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
What happens to the AAs when pK =pH
Equal amounts of protonated and deprotonated forms
26
What AAs are covalent disulphide bonds made between ? Where are these proteins most commonly used?
Cysteine residues | Usually secreted e.g. To go to pancreas which has a hostile environment so need strong bonds holding it together
27
What are electrostatic interactions formed between?
Charged groups e.g. Glu-, Arg +
28
What are hydrogen bonds made between?
Electronegative atom and a hydrogen bound to another electronegative atom
29
What are van der waals forces made between?
Dipole - dipole
30
What is the hydrophobic effect?
Interaction between hydrophobic side chains due to displacement of water
31
What is the name given to a normally folded protein that is functional?
In native conformation
32
What is denaturation and how does it occur?
Disruption of protein structure through breaking forces holding it together E.g by heat, pH, organic solvents affecting hydrophobic interactions
33
What is the folding process of an amino acid sequence driven by? How does it do this without taking too long?
Need to find the most stable conformation Each step involves localised folding with stabilised conformations maintained
34
What are amyloidases?
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!