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CLS4007-B: Biology (Semester 1) > L5 / 6 - Proteins > Flashcards

L5 / 6 - Proteins Flashcards

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1
Q

What does the term ‘polymeric’ mean, with reference to proteins?

A

A chain-like molecule made up of many monomers.

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2
Q

What does it mean that proteins are ‘macromolecules’?

A

They are very large molecules.

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3
Q

How many different proteins can the human body generate? And from how many genes?

A

2 million proteins from approx. 20,000 genes.

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4
Q

What is a polypeptide?

A

A chain of amino acid monomers linked together by peptide bonds.

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5
Q

What determines the shape and function of a protein?

A

The sequence of amino acids.

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6
Q

A polypeptide with how many amino acids, can fold into a defined shape?

A

Greater than 40 amino acids can fold into a defined shape.

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7
Q

What function does a ‘structural’ protein have and can you provide an example?

A

Function: Support
Example: Collagen

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8
Q

What function does a ‘storage’ protein have and can you provide an example?

A

Function: Storage
Example: Casein

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9
Q

What function does a ‘transport’ protein have and can you provide an example?

A

Function: Oxygen transport
Example: Haemoglobin

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10
Q

What function does a ‘hormonal’ protein have and can you provide an example?

A

Function: Metabolism
Example: Insulin

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11
Q

What function does a ‘receptor’ protein have and can you provide an example?

A

Function: Cellular response
Example: β-Adrenergic receptor

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12
Q

What function does a ‘contractile’ protein have and can you provide an example?

A

Function: Movement
Example: Actin, Myosin

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13
Q

What function does a ‘defensive’ protein have and can you provide an example?

A

Function: Protection
Example: Antibodies

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14
Q

What function does a ‘enzymatic’ protein have and can you provide an example?

A

Function: Catalysis
Example: Digestive enzymes

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15
Q

What are all proteins composed of?

A

20 standard proteinogenic amino acids

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16
Q

What is the structure of an α-amino acid?

A
  • Central carbon atom (C)
  • Amino group (NH2)
  • Carboxyl group (COOH)
  • Side chain (R)
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17
Q

What is significant about the Cα?

A

The α-Carbon in all amino acids is a chiral centre (with one exception).

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18
Q

What is significant about the side chain (R group)?

A

It is variable and changes in every amino acid.

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19
Q

What is significant about the carboxyl group (COOH)?

A

It is acidic.

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20
Q

What 2 forms can amino acids exist in?

A

Amino acids can exist as 1 of 2 enantiomers: L or D

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21
Q

Which enantiomer is rarest?

A

In nature, D-amino acids are very rare, so the L form dominates.

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22
Q

What is a zwitterion?

A

An amino acid with NH3+ and COO-.

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23
Q

What is the structure of an amino acid’s acidic form?

A

It has a NH3+ and COOH group.

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24
Q

What is the structure of an amino acid’s basic form?

A

It has a NH2 and COO- group.

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25
Q

What are the hydrogen ion concentrations, [H+] of the acidic and basic forms of amino acids?

A

Acidic: High
Basic: Low

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26
Q

What is the chemical formula of ‘glycine’ (Gly)?

A

C2H5NO2

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27
Q

What is the chemical formula of ‘alanine’ (Ala)?

A

C3H7NO2

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28
Q

What is the chemical formula of ‘proline’ (Pro)?

A

C5H9NO2

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29
Q

What is the chemical formula of ‘valine’ (Val)?

A

C5H11NO2

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30
Q

What is the chemical formula of ‘methionine’ (Met)?

A

C5H11NO2S

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31
Q

What is the chemical formula of ‘leucine’ (Leu)?

A

C6H13NO2

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32
Q

What is the chemical formula of ‘isoleucine’ (Ile)?

A

C6H13NO2

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33
Q

What is the chemical formula of ‘phenylalanine’ (Phe)?

A

C9H11NO2

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34
Q

What is the chemical formula of ‘tryptophan’ (Trp)?

A

C11H12N2O2

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35
Q

Name the 9 amino acids with non-polar R groups.

A
  • Glycine (Gly)
  • Alanine (Ala)
  • Proline (Pro)
  • Valine (Val)
  • Methionine (Met)
  • Leucine (Leu)
  • Isoleucine (Ile)
  • Phenylalanine (Phe)
  • Tryptophan (Trp)
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36
Q

What is the chemical formula of ‘aspartic acid’ (Asp)?

A

C4H7NO4

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37
Q

What is the chemical formula of ‘glutamic acid’ (Glu)?

A

C5H9NO4

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38
Q

Name the 2 acidic amino acids.

A
  • Aspartic Acid (Asp)

- Glutamic Acid (Glu)

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39
Q

What is the chemical formula of ‘lysine’ (Lys)?

A

C6H14N2O2

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40
Q

What is the chemical formula of ‘arginine’ (Arg)?

A

C6H14N4O2

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41
Q

What is the chemical formula of ‘histidine’ (His)?

A

C6H9N3O2

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42
Q

Name the 3 basic amino acids.

A
  • Lysine (Lys)
  • Arginine (Arg)
  • Histidine (His)
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43
Q

What is the chemical formula of ‘tyrosine’ (Tyr)?

A

C9H11NO3

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44
Q

What is the chemical formula of ‘asparagine’ (Asn)?

A

C4H8N2O3

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45
Q

What is the chemical formula of ‘glutamine’ (Gln)?

A

C5H10N2O3

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46
Q

What is the chemical formula of ‘serine’ (Ser)?

A

C3H7NO3

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47
Q

What is the chemical formula of ‘threonine’ (Thr)?

A

C4H9NO3

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48
Q

What is the chemical formula of ‘cysteine’ (Cys)?

A

C3H7NO2S

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49
Q

Name the 6 amino acids with polar R groups.

A
  • Tyrosine (Tyr)
  • Asparagine (Asn)
  • Glutamine (Gln)
  • Serine (Ser)
  • Threonine (Thr)
  • Cysteine (Cys)
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50
Q

At what pH are

  • acidic amino acids’ side chains negatively charged (COO-)
  • and basic amino acids’ side chains positively charged (NxH+)?
A

Physiological pH = 7.4

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51
Q

What bond can cysteine (Cys) residues form?

A
  • Disulphide Bridges

Covalently links 2 polypeptide chains

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52
Q

Between what specific groups is the disulphide bridge between two cysteine residues formed?

A

Between S-H groups on each cysteine residues that forms a S-S bond.

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53
Q

How is a polypeptide chain formed?

A
  • Via linkage of COOH and NH2 groups

- Dehydration synthesis

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54
Q

What is dehydration synthesis (condensation reaction)?

A
  • Removal of a water molecule
  • 2 molecules combine to form a larger molecules
  • Peptide bond formed between amino acids
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55
Q

What are the two parts of a polypeptide chain?

A
  • Peptide backbone

- Side chains projecting from the backbone

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56
Q

How does bond resonance affect a peptide bond?

A

Causes bond to be:

  • Rigid
  • Planar
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57
Q

Why is the trans form of amino acids most common?

A

Rotation at C is usually limited by steric clashes between bulky R groups

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58
Q

Describe the directional nature of a protein.

A
  • Primary amino acid sequence has directionality

- Sequence in one direction is not the same as the sequence in the opposite direction

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59
Q

Describe the 4 levels of protein structure.

A
  • Primary Structure: Amino acid sequence
  • Secondary Structure: Interactions between adjacent amino acids
  • Tertiary Structure: 3D folding of a single polypeptide chain
  • Quaternary Structure: Assembly of multiple proteins into a complex
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60
Q

What are the 4 types of protein secondary structure?

A
  • α-helices
  • β-sheets
  • loops / random coils
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61
Q

How is an amino acid sequence read?

A

From N-terminus to C-terminus.

62
Q

How is the primary sequence determined?

A

By the DNA sequence of the gene for each protein.

63
Q

What does the primary structure dictate, and why?

A

The final protein structure, because sequential arrangement of R groups influences subsequent secondary, tertiary and quaternary structures.

64
Q

What can genetic mutation lead to, and can you provide an example?

A
  • Primary structure changes that can alter structure / function
  • Sickle cell disease
65
Q

What is sickle cell disease caused by?

A

A single mutation in the HbA haemoglobin gene.

66
Q

Describe the secondary structure of proteins.

A
  • Ribbon structures of protein backbone
  • Occur due to parts of polypeptide chains taking on regular patterns of hydrogen bonding
  • Forms α-helices / β-pleated sheets
  • The α-helices / β-pleated sheets are connected by shorter turns and longer loops / random coils
67
Q

Describe the structure of an α-helix.

A
  • Coiled rod-like structure
  • Flexible and elastic
  • Coil of helix = chain not fully extended
68
Q

What is the most common secondary structure?

A

α-helices

69
Q

What is proline?

A

An α-helix structure disrupter (helix breaker).

70
Q

What are α-helices abundant in?

A

Haemoglobin

71
Q

What are α-helices absent in?

A

Chymotrypsin (digestive enzyme)

72
Q

What stabilises α-helices?

A

Extensive intra-chain hydrogen bonding.

73
Q

How many amino acids does an α-helix have per turn?

A

3.6

74
Q

How are α-helices oriented?

A

Right-handed / ‘Clockwise’ from N-terminal to C-terminal end

75
Q

What bonds form the α-helix backbone?

A

Peptide bonds

76
Q

Why do R-groups on α-helices project outwards?

A

To avoid steric hindrance.

77
Q

What is an amphipathic α-helix?

A

An alpha helix with opposing polar and non-polar faces, oriented along the long axis of the helix (secondary structural motif).

78
Q

Describe the structure of a β-helix.

A
  • Flat sheets
  • Pleated
    (strands almost fully extended = surface appears pleated)
79
Q

β-helices are short runs of how many amino acids?

A

5 to 10 amino acids

80
Q

What are the 3 types of β-helix structures?

A
  • Parallel
  • Anti-parallel
  • Mixed
81
Q

Describe the strength of β-helices.

A

Strong and resilient

82
Q

How are multiple sheets connected in a β-helix?

A

By short turns or ‘hairpin’ loops

83
Q

How are β-pleated sheets held together?

A

By hydrogen bonds between peptide bonds on adjacent strands.

84
Q

How many metres in 1Å (Angstrom)?

A

10 ^-10 metres

85
Q

How are side chains of β-sheets arranged?

A

Alternately on opposite sides of the strand.

86
Q

What is the distance between amino acids in a β-helix?

A

3.5Å

87
Q

What is the distance between amino acids in a α-helix?

A

1.5Å

88
Q

What is significant about the distance between amino acids in β-sheets and α-helices?

A

β-sheets are more flexible than α-helices and can be twisted.

89
Q

What is the range of lengths of β-sheets in a protein?

A

2 to 22 residues

90
Q

What is an amphipathic β-helix?

A

A beta helix in which hydrophobic side chains point in one direction, and polar side chains in the other direction.

91
Q

What do loops / random coils connect?

A

Secondary (2°) structural elements

92
Q

Where are loops / random coils usually located?

A

On the surface

93
Q

What are loops / random coils rich in?

A

Polar and charged residues

94
Q

What is the range of lengths of loops / random coils in a protein?

A

2 to 20 residues

95
Q

What are loops / random coils frequently part of?

A

Enzyme active sites

96
Q

What are structural motifs?

A

Arrangements of secondary structures (super-secondary structures) that occur frequently within a protein and can be associated with a specific biological function.

97
Q

What is the tertiary structure?

A

Overall 3D shape of the entire polypeptide

98
Q

What is the tertiary structure held together by?

A
  • Hydrogen bonds
  • Between R groups
  • Ionic bonds (electrostatic attraction)
  • Between Co2- and NH3+ of R groups
  • Disulphide bridges
  • Between cysteine -SH groups (Cys - S - S - Cys)
  • Hydrophobic interactions (Van der Waals interactions)
  • (Hydrophobic R groups cluster inside proteins to shield themselves from water)
99
Q

What are the two structural classifications of proteins? (Provide examples)

A
  • Fibrous (e.g. collagen)

- Globular (e.g. haemoglobin)

100
Q

How are fibrous proteins made?

A

2° structures form long parallel fibres and sheets

101
Q

Describe how fibrous proteins behave in water.

A

They are usually insoluble in water

102
Q

What role do fibrous proteins play?

A

Important roles in providing strength and support.

103
Q

State 2 examples of fibrous proteins.

A
  • Collagen

- Keratins

104
Q

What are the two types of keratins and what are they found in?

A
  • α-keratins
  • Mammalian hair and nails
  • β-keratins
  • Invertebrate silks, reptile scales, reptile claws, avian feathers, avian beaks and avian claws
105
Q

Describe the structure of collagen.

A

Super-helices of Gly-rich triple α-helices (tropocollagen) that assemble into fibrils.

106
Q

What is collagen the main protein in?

A

Connective tissue

107
Q

What is the role of collagen?

A

To support, connect or separate tissues and organs

108
Q

What percentage of total protein is made up of collagen?

A

25%

109
Q

What are α-keratins composed of?

A

Coiled coils of two α-helices that assemble together into larger fibres.

110
Q

State 4 properties of α-keratins.

A
  • Strong
  • Inextensible
  • Insoluble
  • Chemically inert
111
Q

Describe the bonding in α-keratins.

A

Disulphide bridges cross link coiled coils.

112
Q

Describe the structure of β-keratins.

A

Layers of anti-parallel β-sheets rich in Ala and Gly residues.

113
Q

What is fibroin found in?

A

Silk and spider webs

114
Q

What allows the close packing of β-sheets?

A

Small side chains interdigitate to allow close packing of β-sheets.

115
Q

Describe Ehlers Danlos Syndrome (EDS).

A
  • Genetic connective tissue disorder
  • Multiple mutations possible in multiple genes
  • Structure, production and/or processing of collagen is affected
  • Can affect: skin, musculoskeletal, cardiovascular
116
Q

What are globular proteins?

A

A mixture of irregularly folded 2° elements that form a compact 3D shape.

117
Q

Describe how globular proteins behave in water.

A

Usually soluble in water with an inner hydrophobic core.

118
Q

Describe the ease of transport of globular proteins.

A

Transported easily in body fluids.

119
Q

What are globular proteins important in?

A

Important functions in cellular biochemistry (e.g. myoglobin, haemoglobin, immunoglobulins)

120
Q

Describe the structure of haemoglobin.

A
  • Tetramer
  • 4 polypeptide chains / subunits
  • 4 haem molecules
121
Q

What does adult haemoglobin contain?

A
  • 2 α-chains (α2)

- 2 β-chains (β2)

122
Q

Describe the structure of haem.

A
  • Porphyrin ring

- Fe2+

123
Q

What is myoglobin?

A

A globular protein related to haemoglobin, which exists as a single polypeptide.

124
Q

Describe the role of haemoglobin in the body.

A
  • Transports oxygen from the lungs to the rest of the body

- Releases oxygen to permit aerobic respiration to provide energy

125
Q

What can cause diseases such as Sickle Cell Disease and Thalassaemia?

A

Specific mutations in DNA encoding Hb genes.

126
Q

What are immunoglobulins?

A

Y-shaped proteins of the immune system which identify and combat invading foreign organisms.

127
Q

Describe the structure of immunoglobulins.

A

4 chains linked by disulphide bridges:

  • 2 large H (heavy) chains
  • 2 short L (light) chains
128
Q

What do variable structures in H and L chains form?

A

Specific binding sites for non-self targets (antigens)

129
Q

Describe what antigen recognition by an antibody does.

A

Antigen recognition by an antibody marks the antigen for attack by other components of the immune system engaged by constant portions of the H chains.

130
Q

What is Sickle Cell Disease caused by?

A

A single gene defect:

  • A single mutation in the DNA coding region within β-globin gene changes the 1° sequence (Bases: T to A, Amino Acids: Glu to Val)
  • Missense mutation = changes primary structure
131
Q

What bases and amino acids does the Sickle Cell Disease mutation change?

A
  • Bases: T to A

- Amino Acids: Glu to Val

132
Q

What happens to RBCs during Sickle Cell Disease?

A
  • RBCs change shape and become sickle-shaped
  • RBCs become rigid, so they become blocked in capillaries = can cause ischaemia, organ damage and pain
  • Increased haemolysis occurs (RBC destruction) = leads to anaemia and spleen damage
133
Q

What does being a carrier (heterozygous) for the sickle cell gene protect against?

A

Malaria

134
Q

What is the denaturation of proteins?

A

A process in which proteins lose quaternary, tertiary and secondary structure present in their native state due to a change in environment.

135
Q

What does denaturation of proteins result in?

A

A loss of function

136
Q

What does denaturation of proteins occur due to?

A
  • Extreme pH
  • Extreme temperature
  • Organic solvents
137
Q

Ionic bonds are very sensitive to pH. What effect does this have on proteins?

A
  • Ionic bonds can break
  • Tertiary structure is disrupted
  • Can render proteins insoluble in water and cause them to precipitate out of solution
138
Q

Describe H+ concentration at low and high pH.

A

Low pH = High H+ Concentration (acidic)

High pH = Low H+ Concentration (alkaline)

139
Q

What effect does adding H+ have on ionic bonds. Provide an equation?

A
  • Adding H+ neutralises COO- part of ionic bond
  • Removing its charge

H+ + COO- ⇌ COOH

140
Q

What effect does removing H+ have on ionic bonds. Provide an equation?

A
  • Removing H+ neutralises NH3+ part of ionic bond
  • Removing its charge

NH3+ ⇌ NH2 + H+

141
Q

Describe the effect of heat on bonding.

A

Increase in temperature causes vibration, and breaks hydrogen and ionic bonds.

142
Q

What is pyrexia?

A

Increased body temperature and fever (Anti-viral defence mechanism)

143
Q

What is Thermus aquaticus?

A

An extremophile bacterium that lives in hot springs.

144
Q

What temperatures does Thermus aquaticus grow above?

A

70°

145
Q

What does Thermus aquaticus produce?

A

A DNA polymerase enzyme that is stable at very high temperatures.

146
Q

What is Thermus aquaticus an essential component for?

A

Polymerase chain reaction (PCR)

147
Q

State 3 organic solvents.

A
  • Ethanol
  • Acetone
  • Phenol
148
Q

Describe the relationship between solvents and proteins.

A

Solvents form new hydrogen bonds with protein side chains and protein backbones = disrupt intra- and inter- chain H-bonds = causes protein to unfold and denature

149
Q

What are prions?

A

Infectious particles of misfolded proteins that are spread by causing other proteins to misfold and acquire high β-sheet content.

150
Q

State 5 examples of prions disease

A
  • Scrapie (in sheep)
  • Bovine Spongiform Encephalitis (BSE) / Mad Cow Disease
  • Creutzfeldt-Jakob Disease (CJD)
  • Fatal Familial Insomnia
  • Kuru
151
Q

What makes prions disease difficult to tackle?

A
  • Resistant to normal sterilisation methods (including heat, chemicals, and ionising radiation)

CLS4007-B: Biology (Semester 1) (12 decks)

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