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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
Assistance of catalytic activity
Metal and vitamin cofactors - and coenzymes eg Thiamine Pyrophosphate in carbohydrate metabolism
25
What do enzymes do?
Covalent (phosphorylation) or non covalent (allosteric control)
26
Big/ small Km
Small - tight binding and slow unbinding Big - weak binding and quick unbinding7
27
DNA structure
Label heterocyclic nucleobase, purines, pyramidines and to what are they bound as well as nucleosides/ tides, Beta N-glyosidic bond
28
Stability of DNA structure
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
DNA experiments
Avery 1944 - R and S strain pneumonia Watson Crick 1962 - Nobel prize - X ray crystallography and relative quantities of base pairs
30
Larger scale structure DNA
Supercoiling around histones that form nucleosomes, topoisomerases
31
Replication
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
Recombination
Swapping of genetic material and the repair of DSBs
33
Types of DNA repair
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
BRCA1/2
DSB faulty machinery - genetic predisposition to certain cancers
35
What types of problems are seen in DNA breakage
Either deamination (removal of -NH2 from cytosine forms uracil) or depurination and removal of a whole base pair
36
Purpose of DNA
Basic storage unit, survives trans-generationally and encodes for up to 20/25,000 genes with only 4 base pairs
37
Eukaryotic ribosome structure
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
Ribosome paradox
Proteins contained in something that synthesise them, inheritance or free floating tRNA
39
Experiment tRNA
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
tRNA structure
2d translated into L shaped 3d, H complimentary bonding, Holley 1968 NP, 70-90 NTs long
41
Initiation
eIFs (x12) 40S subunit plus eIF = 43s which then scans for AUG and binds with 60S with eIF5B
42
AA onto tRNA
tRNA synthase assisted by EF1 and 2, highly specific with lots of proofreading
43
Elongation
EFs and peptidyl transferase centre catalyses the formation of a peptide bond
44
Wobble hypothesis
WC base pairing not strict on third pair - 61 AAs need a tRNA molecule but not 61 tRNAs
45
Clinical for RNA
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
ABs from RNA
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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