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2. MCBG > 5.2, 6.1 Protein Structure And Function, clinical context > Flashcards

5.2, 6.1 Protein Structure And Function, clinical context Flashcards

1
Q

What is the general structure of an AA?

A

Carbon with attached carboxyl group, amine group, Hydrogen and R group

 NH2 H-C-COOH
 R
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2
Q

What would be the general structure of AA in the following three solutions

1) Acidic (low pH)
2) Neutral
3) Basic (high pH)

A

1) acidic so more H+ ions so NH2 which is a proton acceptor becomes NH3
2) zwitterion, NH3 and COO-
3) COOH group is a proton donor so COO-

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3
Q

How can you differentiate AA from each other?

A

By their chemical and physical properties of R groups

  1. hydrophobic/philic
  2. Polar/non-polar
  3. Acidic/basic/neutral
  4. Aromatic/aliphatic
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4
Q

What is pKa?

A

pKa = -log10(Ka)
Where Ka is the acid dissociation constant
Tells us strength of acid/how likely grps are to loose/gain proteins

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5
Q

Fill in the gaps

Smaller the value of Ka, _______ the value of pKa, _______ extent of dissociation, ________ the acid, H+ _______, more _______

A

Larger, smaller, weaker, acceptor, NH3+

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6
Q

Fill in the gaps

Larger the value of Ka, _______ the value of pKa, _______ extent of dissociation, ________ the acid, H+ _______, more _______

A

Smaller, larger, stronger, donor, COO-

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7
Q

Explain what happens when pK of AA > pH of solution.

A

pK larger so weaker acid so proton acceptor so more NH3+

I.e. R group protonated

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8
Q

Explain what happens when pK of AA < pH of solution.

A

pK smaller, so stronger the acid, proton donor, so more COO-

I.e. R group deprotonated

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9
Q

Negatively charged R groups have a lower/higher pK?

Positively charged R groups have a lower/higher pK?

A

More COO- so proton donor so more acidic so pK smaller

More NH3+ so proton acceptor, so less acidic so pK larger

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10
Q

What bond holds amino acids together?

A

Peptide bond - O=C-N-H

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11
Q

How is the peptide bond rigid if there is a single bond between the Carbon and Nitrogen?

A

It carries partial double bond characteristics

(O-)-C=N-H is in equilibrium with O=C-(N+)-H

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12
Q

Does the peptide bond exhibit cis or trans conformation, and why?

A

Trans
Calphas are on opp sides of bond
Cis conformation not favourable because of steric clashes (repelling)

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13
Q

What bond is present in primary structure of proteins?

A

Peptide/covalent hold primary structure together

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14
Q

What are the secondary structures of a protein and how are they determined?

A

Determined by angles of C-Calpha and Calpha-N

  1. Alpha helix
  2. Beta sheets
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15
Q

How is the alpha helix formed and which AA are good/bad at forming these?

A

H bonds between N-H and C=O 4 AA away

Small hydrophobic residues are strong helix formers
Big not so good

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16
Q

How is the beta sheet formed?

A

Side by side strands run

1) antiparallel stabilised by H bonds
2) parallel - different angles so weaker
3) mixed antiparallel and parallel

17
Q

Describe 3 types of tertiary structure and bonds present

A

3D configuration of protein

Fibrous 
Role - support, shape, protection 
Long strands/sheets
Single type of repeating structure 
E.g. Collagen

Globular
Role - catalysis, regulation
Compact shape
Several types of secondary structure

Water soluble
Role - membrane proteins
Polypeptide chain folds so hydrophobic side chains are buried
Polar chains on surface

Bonds - covalent, ionic, H bonds, van der waals, hydrophobic/philic, disulphide

18
Q

Describe a quarternary structure

A

When 2 or more proteins become held together e.g. Haemoglobin/ribosome

19
Q

What is pI?

A
  1. Isoelectric point

2. pH at which molecule carries no net electrical charge

20
Q

What is the pI of basic proteins?

A

pI>7 and contains many charged AAs (NH3+)

21
Q

What is the pI of acidic proteins?

A

pI<7 and contains many negatively charged AAs (COO-)

22
Q

What happens if pI of AA < pH of solution?

A

More acidic so proton donor so R groups would be deprotonated

23
Q

What happens if pI of AA > pH of solution?

A

More basic, proton acceptor, so R groups would be protonated

24
Q

What does the henderson hasselbach equation used for?

A

Calculate the pH of a buffer solution

pH = pKa + log (base/acid )

25
Q

What happens to the AAs when pK =pH

A

Equal amounts of protonated and deprotonated forms

26
Q

What AAs are covalent disulphide bonds made between ? Where are these proteins most commonly used?

A

Cysteine residues

Usually secreted e.g. To go to pancreas which has a hostile environment so need strong bonds holding it together

27
Q

What are electrostatic interactions formed between?

A

Charged groups e.g. Glu-, Arg +

28
Q

What are hydrogen bonds made between?

A

Electronegative atom and a hydrogen bound to another electronegative atom

29
Q

What are van der waals forces made between?

A

Dipole - dipole

30
Q

What is the hydrophobic effect?

A

Interaction between hydrophobic side chains due to displacement of water

31
Q

What is the name given to a normally folded protein that is functional?

A

In native conformation

32
Q

What is denaturation and how does it occur?

A

Disruption of protein structure through breaking forces holding it together

E.g by heat, pH, organic solvents affecting hydrophobic interactions

33
Q

What is the folding process of an amino acid sequence driven by? How does it do this without taking too long?

A

Need to find the most stable conformation

Each step involves localised folding with stabilised conformations maintained

34
Q

What are amyloidases?

A
  1. Misfolded, insoluble form of a normally soluble protein.
  2. Hence forms aggregates in tissues and organs throughout the body
  3. Causes tissues and organs to stop working properly

Note - the point of this is to note that protein misfolding can cause disease!

2. MCBG (18 decks)

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