Big - weak binding and quick unbinding7

27
Q

DNA structure

A

Label heterocyclic nucleobase, purines, pyramidines and to what are they bound as well as nucleosides/ tides, Beta N-glyosidic bond

28
Q

Stability of DNA structure

A

Pi orbital overlap and H bonds, backbone is hydrolysed but the half life of spontaneous hydrolysis is 200m years, and NTs stack in a way that minimises the hydrophobic surface area of the molecule

29
Q

DNA experiments

A

Avery 1944 - R and S strain pneumonia
Watson Crick 1962 - Nobel prize - X ray crystallography and relative quantities of base pairs

30
Q

Larger scale structure DNA

A

Supercoiling around histones that form nucleosomes, topoisomerases

31
Q

Replication

A

Formation of the replication fork, ORC nicking by DNA gyrase and helicase unwinding the structure, DNAPs catalyse the formation of the phosphodiester bond, primer provides -OH group and ligase disassembly of the machinery

32
Q

Recombination

A

Swapping of genetic material and the repair of DSBs

33
Q

Types of DNA repair

A

Excision - recognition and removal
Mismatch - Mediated by MGMT - removes errors from DNA replication - Lynch syndrome affecting genes MLHL, MSH2, MSH6, PMS2, and EPCAM - colorectal cancer
Transcription mediated - Immediate response at lesion site

34
Q

BRCA1/2

A

DSB faulty machinery - genetic predisposition to certain cancers

35
Q

What types of problems are seen in DNA breakage

A

Either deamination (removal of -NH2 from cytosine forms uracil) or depurination and removal of a whole base pair

36
Q

Purpose of DNA

A

Basic storage unit, survives trans-generationally and encodes for up to 20/25,000 genes with only 4 base pairs

37
Q

Eukaryotic ribosome structure

A

80S overall, 40 s small with 33 proteins and 18S, large is 60S - contains 25s, 5.8S and 5S RNA, peptidyl transferase centre, amino acyl hole for threading, A, P and E sites

38
Q

Ribosome paradox

A

Proteins contained in something that synthesise them, inheritance or free floating tRNA

39
Q

Experiment tRNA

A

Altman and Cech NP 1989
RNAseP from E coli - divided to split - didn’t work in absence of RNA
Studying RNA from Tetrahymena - self split in a test tube

40
Q

tRNA structure

A

2d translated into L shaped 3d, H complimentary bonding, Holley 1968 NP, 70-90 NTs long

41
Q

Initiation

A

eIFs (x12) 40S subunit plus eIF = 43s which then scans for AUG and binds with 60S with eIF5B

42
Q

AA onto tRNA

A

tRNA synthase assisted by EF1 and 2, highly specific with lots of proofreading

43
Q

Elongation

A

EFs and peptidyl transferase centre catalyses the formation of a peptide bond

44
Q

Wobble hypothesis

A

WC base pairing not strict on third pair - 61 AAs need a tRNA molecule but not 61 tRNAs

45
Q

Clinical for RNA

A

HGPS - GGC to GGT mutation should be silent but wrong AA is coded for on the Lamina A 50 th AA - misfolded = extreme ageing

46
Q

ABs from RNA

A

Chloramphenicol - inhibits peptide bond formation
Tetracycline - block site of docking for tRNA
Aminoglycosides - alter 30S subunit

Biochemistry Year 1 (2 decks)

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