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semester 1 > Protein Structure And Function > Flashcards

Protein Structure And Function Flashcards

1
Q

What groups surround the alpha carbon in an amino acid?

A

Variable side chain
Amino group
H atom
Carboxyl group

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2
Q

How are amino acids classified?

A

R groups

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3
Q

Define AA residue.

A

Remnants of AA after it has been joined by a peptide bond to form a protein

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4
Q

What angle is better the alpha carbon and C

A

Psi

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5
Q

Name the angle between the alpha carbon and N

A

Phi

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6
Q

Give features of peptide bond.

A 
Partial double bond character 
Planar 
Rigidity- no rotation 
Resonance 
Stereoisomerism
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7
Q

What is the primary structure?

A

AA sequence

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8
Q

What is the secondary structure?

A

Locals spatial arrangement of polypeptide backbone

Alpha helix and beta sheet

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9
Q

What is tertiary structure?

A

Overall 3D configuration of the protein

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10
Q

What is the quaternary structure?

A

Association between different polypeptides to form multi subunit protein

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11
Q

Define motif

A

Folding pattern of 1+ elements of secondary structure

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12
Q

Domain

A

Polypeptide folded to distinct shape with functional role

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13
Q

Define pI

A

The pH at which a protein has no overall net charge

Exists as a zwitterion

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14
Q

Define pKA. What does pKa tell you about the side chain?

A

PKa is the pH at which there is 50% dissociation. Provides information about how strong an acid is.
High pKa = positively charged R group
Low pKa = negatively charged R group

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15
Q

What happens if pH is smaller than the pKa of a amino acid?

A

Protonated

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16
Q

What happens if pKa is greater than the pH ?

A

Deprotonated

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17
Q

What does an Isoelectic point greater than 7 mean about the amino acids?

A

Basic protein

Increasing number of positive amino acids

18
Q

What happens if the isoelectric point is smaller than 7?

A

Acidic protein

Increasing number of negatively charged amino acids

19
Q

What plot is used to predict the secondary structures of a protein from it primary sequence?

A

Ramachandran

20
Q

What forces stabilise an alpha helix?

A

H bonds between N-H and C=O 4 amino acids apart

21
Q

What happens to the H bonds in a parallel beta sheet compared with a anti parallel beta sheet?

A

Same location however increased bio due angle and therefore weaker

22
Q

What is the Henderson - Hasselbach equation?

A

Henderson- Hasselbach = pH= pKa + log [A-]

[HA]

23
Q

How can you identify an acidic amino acid?

A

Side chain negatively charged- indicated H+ has been lost

24
Q

How can you identify a basic amino acid?

A

Side chain has positive charge indicating it has gained a proton

25
Q

What makes an amino acid polar or non-polar

A

Difference in electronegativity between atoms on side chain

26
Q

What makes an amino acid hydrophilic or hydrophobic?

A 
Polar= hydrophilic
Non-polar= hydrophobic
27
Q

What is an aliphatic amino acid?

A

Straight side chain with H and C

28
Q

What is an aromatic side chain?

A

Side chain with structure similar to that of benzene

29
Q

What is the hydrophobic effect?

A

Internalisation of hydrophobic aa’s leaving hydrophilic aa’s on the surface
Not true from PM proteins

30
Q

What forces stabilise the primary structure?

A

Covalent peptide bonds

31
Q

What forces stabilise the secondary structure?

A

H bonds

32
Q

What forces stabilise the tertiary and quaternary structures?

A 
Covalent disulphide bonds
Ionic 
H bonds 
Vdw 
Hydrophobic effect
33
Q

Where do ionic interactions occur?

A

Between charged side chains form salt bridge

34
Q

Where do disulphide bonds form? Which proteins are they most commonly found in?

A

Between cysteine residues

Found in secreted proteins as extracellular environment is harsher

35
Q

Where do h bonds form?

A

Between electronegative atom and a H bound to another electronegative atom
NOF

36
Q

What are vdw forces?

A

Dipole-dipole interactions that result form the transient localisation of electrons at any given moment.
Intrinsic to any bond type

37
Q

What is the native conformation of a protein?

A

Folded protein that is functional

38
Q

How to detergents and organic solvents cause desaturation of a protein?

A

Disrupt hydrophobic interactions

39
Q

How does a change in pH alter protein structure?

A

Change in ionisation state of amino acids

40
Q

Outline how proteins fold

A

Ordered process as would take too long other wise
Localised folding whereby stable conformations maintained
Process driven by need to find most stable conformation

41
Q

Why does protein misfolding cause disease?

A

Misfolded proteins non functional therefore unable to work
Can cause other proteins to misfold
Accumulate in cells

semester 1 (45 decks)

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