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Foundations of Medicine > Proteins > Flashcards

Proteins Flashcards

1
Q

What are the various classes of naturally occurring amino acids?

A

Non-polar amino acids
Polar amino acids
Polar basic amino acids
Polar acidic amino acids

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2
Q

How many naturally occurring amino acids are there?

A

20

Out of the 20 amino acids, 9 are the essential amino acids, and the others are non-essential amino acids.

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3
Q

What makes up an amino acid?

A

Amine group ( -NH2)
Carboxyl group (-C02H)

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4
Q

What does polar mean vs non polar?

A

The polar (or hydrophilic) amino acids have side chains that interact with water, while those of the nonpolar (or hydrophobic) amino acids do not.

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5
Q

What are the non-polar amino acids?

A

Alanine
Cysteine
Glycine
Isoleucine
Leucine
Methionine
Proline
Phenylalanine
Tryptophan
Valine

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6
Q

What are the polar amino acids?

A

Arginine (Arg)
Asparagine (Asn)
Aspartate (Asp)
Glutamine (Gln)
Glutamate (Glu)
Histidine (His)
Lysine (Lys)
Serine (Ser)
Threonine (Thr)
Tyrosine (Tyr)

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7
Q

What are the essential amino acids?

A

Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine

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8
Q

What makes a non-polar amino acid?

A

When the R group is:

H
CH3
Alkyl groups
Aromatic

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9
Q

What makes an amino acid polar?

A

When the R group is:

-CH2OH
-CH2SH
-CH2CO-NH2

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10
Q

What makes an amino acid polar acidic?

A

When the R group contains:

-COOH group

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11
Q

What makes an amino acid polar basic?

A

When the R group contains:

-NH2

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12
Q

What are the polar basic amino acids?

A

Lysine
Arginine
Histidine

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13
Q

What are the polar acidic amino acids?

A

Asparate
Glutamate

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14
Q

What is a polypeptide?

A

Peptides are short chains of amino acids linked by peptide bonds.

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15
Q

What is the difference between a polypeptide and a protein?

A

A polypeptide is a polymer formed by a defined sequence of amino-acids linked together through covalent peptide bonds.

A protein is a structurally and functionally complex molecule formed by the folding of one or many polypeptide chains.

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16
Q

What is a polymer?

A

A polymer is a substance or material consisting of very large molecules called macromolecules, composed of many repeating subunits.

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17
Q

What are the types of protein?

A

Structural proteins
Enzymatic
Receptor proteins
Hormonal proteins
Transport proteins
Storage proteins
Defensive proteins
Contractile proteins

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18
Q

What is the function of structural proteins?

A

Providing support within connective tissues eg collagen and cartilage

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19
Q

What is the function of enzymatic proteins?

A

Selective acceleration of chemical reactions eg digestive enzymes penalise which catablosies starch into simple sugars

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20
Q

What is the function of a receptor protein?

A

Family of G protein coupled receptors which are signalling proteins that play a pivotal role in many physiological processes

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21
Q

What is the function of hormone proteins?

A

Coordinating metabolic function, eg insulin which is involved in glucose homeostasis

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22
Q

What is the function of transport proteins?

A

Responsible for transporting resources eg haemoglobin which carries oxygen in the blood however there are also important membrane transport proteins like the sodium potassium pump

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23
Q

What is the function of storage proteins?

A

Responsible for storage, ferritin - storage protein for iron

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24
Q

What is the function of a defensive protein?

A

Providing protection against disease for example immunoglobulins and major histocompatibility complexes that aid the body in self recognition

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25
Q

What is the function of contractile proteins?

A

Actin and myosin are examples of proteins that help facilitate motion through the contraction of muscle fibres

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26
Q

What are the four types of protein structure?

A

Primary
Secondary
Tertiary
Quaternary

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27
Q

Describe the primary structure of a protein

A

The sequence of amino acids bonded by peptide bonds

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28
Q

What are peptide bonds?

A

A peptide bond is a chemical bond that is formed by joining the carboxyl group of one amino acid to the amino group of another.

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29
Q

Describe the secondary structure of a protein

A

Local folded structures that form within a polypeptide due to interactions between atoms of the backbone.

The backbone just refers to the polypeptide chain apart from the R groups.

Held in place by hydrogen bonds

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30
Q

What are the two main types of secondary structure proteins?

A

The α helix and the β pleated sheet

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31
Q

How are the α helix and the β pleated sheet held together?

A

Both structures are held in shape by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another.

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32
Q

Discuss the structure of a α helix.

A

The carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain.

The R groups of the amino acids stick outward from the α helix, where they are free to interact.

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33
Q

What stabilises the alpha helix structure?

A

H bonds between the NH groups and the CO groups in the next turn of the helix

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34
Q

How are the α helix and the β pleated sheet held together?

A

α helix - hydrogen bonding between every 4th amino acid

β pleated sheet - hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet.

35
Q

What stabilises the beta sheets?

A

H bonds between the amide groups of the linear polypeptide chains

36
Q

Describe the tertiary structure of a protein

A

Three-dimensional structure of a polypeptide.

The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein.

R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces – basically, the whole gamut of non-covalent bonds.

Finally, there’s one special type of covalent bond that can contribute to tertiary structure: the disulfide bond.

37
Q

What are disulphide bonds?

A

A disulfide bond is a covalent bond between two sulfur atoms (–S–S–) formed by the coupling of two thiol (–SH) groups.

They are common in extra-cellular proteins

They can occur between as well as within a polypeptide

38
Q

What is the role of a disulphide bond?

A

Disulphide bonds function to stabilise the tertiary and/or quaternary structures of proteins

39
Q

Discuss the quaternary structure of a protein

A

Some proteins are made up of multiple polypeptide chains, also known as subunits. When these subunits come together, they give the protein its quaternary structure.

40
Q

Bonds in the quaternary protein structure

A

Hydrophobic interactions and disulphide bonds

41
Q

What is an important molecule with quaternary structure?

A

Hemoglobin
As mentioned earlier, hemoglobin carries oxygen in the blood and is made up of four subunits, two each of the α and β types.

DNA polymerase
An enzyme that synthesises new strands of DNA and is composed of ten subunits

42
Q

Why does haemoglobin have four subunits?

A

The binding of O2 to one sub unit alters its shape
This in turn causes a change in shape of the other sub-units so that they bind O2 more easily

Co-operative binding

43
Q

What can cause protein denaturing?

A

Acids
Heat
Solvents (ethanol)
Cross linking reagents (formaldehyde)
Chaotropic agents (urea)
Disulphide bond reducers (2 mercaptoehanol)

44
Q

What is the tertiary structure held together by?

A

Van der waals forces
Ionic interactions

Hydrogen bonds
Disulphide bridges
Hydrophobic interactions

45
Q

Where do ionic interactions take place?

A

Between two oppositely charged R groups

46
Q

What environment is needed for intra polypeptide hydrophobic interactions to occur?

A

An environment within proteins from which water is excluded

47
Q

What is denaturing?

A

Occurs when a protein’s chemical bonds are disrupted - possibly destroyed - within its secondary and tertiary structure.

48
Q

What structure remains in tact after denaturation?

A

Denaturation processes are rarely strong enough to break the primary structure of individual peptide bonds so the primary structure remains the same even after denaturation.

49
Q

Effect of denaturation

A

Decrease in solubility
Altered water binding capacity
Loss of biological activity
Improved digestibility

50
Q

What is co-translational modification?

A

All biologically active structures will have at least a tertiary structure however proteins can be modified further still, contributing to its quaternarty structure.

This relates to post-translational modification - modification occurring after the protein has been transcribed, ocassionally taking place while translation.

Process is termed co-translational modification.

51
Q

What are conjugated proteins?

A

Following post or co-translational modification, proteins are conjugated proteins.

A protein with additional units, such as a nucleic acid, a lipid or a metal etc., are conjugated proteins.

52
Q

What are three conjugated proteins?

A
  1. Glycoproteins
  2. Lipoproteins
  3. Metalloproteins
53
Q

What are glycoproteins?

A

Any of a class of proteins which have carbohydrate groups covalently attached to the polypeptide chain.

Co-translational or post-translational modification where oligosaccharide chains are attached to a protein

54
Q

What is glycosylation?

A

Glycosylation, the attachment of carb/sugar moieties to proteins, is a post-translational modification (PTM) that provides greater proteomic diversity than other PTMs.

55
Q

What are the effects of glycosylation?

A
  1. Increased stability
  2. Altered solubility
  3. Cell signalling (most important reason for glycoproteins being modified this way)
  4. New configurations that can change how the orginal protein orientates itself in space.
56
Q

Give an example of a glycoprotein

A

Immunoglobulins

57
Q

What are lipoprteins?

A

Proteins can combine with lipids to form lipoproteins

58
Q

Where are lipoproteins found and what do they do?

A

Lipoproteins are found in cell membranes and transport hydrophobic molecules (e.g. cholesterol and fat transport in the blood)

59
Q

What are metalloproteins?

A

Protein molecules with metal ions within their structures (co-factors)

60
Q

Function of metalloprotein

A

Various functions (e.g. enzymatic, signal transduction, transport, and storage) however the most important metallaprotein to learn about is haemoglobin.

61
Q

What makes up haemoglobin?

A

Haemoglobin has a large quaternary structure and is made up of four polypeptide chains ( 2 alpha subunits, 2 beta subunits)

The interfaces where these subunits contact are usually non-polar and this plays an important role in transmitting information between the individual subunits about their individual activities.

62
Q

What does each subunit of haemoglobin consist of?

A

Each subunit contains the organic molecule heme and in each heme molecule sits an atom of iron.

The interaction between iron, its associated heme molecule and the polypeptide subunit that allows haemoglobin to transport one molecule of oxygen thus each haemoglobin molecule with four subunits can carry four molecule of oxygen.

63
Q

Fibrous proteins vs Globular proteins:

Structure

A

G: Round and spherical
F: Made up of long and narrow sheet-like structure which are filamentous

64
Q

Fibrous proteins vs Globular proteins:

Function

A

Globular protein act as a functional protein performing functions like enzymes, as messengers, in the transportation of molecules and regulators

Fibrous protein help in providing protection and play a structural role in organisms

65
Q

Fibrous proteins vs Globular proteins:

Amino acid sequence

A

The amino acid sequence is irregular in globular proteins

Fibrous proteins are made up of regular amino acid strands

66
Q

Fibrous proteins vs Globular proteins:

Sensitivity

A

Globular proteins are sensitive to any changes in pH, temperature etc.

Fibrous proteins are less sensitive to any changes in temperature or pH

67
Q

Fibrous proteins vs Globular proteins:

In water

A

Globular proteins are generally soluble in water and form colloids

Fibrous proteins are not soluble in water

68
Q

Fibrous proteins vs Globular proteins:

Examples

A

Examples of globular proteins are - Haemoglobin, insulin, myoglobin etc

Examples of fibrous protein are- Collagen, fibrin, keratin, actin etc

69
Q

What are membrane proteins?

A

Proteins imbedded within cell membranes

Important role in transporting substances into and out of cells such as aqua-porins which transport water

  • Membrane transporter
  • Membrane enzymes
  • Cell adhesion molecule
70
Q

What is familial hypercholesterolemia?

A

Familial hypercholesterolemia (FH) is a diagnosis which refers to individuals with very significantly elevated low-density lipoprotein (LDL) cholesterol (LDL-C) or “bad cholesterol” and an increased risk of early onset of coronary artery disease if not sufficiently treated.

71
Q

What are the possible mutations of the LDL receptor?

A

No receptors produced
Receptors never reach cell surface
Receptors can’t bind LDL
Receptors don’t internalise on binding LDL
Receptors don’t release LDL

72
Q

How does sickle cell anaemia arise?

A

Substitution of one amino acid, hydrophilic glutamic acid is replaced with hydrophobic amino acid Valine

73
Q

How does sickle cell anaemia arise?

A

Substitution of one amino acid, hydrophilic glutamic acid is replaced with hydrophobic amino acid Valine

74
Q

What are the clinical features of sickle cell anaemia?

A

Severe haemolytic anaemia
Oxygen is given up more easily in the tissues

75
Q

What is the effect of scurvy?

A

Vitamin C deficiency, there is less hydroxyproline and hydroxylysine which are essential in stabilising cross links between chains of collagen, so collagen produced is weaker

76
Q

What is the effect of osteogenesis imperfecta?

A

Osteogenesis imperfecta (OI) is an inherited (genetic) bone disorder that is present at birth. It is also known as brittle bone disease.

Protein cannot form into a tight coil due to amino acid substitution

There is less interaction between fibrils

Loss of secondary and tertiary structure

Weakened and brittle collagen is produced

77
Q

What is PKU?

Phenylketonuria

A

PKU is an autosomal recessive inherited metabolic condition.

An inborn error of aromatic amino acid metabolism in which the body is unable to break down phenylalanine and blood levels accumulate causing neurological damage.

It occurs as a result of a substitution mutation. This results in the enzyme needed to convert phenylalanine into tyrosine being non-functional.

78
Q

PKU treatment

A

PKU is managed by cutting back on protein to limit the intake of phenylalanine meaning that diets have to be adjusted appropriately.

79
Q

What is the structure of collagen?

A

Polypeptides coil to form a helix

Held together by hydrogen bonds
Interactions form fibrils which increases strength

80
Q

Describe elastins

A

Elastin is another key structural protein found in the ECMs of connective tissues (e.g., blood vessels, esophagus, skin) that need to stretch and retract following mechanical loading and release. It is found predominantly in the walls of arteries, lungs, intestines, and skin, as well as other elastic tissues.

81
Q

Discuss keratins

A

Alpha-keratins, which are found in the hair, the skin, and the wool of mammals, are primarily fibrous and helical in structure.

82
Q

What is renaturation and how does it happen?

A

Renaturation in molecular biology refers to the reconstruction of a protein or nucleic acid (such as DNA) to their original form especially after denaturation. This process is therefore the inverse of denaturation.

83
Q

What are the essential amino acids?

A

Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine

Foundations of Medicine (56 decks)

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