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Molecular Medicine > Proteins > Flashcards

Proteins Flashcards

0
Q

Aromatic amino acids

A

Tyrosine, tryptophan, phenylalanine

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1
Q

Aliphatic amino acids

A

Glycine, alanine, valine, lucine, isolucine

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2
Q

Sulfur containing amino acids

A

Cysteine, methionine

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3
Q

Cyclic amino acids

A

Proline

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4
Q

Basic amino acids

A

Histidine, lysine, arginine

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5
Q

Hydroxy amino acids

A

Serine, threonine

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6
Q

Amide amino acids

A

Asparginine, glutamine

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7
Q

Acidic amino acids

A

Aspartic acid, glutamic acid

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8
Q

Hydrophilic amino acids

A

Cysteine, serine, threonine, histidine, lysine, aspartic acid

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9
Q

Isoelectric point

A

pH at which molecules have no net charge

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10
Q

Why is ionization NB

A

Closure pka of drug to tissue the more effective it is. Eg. Alkalinise tissue when giving anaesthetic.

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11
Q

Chiral molecule

A

Lacks internal plane of symmetry

Non superimposable mirror image

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12
Q

D, L enantiomers indicate..

A

Different optical activities. (Ability to rotate a plane of polarised light)

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13
Q

Protein assembly involves what reactions?

A

Dehydration synthesis and polymerization of aas.

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14
Q

Principles of Ramachandran plot

A
  1. Bond length and angles must be similar to aas
  2. Peptide bonds are planar
  3. No overlaps
  4. Stabilisation - steric a permit H-bonds
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15
Q

Protein interaction promoted by:

A

Chaperones
Membrane proteins
Cystolic/extra cellular elements

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16
Q

Class

A

2ndry structure composition

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17
Q

Motif

A

Small specific combinations of secondary structure elements

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18
Q

Fold/ architecture

A

Shape/ orientation of secondary structure

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19
Q

Domain

A

Functional property of fold

20
Q

Recognition motif for glycosylation

A

Asn-xaa- ser/thr

21
Q

The role of glycosylation in protein folding

A

Glucose trimmed. Protein interacts with calnexin. Glucosidase cleaves glucose. If still misfolded, glucosyl transferase adds protein. REPEAT. when folded correctly, exit ER.

22
Q

Process of glycosylation

A

Precursor oligosaccharide formed on dolichol lipid.

Transferred to growing protein on recognition motif.

23
Q

Functions of glucosidation

A
  1. Stabilize proteins against proteolysis.
  2. Modulation of immune response.
  3. Provide sorting signals.
  4. Contributes to events in development.
24
Q

What do motor proteins do?

A

Move chromosomes
Move organelles
Move enzymes along DNA

25
Q

Phosphorylation of … Regulates protein synthesis

A

Eukaryote initiation factor 2

26
Q

Process of ubiquitin conjugation

A

High energy thiol ester formed between ubiquitin C-terminal Gly and Cys on E1.
Ub transferred to Cys of E2.
Peptide bond forms between Ub Gly and e-amino group of lysine on target protein.

27
Q

… recognized for Ub degradation

A

Lys 48 linked chain

28
Q

Define an enzyme

A

Substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change.

29
Q

Factors that effect the rate of enzyme reactions

A

Enzyme concentration
Ligand concentrations
Physical conditions (pH, temp, ionic strength)

30
Q

Assumptions of Michaelis-Menten kinetics

A

Formation of enzyme substrate complex
Assumes ES is in rapid equilibrium with free enzyme
K-1 is faster than k2.

31
Q

What is Km under assumed conditions?

A

The measure of binding affinity between E and S

32
Q

What does Vmax mean?

A

The maximum reaction rate for a given range of substrate with a fixed amount of enzyme.

33
Q

What is Kcat?

A

'’Turnover number’’ the number of substrate molecules turned into product per molecule of enzyme in a unit time (when enzyme is totally saturated with substrate.

34
Q

How are enzymes controlled?

A

Transcription
Compartmentalisation
Enzyme regulation
Kinetic regulation

35
Q

Competitive inhibitors..

A

Bind active site.

Increases Km.

36
Q

Non-competitive inhibitors..

A

Bind allosteric site.

Lowers Vmax

37
Q

Major players in protein folding.

A 
Chaperones/ chaperonins
ATP
Peptide binding proteins
Disulfide isomerase
Peptidyl Prolyl cis/trans isomerase
38
Q

Features of improperly folded proteins

A

Aggregate
Non-functional
Resource drain
Target for degradation

39
Q

Two units of chaperone complex

A

GroEL and GroES

40
Q

What does a folio some consist of ?

A

DnaJ (Hsp40) and DnaK (Hsp70)

41
Q

What does calnexin do?

A

Keen misfolded protein in ER.

42
Q

CATH

A

Class
Architecture
Topology
Homologous superfamily

43
Q

Models to determine protein structure

A

Repositories - protein data bank, molecular modelling database
Resolution - X-ray crystallography, NMR spectroscopy, EM

Databases - CATH, SCOP
Prediction - Ab-initio, theoretical modeling, conformation space search. Energy minimalisation. Threading.

44
Q

Write down enzyme equations

A

…

45
Q

Process of protein structure

A
  • assembly
  • folding
  • packing
  • interaction
46
Q

Why are proteins modified?

A
  • regulation of activity
  • protein-protein interaction
  • sub cellular localization
  • aging
47
Q

Functions of glycosylation

A
  • stabilize proteins against proteolysis
  • modulation of immune response
  • provide sorting signals
  • differentiation in development

Molecular Medicine (12 decks)

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