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FMCI-Genetics LUSUMA (COPY) > S4-5) Protein Structure > Flashcards

S4-5) Protein Structure Flashcards

1
Q

Describe the molecular structure of an amino acid

A

Each amino acid (except for proline) has the following bonded to the α-carbon atom:

  • A carboxyl group
  • A primary amino group
  • A distinctive side chain (“R-group”)
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2
Q

How are amino acids be classified?

A
  • Amino acids are classified according to the properties of their side chains
  • The nature of the side chains dictates the role an amino acid plays in a protein
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3
Q

How do amino acids bond together?

A

Peptide bonds are formed to link two amino acids together accompanied by the abstraction of a molecule of water (condensation reaction/dehydration synthesis)

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4
Q

Describe the 4 unique features of peptide bonds

A
  • Peptide bonds are planar
  • Peptide bonds are rigid
  • Peptide bonds exhibit a trans conformation
  • Bonds on either side of the peptide bond are free to rotate
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5
Q

How might amino acids be classified?

A
  • Polar: uneven distribution of electrons
  • Nonpolar: even distribution of electrons
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6
Q

Describe the structure and formation of a disulphide bond

A
  • The side chain of cysteine contains a sulfhydryl group (–SH)
  • In proteins, the –SH groups of two cysteines can become oxidized to form a dimer, cystine, which contains a covalent cross-link called a disulphide bond (–S–S–)
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7
Q

What is the significance of disulphide bonds?

A
  • Important component in the active site of many enzymes
  • Many extracellular proteins are stabilized by disulphide bonds e.g. Albumin
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8
Q

How can one characterise basic and acidic amino acids respectively?

A
  • Acidic amino acids: negatively charged at physiological pH
  • Basic amino acids: positively charged at physiological pH
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9
Q

What is the value of physiological pH?

A

pH = 7.35 - 7.45

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10
Q

Identify the 2 amino acids with acidic side chains

A
  • Aspartate
  • Glutamate
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11
Q

Outline the behaviour of amino acids with acidic side chains

A
  • The aspartic and glutamic acid are proton donors
  • At physiological pH, the side chains of these amino acids are fully ionized, containing a negatively charged carboxylate group (–COO-)
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12
Q

Outline the behaviour of amino acids with basic side chains

A
  • The side chains of the basic amino acids accept protons
  • At physiological pH the side chains of strongly basic amino acids are fully ionized and positively charged
  • At physiological pH, the side chains of weakly basic amino acids the free amino acid is largely uncharged
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13
Q

Identify the 3 amino acids with basic side chains

A
  • Arginine (strongly basic)
  • Lysine (strongly basic)
  • Histidine (weakly basic)
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14
Q

What is the Henderson-Hasselbalch equation?

A
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15
Q

What is the significance of the Henderson-Hasselbalch equation?

A

The Henderson-Hasselbalch equation expresses the quantitative relationship between the pH of a solution and the [weak acid] and the [conjugate base]

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16
Q

What encodes for the amino acid sequence of a protein?

A

The nucleotide sequence of a gene determines the amino acid sequence of a protein

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17
Q

What is determined by the amino acid sequence of a protein?

A
  • The way the polypeptide chain folds
  • The physical characteristics of the protein
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18
Q

Proteins are polypeptides.

What are polypeptides?

A
  • Polypeptides are macromolecules composed of amino acids
  • Amino acids join covalently through peptide bonds to form the sequence of the protein
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19
Q

Identify two contrasting factors which influences the way in which a protein folds?

A
  • Chemical properties of the amino acids
  • Physical properties of the amino acids
20
Q

How can amino acids be classified based on their chemical properties?

A
  • Hydrophobic / Hydrophilic
  • Polar / Non-polar
  • Acidic / Basic / Neutral
21
Q

How can amino acids be classified based on their physical properties?

A

Aliphatic / Aromatic

22
Q

What are amino acid residues?

A

Amino acid residues are what remains of an amino acid after it has been joined by a peptide bond to form a protein

23
Q

How do pKa values vary across acidic and basic amino acids?

A

- Basic amino acids:

I. Positively charged R groups

II. Higher pKa values (6.0 - 12.5)

- Acidic amino acids:

I. Negatively charged R groups

II. Lower pKa values (2.8 - 4.3)

24
Q

Illustrate the relationship between pK values and pH in terms of amino acids

A
  • pH of the solution < pK value of amino acid = R group is protonated
  • pH of the solution > pK value of amino acid = R group is deprotonated
25
Q

What is meant by the isoelectric point of proteins?

A

Isoelectric point (pI) of proteins: the pI of a protein is the pH at which there is no overall net charge

26
Q

How do pI values vary across acidic and basic proteins?

A
  • Basic proteins have a pI > 7 and contain many positively charged (basic) amino acids
  • Acidic proteins have a pI < 7 and contain many negatively charged (acidic) amino acids
27
Q

Illustrate the relationship between pI values and pH in terms of proteins

A
  • If the pH < pI then the protein is protonated
  • If the pH > pI then the protein is deprotonated
28
Q

What are conjugated proteins?

A

Conjugated proteins are proteins which have other chemical components covalently linked in addition to amino acids e.g. haemoglobin

29
Q

Identify 5 biochemical roles of proteins

A
  • Catalysts e.g. enzymes
  • Transporters e.g. haemoglobin carries O2
  • Structural support e.g. collagens in skin and bone
  • Immune protection e.g. immunoglobulins
  • Receptors e.g. for hormones, neurotransmitters, etc
30
Q

Identify the 4 different components to protein structure

A
31
Q

Describe the primary structure of the protein

A

Primary structure is the linear amino acid sequence of the polypetide chain

32
Q

Describe the secondary structure of the protein

A

Secondary structure is the local spatial arrangement of polypeptide backbone consisting of alpha helixes and beta pleated sheets

33
Q

Which type of bond stabilises the secondary structure of a protein?

A

H2 bonds

34
Q

Describe the tertiary structure of the protein

A

Tertiary structure is the overall 3D configuration of the protein

35
Q

Describe the quaternary structure of the protein

A

Quaternary structure is the association between different polypeptides to form a multi-subunit protein

36
Q

Identify the 4 interactions which stabilise the tertiary structure

A
  • Disulphide bonds
  • Hydrophobic interactions
  • Hydrogen bonds
  • Ionic interactions
37
Q

Which bonds hold subunits together in the quaternary structure of the protein?

A

Non-covalent interactions:

  • Hydrogen bonds
  • Ionic bonds
  • Hydrophobic interactions
38
Q

How do subunits function in the quaternary structure of proteins?

A
  • Subunits can function independently
  • Subunits can function cooperatively e.g. haemoglobin
39
Q

Describe the role and structure of fibrous proteins and include an example

A
  • Role: support, shape, protection
  • Structure: single type of repeating secondary structure, forms long strands or sheets
  • Examples: collagen & keratin
40
Q

Describe the role and structure of globular proteins and include an example

A
  • Role: catalysis, regulation, transport
  • Structure: several types of secondary structure
  • Examples: myoglobin, haemoglobin, carbonic anhydrase
41
Q

Identify the 2 types of secondary structures found in globular proteins

A
  • Motifs
  • Domains
42
Q

Describe the 2 types of secondary structures found in globular proteins

A
  • Motifs which are folding patterns containing 1/more elements of secondary structure
  • Domains which are the parts of a polypeptide chain that fold into a distinctive shape
43
Q

How do membrane proteins fold?

A

Membrane proteins fold to express hydrophobic amino acids on the exterior cell surface and hydrophilic amino acids on the interior forming channels

44
Q

How do water soluble proteins fold?

A

In water soluble proteins, polypeptide chains fold so the hydrophobic side chains are buried and polar and the charged side chains are on the cell surface

45
Q

Describe the relative amount of amino acids in the following:

  • Peptides/oligopeptides
  • Polypeptides/proteins
A
  • Peptides/oligopeptides: few amino acids in length
  • Polypeptides/proteins: many amino acids in length

FMCI-Genetics LUSUMA (COPY) (23 decks)

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