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Y1 SEM 1: Medical Cell Biology and Genetics > 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
What is meant by the isoelectric point of proteins?
**Isoelectric point (pI) of proteins:** the pI of a protein is the pH at which there is no overall net charge
26
How do pI values vary across acidic and basic proteins?
- **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
Illustrate the relationship between pI values and pH in terms of proteins
- If the pH \< pI then the protein is **protonated** - If the pH \> pI then the protein is **deprotonated**
28
What are conjugated proteins?
Conjugated proteins are proteins which have other chemical components covalently linked in addition to amino acids *e.g. haemoglobin*
29
Identify 5 biochemical roles of proteins
- **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
Identify the 4 different components to protein structure
31
Describe the primary structure of the protein
**Primary structure** is the linear amino acid sequence of the polypetide chain
32
Describe the secondary structure of the protein
**Secondary structure** is the local spatial arrangement of polypeptide backbone consisting of alpha helixes and beta pleated sheets
33
Which type of bond stabilises the secondary structure of a protein?
H2 bonds
34
Describe the tertiary structure of the protein
**Tertiary structure** is the overall 3D configuration of the protein
35
Describe the quaternary structure of the protein
**Quaternary structure** is the association between different polypeptides to form a multi-subunit protein
36
Identify the 4 interactions which stabilise the tertiary structure
- Disulphide bonds - Hydrophobic interactions - Hydrogen bonds - Ionic interactions
37
Which bonds hold subunits together in the quaternary structure of the protein?
**Non-covalent interactions:** - Hydrogen bonds - Ionic bonds - Hydrophobic interactions
38
How do subunits function in the quaternary structure of proteins?
- Subunits can function **independently** - Subunits can function **cooperatively** *e.g. haemoglobin*
39
Describe the role and structure of fibrous proteins and include an example
- **Role**: support, shape, protection - **Structure**: single type of repeating secondary structure, forms long strands or sheets - **Examples**: collagen & keratin
40
Describe the role and structure of globular proteins and include an example
- **Role**: catalysis, regulation, transport - **Structure**: several types of secondary structure - **Examples**: myoglobin, haemoglobin, carbonic anhydrase
41
Identify the 2 types of secondary structures found in globular proteins
- Motifs - Domains
42
Describe the 2 types of secondary structures found in globular proteins
- **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
How do membrane proteins fold?
**Membrane proteins** fold to express hydrophobic amino acids on the exterior cell surface and hydrophilic amino acids on the interior forming channels
44
How do water soluble proteins fold?
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
Describe the relative amount of amino acids in the following: - Peptides/oligopeptides - Polypeptides/proteins
- **Peptides/oligopeptides:** few amino acids in length - **Polypeptides/proteins:** many amino acids in length

Y1 SEM 1: Medical Cell Biology and Genetics (23 decks)

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