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Biological chemistry > Proteins > Flashcards

Proteins Flashcards

1
Q

What are the 4 main functions of proteins?

A
  • defence: external covering (hair,skin) and immunity (antibodies)
  • structure: coordinated movement (muscle) and mechanical support (silk)
  • catalysis-enzymes
  • transport (e.g. oxygen via haemoglobin)
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2
Q

Describe the basic structure of an amino acid

A
  • central alpha carbon, bound to a hydrogen
  • R group/side chain (variable)
  • amino group (NH2)
  • carboxyl group (carbon with double bond to O and bond to OH)
  • tetrahedral molecule
  • chiral = different molecules with same groups but arranged differently (mirror images)
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3
Q

Describe the relationship between the carboxyl group and amine group of amino acids

A

Acidic carboxyl group has tendency to lose proton

Basic amine group has tendency to gain a proton

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4
Q

Normal configuration of amino acid

A

L-configuration (left handed)n

D-configuration (right handed) exist but not in proteins encoded for by DNA

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5
Q

Describe amino acid glycine

A

Abbreviations: G, gly
R = H
Simplest amino acid

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6
Q

Describe amino acid alanine

A

Abbreviations = Ala, A
R = CH3
Used for biosynthesis of proteins

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7
Q

Describe amino acid serine

A

Abbreviations: Ser, S
R = CH2OH
needed for the metabolism of fats, fatty acids, and cell membranes; muscle growth; and a healthy immune system

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8
Q

Describe amino acid cysteine

A

Abbreviations: Cys, C
R= CH2SH
Important structural role in a lot of enzymes

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9
Q

Describe amino acid histidine

A

Abbreviations: His, H

R = ring structure with 2 nitrogen groups

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10
Q

Zwitterion

A

Amino acid containing 2 ions, one with a positive charge and one with a negative charge = neutral overall

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11
Q

Isoelectric point of amino acids and equation

A

Isoelectric point = point along the PH scale where an amino acid has a net 0 charge

PI (isoelectric point) = (PKa 1 (equilibrium constant of acid) + PKa 2 (equilibrium constant of base)) / 2

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12
Q

Describe how amino acids bond

A
  • carboxyl group of one amino acid interacts with amine group of another amino acid = peptide bond + H2O molecule released
  • Double bonds between backbone C and O delocalise and peptide bond becomes partial double bond = stops rotation
  • Central carbon atom held in backbone by 2 rotatable bonds: psi and phi (dihedral angles)
  • most psi/phi rotations impossible as 2 atoms cannot occupy the same space
  • one end of chain has free H3N+ = n terminal and other has free COO- = C terminal
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13
Q

What are the 2 secondary structures of proteins

A

Alpha helix

Beta sheet

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14
Q

Describe hydrogen bonding in structure

A

Forms between lone pair of an oxygen atom (in the double bond with C) and hydrogen atom (attached to nitrogen atom) of amino group of another peptide

Protein backbone segments involved in hydrogen bonding can be 2 segments from 2 different backbones or the same backbone that’s folded up on itself

Individually weak but cumulatively strong

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15
Q

Describe alpha helix structure

A

H bonded: orientated parallel to axis of the helix
Carbonyl 1 links to amino 5 etc (n+4 linkage)
3.6 residues a turn
Easy to stretch but rigid side to side
R groups point away from centre of spiral = free to interact with other parts of protein
R groups project 100 degrees to preceding one

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16
Q

Helix formers and e.g’s (8)

A 
Certain amino acids with a high propensity to be in alpha helixes 
E.g. 
glutamate
Glutamine
Alanine
Histidine
Methionine
Leucine 
Lysine 
Arginine
17
Q

Helix breaker and e.g. (1)

A

Amino acids that dont have geometry required to be part of an alpha helix so will break the chain e.g. proline: R group bonds back to N terminus so cannot rotate and make coil structure

18
Q

Helix destabilisers and e.g. (1)

A

Amino acids that dont always form alpha helixes e.g. tyrosine

19
Q

What are the 2 types of beta sheet?

A

Parallel and anti-parallel

20
Q

Describe the structure of an anti parallel beta sheet

A

The beta sheets run in opposite directions

  • stabilise via hydrogen bonding (h bonds to O)
  • Will be carbonyl and amino groups facing outwards allowing for more strands to bond
  • anti parallel H bonds are pretty straight so are fairly strong
  • if B pleated sheet only involves 1 molecule than several U turns will be made (common)
  • strands inter digitate (fit like Lego)
21
Q

Describe silk fibroin

A
  • made from anti parallel beta sheets
  • highly insoluble
  • fibrous protein
  • produced mainly by silk worms
  • 90% aa’s are glycine (projects up) and alanine (projects down)
  • useful biomaterial (fibre and film)
  • wont stretch in longitudinal direction but very flexible laterally
22
Q

Describe parallel beta sheets

A

Strands running in the same direction
H bonds not quite so parallel so not as stable

(Can have a mix of parallel and non parallel = mixed beta sheets)

23
Q

Describe structural motifs

A

Short segments of 3D protein that are spatially close but not always adjacent in the sequence.

  • in a large number of proteins
  • may play structural or functional role
24
Q

Give 3 examples of structural motifs

A

triosephosphate isomerase

  • repeating a and b strands = barrel like structure
  • metabolic enzyme and also contributes towards production of products that alter proteins, DNA and lipids

Myoglobin:

  • iron and oxygen binding protein
  • found in vertebrate muscle tissue

Immunoglobulin (IgG)

  • type of antibody
  • formed from 4 different polypeptide chains
25
Q

Describe tertiary folding

A
  • creates 3 structure

- from interactions between amino acid side chains

26
Q

Name 3 hydrophobic sidechains

A

Valid
Leucine
Phenylalanine

27
Q

Name 3 hydrophilic sidechains

A

Aspartate
Lysine
Serine

28
Q

Describe the hydrophobic effect

A

Determines tertiary structure

  • in aqueous solution proteins have polar R groups facing outwards and non polar R groups facing inwards = non polar interact with each other
  • van der waals play a role in this
  • hydrophobic interactions weak but have strong cumulative effect
29
Q

Describe the van der waals interactions

A

Holds tertiary structure

  • non covalent associations between electrically neutral molecules
  • both very weak and only occur in short range
  • 1000’s in a protein strong cumulatively

Permanent dipoles:
- slight neg and pos attractions of 2 different molecules attract eachother

Induced dipoles: (London forces)

  • caused by randomness of movement of electron cloud
  • same attractive forces between 2 molecules
30
Q

Entropic effect

A

Hydrophobic molecules in tertiary structure form a cage from water molecules = water molecules more ordered than if no hydrophobic molecule

More order = less entropy

Biological chemistry (11 decks)

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