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FTM week 1-3 > Proteins and AAs > Flashcards

Proteins and AAs Flashcards

1
Q

Why does proline differ from other AAs?

A
  • peptide bonds take specific shape (has a secondary amino group and side chain causes rigid ring). Leads to bends in the protein chain. Interrupt alpha helical xture. Proline is an alpha helix breaker
  • Collagen is rich in proline residues
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2
Q

AAs with nonpolar, aliphatic, non branched side chains

A

Glycine, alanine, proline

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3
Q

AAs with non polar, aliphatic, branched side chains

A

Valine, leucine, isoleucine

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4
Q

AAs with aromatic side chains

A
  1. Phenylalanine - no UV light absorbance
  2. Tryptophan- absorb UV light 4x better than tyr
  3. Tyrosine

all non polar but slightly increase in polarity (1 –> 3)

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5
Q

AAs that contain sulfur

A

Methionine (met) - also non polar

Cysteine (cys) - uncharged, polar. 2 cysteins orms disulfide bond to form CYSTINE

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6
Q

AAs polar, uncharged

A

Asparagine (asn) - derivative of aspartate

Glutamine (gln) - amine group added to glutamate

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7
Q

Polar, uncharged

A

Serine
Threonine

Both contain -OH group that can be phosphorylated and glycosylated

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8
Q

Which AAs have -OH group

A

Serine and threonine

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9
Q

AAs with negative (acidic) side chains

A

Aspartate (asp)

Glutamate (glu)

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10
Q

AAs with positive (basic) side chains

A

Arginine (Arg)
Lysine (lys)
*Histidine – sometimes, dependent on exact pH

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11
Q

Amphoteric

A

Can act as either acid or base

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12
Q

Histidine side chain buffer

A
  • has imidazole ring (pKa 6) which allows buffering of possible drop in intracellular pH (pH 7)
  • pKa of his may be shifted in proteins to 6-7 due to local chem envir of the protein
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13
Q

Why is hb a good buffer?

A

Rich in his

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14
Q

What are the the main blood buffer systems?

A

phosphate
Hb
bicarb

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15
Q

biologically active amines and mech

A

AAs are precursors for many biological active amines

  • Amino group is retained and alpha-carboxyl group is enzymatically removed as CO2 (decarboxylation)
    ex) GABA, histamine, serotonin
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16
Q

How is GABA formed

A

decarboxylation of glutamate (also alpha carbon is now gamma)

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17
Q

How is histamine formed

A

decarboxylation of histidine

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18
Q

How is serotonin synth

A

Tryptophan is hydroxylated to 5-hydroxy tryptophan

5 hydroxy tryptophan is decarboxylated to serotonin

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19
Q

Catecholamine synth

A

Tyrosine hydroxylated to DOPA

Dopa decarboxylated to dopamine

dopamine –> norepi –> epi

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20
Q

Where are catecholamines synth

A

adrenal medulla

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21
Q

What is not synth by normal translation?

A

glutathione

22
Q

Characteristics of peptide bond

A
  • partial (40% double bond character)
  • rigid and planar
  • uncharged but polar
  • can form H-bonds –stabilizes alpha helical and beta sheet xtures
23
Q

Which configuration of peptide bond minimizes steric hindrance?

A

trans

24
Q

Where on peptide bond is rotation possible?

A

alpha carbons

25
Q

Which bond does not break during denaturation of proteins?

A

peptide bond

26
Q

General functions of proteins

A

Regulatory: repressors and activators

Defernse: antibiotics, blood clotting

27
Q

Where do polar AAs cluster on the soluble proteins?

A

On the surface

28
Q

Where do non polar AAs cluster on membrane proteins?

A

Embedded in the membrane

29
Q

AA primary xture

A

-determines the 3D xture of the protein

30
Q

Covalent bonds

A
  • Strong ( >50 kcal mol-1)
  • Not meant to be broken other than during protein degradation
  • Ex) peptide bonds, disulfide bonds
31
Q

Non covalent bonds

A
  • Weaker than covalent ( 1-7 kcal mol-1)
  • These “weak attractive forces” specify protein folding and conformational changes. Additive, so in aggregate they may provide strong stabilizing force
  • Hydrophobic forces- water excludes cmpds that don’t form H-bonds (formed bw 2 non polar AAs)
  • H-bonds- formed bw polar uncharged side chains (ex- ser or asn) or bw one charged side chain and one polar (ex -OH or COO-) (also called ion dipole)
  • ionic bonds– 2 opp charged side chains
  • Van der Waals (london) forces
32
Q

Secondary xture

A
  • Stabilized by H bonds involving atoms of the peptide bond
  • Alpha helix – SPECIAL HELIX, tightly packed and right handed helix. H-bonds parallel to axis, side chains stick out (may lead to constraints, but dep on primary xture)
  • Beta sheet- perpendicular H-bonds bw peptide atoms and AA side chains alternatiec above and below the plane of the pleated sheet. Parallel or anti parallel
33
Q

H-bond

A

non covalent

-stabilizes secondary xture (H-bonds of atoms of peptide bond)

34
Q

Interruption of the alpha helix

A
  • electrostatic repulsion bw successive AAs with charged R groups
  • Bulkiness of adjacent R groups
  • Helix disruption by specific residues – proline (bend, kink), glycine (rotation)
35
Q

tertiary xture? How is it stabilized

A
  • refers to 3D conformation of a protein
  • water soluble protins hold into #D xture with non polar side chains to inside – “hydrophobic core”
  • stabilized by AA side chains –non covalent associates, S-S (covalent), ionic interactions
36
Q

H bonds can be formed bw _____ or _____

A

polar uncharged side chains or bw one charged side chain and one polar

37
Q

Which type of proteins often have several S-S bonds?

A

extracellular

-intracellular proteins usually lack S-S

38
Q

Insulin xture

A

2 inter-chain disulfide bonds hold A & B chains together

Intra-chain disulfide bond in A chain holds the peptide and needed for receptor recognition

39
Q

Why is c peptide needed?

A

needed for proper formation of disulfide bonds in insulin

40
Q

Myoglobin xture

A
  • described in terms of tertiaty xture
  • contains 80% alpha helix secondary xture
  • devoid of beta sheet
41
Q

Monomeric proteins lead to ____ xture

A

tertiary

42
Q

multimeric proteins lead to ____ xture

how do the subunits assoc?

A

quaternary xture

-subunits assoc via NON COVALENT attractive forces

Ex) Hb, some enzymes

43
Q

Chaperones

A

Facilitate proper folding

  • Hsp70 – prevent aggregation of unfolded protein
  • Hsp60 – proteins have BARREL SHAPE and are req for correct folding of proteins that don’t fold spontaneously. Also help refold protein after crossing cellular membrane
44
Q

Defective proteins are tagged by _____ and degraded in the ______

A

ubiquitin, proteasome

ATP dep

45
Q

Protein misfolding diseases

A
  • Alzheimers, prion disease (Transmissible Spongiform Encephalopathy, TSE)
  • the diseased protein is very stable
  • abnormal proteins accumulate
  • damage the brain
46
Q

Transmissible Spongiform Encephalopathy

A
  • Prion disease
  • 3 routes to acquire: sporadic, infection, genetic predisposition
  • diseased brain develops holes
  • Symptoms include dementia and loss of coordination, leading to death.
47
Q

Prion

A

Proteinaceous infectious agent

  • infectious agent is a single protein names PrP
  • PrP is normal constituent of cells in brain
  • PrP-SC (scrapie) is abnormal form. PrP-SC acts like template and leads to conversion of PrP to large aggregates of PrP-SC. Abnormal protein is highly infective and not destroyed by sterilization
48
Q

To get from PrP to PrP-SC, the _____ is changed to _______

A

alpha helix, beta sheet

49
Q

Denaturing proteins in the lab

A
  • Heat urea, salt to break H-bonds
  • Strong acids/bases to break ionic bonds
  • SDS detergent to break hydrophobic interactions
  • Thiol containing compounds to red S-S
    - Beta-mercaptoethanol
    - 2-mercaptoethanol
50
Q

Creutzfeldt-Jakob disease

A

prion disease

FTM week 1-3 (4 decks)

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