L5 / 6 - Proteins Flashcards
(151 cards)
1
Q
What does the term ‘polymeric’ mean, with reference to proteins?
A
A chain-like molecule made up of many monomers.
2
Q
What does it mean that proteins are ‘macromolecules’?
A
They are very large molecules.
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.
4
Q
What is a polypeptide?
A
A chain of amino acid monomers linked together by peptide bonds.
5
Q
What determines the shape and function of a protein?
A
The sequence of amino acids.
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.
7
Q
What function does a ‘structural’ protein have and can you provide an example?
A
Function: Support
Example: Collagen
8
Q
What function does a ‘storage’ protein have and can you provide an example?
A
Function: Storage
Example: Casein
9
Q
What function does a ‘transport’ protein have and can you provide an example?
A
Function: Oxygen transport
Example: Haemoglobin
10
Q
What function does a ‘hormonal’ protein have and can you provide an example?
A
Function: Metabolism
Example: Insulin
11
Q
What function does a ‘receptor’ protein have and can you provide an example?
A
Function: Cellular response
Example: β-Adrenergic receptor
12
Q
What function does a ‘contractile’ protein have and can you provide an example?
A
Function: Movement
Example: Actin, Myosin
13
Q
What function does a ‘defensive’ protein have and can you provide an example?
A
Function: Protection
Example: Antibodies
14
Q
What function does a ‘enzymatic’ protein have and can you provide an example?
A
Function: Catalysis
Example: Digestive enzymes
15
Q
What are all proteins composed of?
A
20 standard proteinogenic amino acids
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)
17
Q
What is significant about the Cα?
A
The α-Carbon in all amino acids is a chiral centre (with one exception).
18
Q
What is significant about the side chain (R group)?
A
It is variable and changes in every amino acid.
19
Q
What is significant about the carboxyl group (COOH)?
A
It is acidic.
20
Q
What 2 forms can amino acids exist in?
A
Amino acids can exist as 1 of 2 enantiomers: L or D
21
Q
Which enantiomer is rarest?
A
In nature, D-amino acids are very rare, so the L form dominates.
22
Q
What is a zwitterion?
A
An amino acid with NH3+ and COO-.
23
Q
What is the structure of an amino acid’s acidic form?
A
It has a NH3+ and COOH group.
24
Q
What is the structure of an amino acid’s basic form?
A
It has a NH2 and COO- group.
25
What are the hydrogen ion concentrations, [H+] of the acidic and basic forms of amino acids?
Acidic: High
Basic: Low
26
What is the chemical formula of 'glycine' (Gly)?
C2H5NO2
27
What is the chemical formula of 'alanine' (Ala)?
C3H7NO2
28
What is the chemical formula of 'proline' (Pro)?
C5H9NO2
29
What is the chemical formula of 'valine' (Val)?
C5H11NO2
30
What is the chemical formula of 'methionine' (Met)?
C5H11NO2S
31
What is the chemical formula of 'leucine' (Leu)?
C6H13NO2
32
What is the chemical formula of 'isoleucine' (Ile)?
C6H13NO2
33
What is the chemical formula of 'phenylalanine' (Phe)?
C9H11NO2
34
What is the chemical formula of 'tryptophan' (Trp)?
C11H12N2O2
35
Name the 9 amino acids with non-polar R groups.
- Glycine (Gly)
- Alanine (Ala)
- Proline (Pro)
- Valine (Val)
- Methionine (Met)
- Leucine (Leu)
- Isoleucine (Ile)
- Phenylalanine (Phe)
- Tryptophan (Trp)
36
What is the chemical formula of 'aspartic acid' (Asp)?
C4H7NO4
37
What is the chemical formula of 'glutamic acid' (Glu)?
C5H9NO4
38
Name the 2 acidic amino acids.
- Aspartic Acid (Asp)
| - Glutamic Acid (Glu)
39
What is the chemical formula of 'lysine' (Lys)?
C6H14N2O2
40
What is the chemical formula of 'arginine' (Arg)?
C6H14N4O2
41
What is the chemical formula of 'histidine' (His)?
C6H9N3O2
42
Name the 3 basic amino acids.
- Lysine (Lys)
- Arginine (Arg)
- Histidine (His)
43
What is the chemical formula of 'tyrosine' (Tyr)?
C9H11NO3
44
What is the chemical formula of 'asparagine' (Asn)?
C4H8N2O3
45
What is the chemical formula of 'glutamine' (Gln)?
C5H10N2O3
46
What is the chemical formula of 'serine' (Ser)?
C3H7NO3
47
What is the chemical formula of 'threonine' (Thr)?
C4H9NO3
48
What is the chemical formula of 'cysteine' (Cys)?
C3H7NO2S
49
Name the 6 amino acids with polar R groups.
- Tyrosine (Tyr)
- Asparagine (Asn)
- Glutamine (Gln)
- Serine (Ser)
- Threonine (Thr)
- Cysteine (Cys)
50
At what pH are
- acidic amino acids' side chains negatively charged (COO-)
- and basic amino acids' side chains positively charged (NxH+)?
Physiological pH = 7.4
51
What bond can cysteine (Cys) residues form?
- Disulphide Bridges
| Covalently links 2 polypeptide chains
52
Between what specific groups is the disulphide bridge between two cysteine residues formed?
Between S-H groups on each cysteine residues that forms a S-S bond.
53
How is a polypeptide chain formed?
- Via linkage of COOH and NH2 groups
| - Dehydration synthesis
54
What is dehydration synthesis (condensation reaction)?
- Removal of a water molecule
- 2 molecules combine to form a larger molecules
- Peptide bond formed between amino acids
55
What are the two parts of a polypeptide chain?
- Peptide backbone
| - Side chains projecting from the backbone
56
How does bond resonance affect a peptide bond?
Causes bond to be:
- Rigid
- Planar
57
Why is the trans form of amino acids most common?
Rotation at C is usually limited by steric clashes between bulky R groups
58
Describe the directional nature of a protein.
- Primary amino acid sequence has directionality
| - Sequence in one direction is not the same as the sequence in the opposite direction
59
Describe the 4 levels of protein structure.
- 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
60
What are the 4 types of protein secondary structure?
- α-helices
- β-sheets
- loops / random coils
61
How is an amino acid sequence read?
From N-terminus to C-terminus.
62
How is the primary sequence determined?
By the DNA sequence of the gene for each protein.
63
What does the primary structure dictate, and why?
The final protein structure, because sequential arrangement of R groups influences subsequent secondary, tertiary and quaternary structures.
64
What can genetic mutation lead to, and can you provide an example?
- Primary structure changes that can alter structure / function
- Sickle cell disease
65
What is sickle cell disease caused by?
A single mutation in the HbA haemoglobin gene.
66
Describe the secondary structure of proteins.
- 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
Describe the structure of an α-helix.
- Coiled rod-like structure
- Flexible and elastic
- Coil of helix = chain not fully extended
68
What is the most common secondary structure?
α-helices
69
What is proline?
An α-helix structure disrupter (helix breaker).
70
What are α-helices abundant in?
Haemoglobin
71
What are α-helices absent in?
Chymotrypsin (digestive enzyme)
72
What stabilises α-helices?
Extensive intra-chain hydrogen bonding.
73
How many amino acids does an α-helix have per turn?
3.6
74
How are α-helices oriented?
Right-handed / 'Clockwise' from N-terminal to C-terminal end
75
What bonds form the α-helix backbone?
Peptide bonds
76
Why do R-groups on α-helices project outwards?
To avoid steric hindrance.
77
What is an amphipathic α-helix?
An alpha helix with opposing polar and non-polar faces, oriented along the long axis of the helix (secondary structural motif).
78
Describe the structure of a β-helix.
- Flat sheets
- Pleated
(strands almost fully extended = surface appears pleated)
79
β-helices are short runs of how many amino acids?
5 to 10 amino acids
80
What are the 3 types of β-helix structures?
- Parallel
- Anti-parallel
- Mixed
81
Describe the strength of β-helices.
Strong and resilient
82
How are multiple sheets connected in a β-helix?
By short turns or 'hairpin' loops
83
How are β-pleated sheets held together?
By hydrogen bonds between peptide bonds on adjacent strands.
84
How many metres in 1Å (Angstrom)?
10 ^-10 metres
85
How are side chains of β-sheets arranged?
Alternately on opposite sides of the strand.
86
What is the distance between amino acids in a β-helix?
3.5Å
87
What is the distance between amino acids in a α-helix?
1.5Å
88
What is significant about the distance between amino acids in β-sheets and α-helices?
β-sheets are more flexible than α-helices and can be twisted.
89
What is the range of lengths of β-sheets in a protein?
2 to 22 residues
90
What is an amphipathic β-helix?
A beta helix in which hydrophobic side chains point in one direction, and polar side chains in the other direction.
91
What do loops / random coils connect?
Secondary (2°) structural elements
92
Where are loops / random coils usually located?
On the surface
93
What are loops / random coils rich in?
Polar and charged residues
94
What is the range of lengths of loops / random coils in a protein?
2 to 20 residues
95
What are loops / random coils frequently part of?
Enzyme active sites
96
What are structural motifs?
Arrangements of secondary structures (super-secondary structures) that occur frequently within a protein and can be associated with a specific biological function.
97
What is the tertiary structure?
Overall 3D shape of the entire polypeptide
98
What is the tertiary structure held together by?
- 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
What are the two structural classifications of proteins? (Provide examples)
- Fibrous (e.g. collagen)
| - Globular (e.g. haemoglobin)
100
How are fibrous proteins made?
2° structures form long parallel fibres and sheets
101
Describe how fibrous proteins behave in water.
They are usually insoluble in water
102
What role do fibrous proteins play?
Important roles in providing strength and support.
103
State 2 examples of fibrous proteins.
- Collagen
| - Keratins
104
What are the two types of keratins and what are they found in?
- α-keratins
- Mammalian hair and nails
- β-keratins
- Invertebrate silks, reptile scales, reptile claws, avian feathers, avian beaks and avian claws
105
Describe the structure of collagen.
Super-helices of Gly-rich triple α-helices (tropocollagen) that assemble into fibrils.
106
What is collagen the main protein in?
Connective tissue
107
What is the role of collagen?
To support, connect or separate tissues and organs
108
What percentage of total protein is made up of collagen?
25%
109
What are α-keratins composed of?
Coiled coils of two α-helices that assemble together into larger fibres.
110
State 4 properties of α-keratins.
- Strong
- Inextensible
- Insoluble
- Chemically inert
111
Describe the bonding in α-keratins.
Disulphide bridges cross link coiled coils.
112
Describe the structure of β-keratins.
Layers of anti-parallel β-sheets rich in Ala and Gly residues.
113
What is fibroin found in?
Silk and spider webs
114
What allows the close packing of β-sheets?
Small side chains interdigitate to allow close packing of β-sheets.
115
Describe Ehlers Danlos Syndrome (EDS).
- 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
What are globular proteins?
A mixture of irregularly folded 2° elements that form a compact 3D shape.
117
Describe how globular proteins behave in water.
Usually soluble in water with an inner hydrophobic core.
118
Describe the ease of transport of globular proteins.
Transported easily in body fluids.
119
What are globular proteins important in?
Important functions in cellular biochemistry (e.g. myoglobin, haemoglobin, immunoglobulins)
120
Describe the structure of haemoglobin.
- Tetramer
- 4 polypeptide chains / subunits
- 4 haem molecules
121
What does adult haemoglobin contain?
- 2 α-chains (α2)
| - 2 β-chains (β2)
122
Describe the structure of haem.
- Porphyrin ring
| - Fe2+
123
What is myoglobin?
A globular protein related to haemoglobin, which exists as a single polypeptide.
124
Describe the role of haemoglobin in the body.
- Transports oxygen from the lungs to the rest of the body
| - Releases oxygen to permit aerobic respiration to provide energy
125
What can cause diseases such as Sickle Cell Disease and Thalassaemia?
Specific mutations in DNA encoding Hb genes.
126
What are immunoglobulins?
Y-shaped proteins of the immune system which identify and combat invading foreign organisms.
127
Describe the structure of immunoglobulins.
4 chains linked by disulphide bridges:
- 2 large H (heavy) chains
- 2 short L (light) chains
128
What do variable structures in H and L chains form?
Specific binding sites for non-self targets (antigens)
129
Describe what antigen recognition by an antibody does.
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
What is Sickle Cell Disease caused by?
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
What bases and amino acids does the Sickle Cell Disease mutation change?
- Bases: T to A
| - Amino Acids: Glu to Val
132
What happens to RBCs during Sickle Cell Disease?
- 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
What does being a carrier (heterozygous) for the sickle cell gene protect against?
Malaria
134
What is the denaturation of proteins?
A process in which proteins lose quaternary, tertiary and secondary structure present in their native state due to a change in environment.
135
What does denaturation of proteins result in?
A loss of function
136
What does denaturation of proteins occur due to?
- Extreme pH
- Extreme temperature
- Organic solvents
137
Ionic bonds are very sensitive to pH. What effect does this have on proteins?
- Ionic bonds can break
- Tertiary structure is disrupted
- Can render proteins insoluble in water and cause them to precipitate out of solution
138
Describe H+ concentration at low and high pH.
Low pH = High H+ Concentration (acidic)
| High pH = Low H+ Concentration (alkaline)
139
What effect does adding H+ have on ionic bonds. Provide an equation?
- Adding H+ neutralises COO- part of ionic bond
- Removing its charge
H+ + COO- ⇌ COOH
140
What effect does removing H+ have on ionic bonds. Provide an equation?
- Removing H+ neutralises NH3+ part of ionic bond
- Removing its charge
NH3+ ⇌ NH2 + H+
141
Describe the effect of heat on bonding.
Increase in temperature causes vibration, and breaks hydrogen and ionic bonds.
142
What is pyrexia?
Increased body temperature and fever (Anti-viral defence mechanism)
143
What is Thermus aquaticus?
An extremophile bacterium that lives in hot springs.
144
What temperatures does Thermus aquaticus grow above?
70°
145
What does Thermus aquaticus produce?
A DNA polymerase enzyme that is stable at very high temperatures.
146
What is Thermus aquaticus an essential component for?
Polymerase chain reaction (PCR)
147
State 3 organic solvents.
- Ethanol
- Acetone
- Phenol
148
Describe the relationship between solvents and proteins.
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
What are prions?
Infectious particles of misfolded proteins that are spread by causing other proteins to misfold and acquire high β-sheet content.
150
State 5 examples of prions disease
- Scrapie (in sheep)
- Bovine Spongiform Encephalitis (BSE) / Mad Cow Disease
- Creutzfeldt-Jakob Disease (CJD)
- Fatal Familial Insomnia
- Kuru
151
What makes prions disease difficult to tackle?
- Resistant to normal sterilisation methods (including heat, chemicals, and ionising radiation)
