Tutorial - Week 4 - Amino acids, protein structure & function Flashcards

1
Q

Key concept: describe the structure and properties of amino acids

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2
Q

Key concept: describe the primary structure of proteins

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3
Q

Key concept: Describe polymerisation of amino acids

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4
Q

Key concept: Describe peptide bonds

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5
Q

Key concept: Describe intramolecular bonds

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6
Q

Key concept: Describe secondary structure of proteins

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7
Q

Key concept: Describe tertiary structure of proteins

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8
Q

Key concept: Describe quaternary structure of protein

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9
Q

Key concept: Describe proteins associated with membranes

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10
Q

Key concept: Describe denaturation

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11
Q

Key concept: Describe isoelectric point

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12
Q

How many common amino acids are there and how are the groups they are divided into classified?

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20

Classified based on the chemistry of the side chain

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13
Q

What are the different side chain groups?

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  1. Non-polar or hydrophobic (means that their side chain has hydrophobic properties)
  2. Uncharged Polar (soluble in water because they have groups that can establish hydrogen bonding - e.g: hydroxyl groups, carbonyl groups)
  3. Charged Polar
    3.1 Acidic (-)
    3.2 Basic (+)
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14
Q

T/F: Cysteine also has a group that can establish hydrogen bonding? Why is it special and different to others in it’s group?

A

True (But is a special amino acid and doesn’t have the regular hydroxyl group or carbonyl group like the other amino acids in the uncharged polar category

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15
Q

Aspartate and glutamate are also named what?

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Aspartic acid and glutamic acid

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16
Q

Are aromatic amino acids similar to non-polar/hydrophobic AA’s? How do they differ?

A

Yes, they are also part of the non-polar/hydrophobic group

Differ because they also have their own properties and have the benzine ring/rings within their structure

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17
Q

T/F: Depending on certain properties of amino acids they can be grouped differently and often are grouped slightly differently depending on what the focus is?

A

True

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18
Q

Aromatic residues (Trp, Tyr and Phe) can be classified in different groups - name the groups they belong to:

A
  • Tyr (aromatic, polar or amphipathic)
  • Trp (aromatic, apolar or amphiphatic)
  • Phe (aromatic, or apolar)
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19
Q

What is unique about proline (Pro)?

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Proline has a cyclic structure where the side chain is fused with the amino group.

The amino group is slightly different because of this and proline has some unique properties because of it

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20
Q

What are the two amino acids that we focused on in this tut that have a cyclic structure?

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Proline (Pro) and histidine (His)

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21
Q

T/F: Histidine (His) has a cyclic structure in the side
chain, involving an amino group.

How is histidine different to proline and aromatic AAs?

A

True

Histidine’s cyclic structure doesn’t attach to it’s side chain. Other aromatic AAs have benzine rings but histidine doesn’t have that, it just has a cyclic structure without the proper benzine ring

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22
Q

T/F: histidine is ALWAYS classified as a basic amino acid

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True

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23
Q

Describe two main points about Non-polar, aliphatic amino acids (R-groups and what they participate in)

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  1. R groups are non-polar and are hydrophobic
  2. Participate in the hydrophobic effect. The side chains
    of these amino acids tend to cluster together inside
    the protein (i.e. not accessible to the surrounding
    aqueous environment)
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24
Q

Aromatic amino acids:

What are their side chains classed as?

A

Aromatic

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25
Phenylalynine is an aromatic AA but is ________ therefore often classes as a ___________ AA
Non-polar Hydrophobic
26
What effect can aromatic amino acids contribute to?
The hydrophobic effect
27
Tyr and Trp are __________, meaning?
amphipathic they have hydrophilic and hydrophobic properties
28
Tyr – has an _____________ group that can form ________. Often classes as?
(-OH) hydroxyl H-bonds (often classified as polar uncharged)
29
Trp has what in the indole ring? What does it form?
Nitrogen in the indole ring, forms pi-bonds and H-bonds
30
What is an indole ring?
Indole is an aromatic, heterocyclic, organic compound with the formula C 8H 7N. It has a bicyclic structure, consisting of a six-membered benzene ring fused to a five-membered pyrrole ring
31
What do aromatic residues absorb?
UV Light
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What do these AAs all have in common in terms of what they absorb?
UV Light
33
Why are Tyr and Trp often used in spectrophotometry in the lab? Why is Phe not used?
Because Tyr and Trp absorb light with a maximum close to 280 nm Absorbance at 280 nm is commonly used in the lab to quantify the concentration of proteins using the spectrophotometer Phe has an absorbance spectrum that is too low therefore doesn't have enough sensitivity to be quantified using spectrophotometry
34
What is the molar coefficient of trp?
e280 (Trp) = 5.500 M-1 .cm-1
35
Label
36
Why is cysteine a unique AA? Why is it important?
because it can make a disulfide bond (covalent bond between 2 sulfur atoms (S-S)) Very important for the structure of proteins
37
Why are disulfide bonds important?
- Disulfide bonds play an important role in the 3D structure of many proteins - Disulfide bonds stabilise the structure and are important for the function
38
What is important about polar charged amino acids?
Form ionic bonds (electrotactic interactions, salt bridge) They have charge and the charges can establish electrostatic interactions which are very important for structure
39
Whats the difference between a peptide, a polypeptide, and a protein?
1. Peptide is a chain of 2 to 50 amino acids (AAs) joined together by peptide bonds that can have a 3D structure 2. Polypeptide is a chain of more than 50 AAs joined together by peptide bonds 3. Protein contains more than 50 AAs residues from one or more polypeptide chains, it has a 3D structure and normally refers to a functional identity
40
What is an example of a peptide?
41
What is an example of a polypeptide chain?
42
What is an example of a protein?
43
What is the key difference between polypeptides and proteins?
Polypeptides are a single strand of AAs, have no function. However a protein is a combination of multiple, different polypeptides and is folded into a structure that has function
44
When is a newly synthesised polypeptide (chain of amino acids) is obtained?
At the end of translation
45
To achieve its biological active form, the new polypeptide must...?
Fold into its proper 3D structure
46
The polypeptide might have ________________________ by having other molecules/groups added Examples?
post-translational modifications (Phosphorylation) or intramolecular covalent bonds (e.g. disulfide bonds)
47
What might protein folding also involve but not necessarily?
It might undergo enzymatic processing (e.g. cleavage)
48
Name the levels of protein structure and describe them
49
What kind of bonds are peptide bonds and where do they form?
They are stable covalent bonds and form between the amino group and carbonyl group of amino acids
50
Amino acids ________ to form _________ & ________ via ________ bonds
polymerise peptides proteins peptide
51
What is released during the formation of the peptide bond? What is this process called?
1 molecule of water is released during the formation of the peptide bond (condensation, or dehydration)
52
T/F: Peptide bonds are ionic bonds that link amino acids together to form proteins only
False Peptide bonds are covalent bonds that link amino acids together to form peptides, and proteins
53
What is the process of 1 water molecule being released when peptide bonds are formed called?
Dehydration
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What is the process of 1 water molecule being added when peptide bonds are broken called?
Condensation
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What is this called?
A dipeptide
56
What is important about the structure of the peptide bond?
Peptide bond is planar: the bonds involved in the peptide bond resonance (C=O and C-N), are all in a single plan. * There is no rotation around C-N or C-O bonds, this makes the peptide bond very stable * There is rotation around the C-N and C-C bonds with the alpha-carbon
57
Is there any flexibility between covalent bonds?
No - no movement and is very strong in structure
58
Why is the peptide bond so strong?
There is a pair of electrons from the Nitrogen shared between the two atoms C-N This pushes the electrons from the carbonyl double bond towards the oxygen, forming an oxygen anion
59
Describe Peptide bond resonance:
Shared electrons between C-O and C-N. Resonance effect increases stability of the C-N bond, makes it shorter, and decreases rotation around that bond
60
T/F: Peptide bond has H-bond donor and H-bond acceptor. Explain
True NH group is a H-bond donor, the C-O group is a H-bond receptor
61
T/F: Peptide bond in the polypeptide sequence can establish H-bonds and be involved in...?
True Secondary structure
62
Chemical groups in the peptide bond and side chains of amino acids are involved in ___________________ Name them
intramolecular interactions 1. Ionic bonds 2. Hydrogen bonds 3. Disulfide bonds 4. van der Waals Forces
63
What are ionic bonds referred to as? Where do they occur?
Also referred to as electrostatic interactions and salt bridges): between side chains of basic and an acidic amino acid
64
Hydrogen bonds also known as? Where do they occur?
(H-bonds): between peptide bonds and/or between side chains of polar amino acids
65
Disulfide bonds also known as? Where do they occur?
(also referred to as disulfide bridges, or disulfide linkages): a covalent bond between two Cys
66
van der Waals forces also referred to as? Where do they occur?
Sometimes referred to as hydrophobic interactions, or London dispersion forces): between two hydrophobic amino acids
67
The sequence of amino acids (primary structure) determines ___________ bonds
Intramolecular
68
Why are chemical interactions that stabilise higher levels of protein structure imporant?
These interactions are important to fold the polypeptide chain into a 3D shape, which is essential to obtain a functional peptide/protein.
69
What are the two types of secondary structures? Label these
𝛼-helices β-sheets * Antiparallel * Parallel Turns or loops (connecting 𝛼-helices or β-sheets)
70
What is a secondary structure?
Secondary structure: portions of the polypeptide chain that fold into a local spatial arrangement
71
Describe the a-helix secondary structure (3 points)
1. Each turn is made of 3 AAs 2. Each AA in a polypeptide chain has an intrinsic propensity to form a helix, which depends on the side chain 3. Position and the neighbour amino acids are also important: - Positive and negatively-charged residues are conveniently located 3 positions apart to establish ionic interactions
72
What level of structures are these?
Secondary structures
73
What are helix breakers? What are examples of helix breakers?
AAs that really don't like to be in a helical conformation 1. Proline (with the amino group in a cyclic structure it cannot establish H-bonds and it induces a kink in the helix) 2. Glycine (given its small size, too much flexibility) 3. Long block of only negatively-charged, or of only positively-charged AAs (due to electrostatic repulsions 4. Asparagine, Serine, Threonine and Cysteine if close together in the chain
74
What kind of shape is the beta pleated sheet?
Zigzag structure
75
In a beta pleated sheet, The side chains of adjacent amino acids protrude from...?
protrude from the zigzag structure in opposite directions, creating the alternating pattern seen in the side view
76
_________ are formed between the peptide bonds of adjacent β- strands to form a β-sheet
H-bonds
77
The individual β-strands that form a β sheet are usually __________ on the polypeptide chain but can also be quite _______
nearby distant
78
T/F: β sheets can be antiparallel (formed with nearby sequences). β sheets can be parallel (formed with more distant portions of the polypeptide).
True
79
What is shown here?
Turns or loops connect segments of α helix or of β strands.
80
What do B turns often contain? What do they connect?
β turns, which often contain Gly or Pro residues, connect segments of antiparallel or parallel β sheets.
81
Tertiary structure is the overall _____ structure
3D
82
Proteins fold to achieve the most stable structure, which contains: (5 points)
1. A network of H-bonds 2. Regions with secondary structure wherever possible 3. Helices and sheets packed closely together 4. Reduction of surface area 5. Disulfide bonds to help holding the structure
83
Proteins typically contain a mixture of polar and hydrophobic AAs: (2 points)
1. AAs with hydrophobic side chains tend to be folded in the interior of the protein (to avoid contact with water: hydrophobic effect) 2. AAs with polar side chains tend to be exposed on the surface of the molecule (they establish ionic interactions and/or H-bonds with other side chains or with water)
84
Generally based on the 3D shape, proteins can be classified as? (3 points)
1. Fibrous proteins 2. Globular proteins 3. Disordered proteins
85
What do the blue dashes indicate?
Hydrogen bonding between oxygen and hydrogen
86
Define Quaternary structure:
proteins with more than one polypeptide
87
Do the polypeptide chains that form protein have to be identical?
No, they can be identical or different too
88
What does the arrangement of polypeptide chains into a 3D structure constitute?
Quarternary structure
89
Are individual subunits normally functional?
No
90
T/F: The active protein requires the quaternary structure (made of two of more subunits)
True
91
What is this protein? Describe
Hemoglobin: 2 alpha-subunits (in grey) and 2 beta-subunits (in blue)
92
What is this protein? Describe
Lactate Dehydrogenase-5 (LDH5): Homotetramer made of 4 identical subunits (LDHA); each subunit is here shown with a different colour
93
Tertiary & quaternary structure: fibrous proteins - describe what they are (6 points) 1. Structure of subunits and how are they packed? 2. Made of? 3. Shape? 4. How are the chains held together? 5. Water solubility? 6. Protein molecules might align together to form...?
1. Elongated polypeptide chains packed in parallel to each other 2. Simple repeating elements of secondary structure 3. Rope like shape 4. Chains are held together by H-bonds 5. Normally water insoluble 6. Protein molecules might align together to form fibres
94
Give examples of tertiary and quaternary structure, fibrous proteins
1. Alpha-keratin of hair: 2 𝛼-helices each hold by H-bonds, and cross-linked by disulfide bonds; tough, insoluble 2. Collagen of tendons, bone matrix: 3 𝛼-helices, from 3 independent polypeptide chains; high tensile strength, no stretch 3. Silk fibroin: β-strands; soft, flexible filaments
95
Tertiary & quaternary structure: globular proteins... 1. Shape? 2. Compact (more than fibrous? 3. Complexity? Explain 4. Structural diversity required for...? 5. Common? What do they fulfil? 6. Water solubility and present in?
1. Spherical (‘globe-like’ shape) 2. More compact shape than fibrous proteins 3. More complicated 3D structures: often containing several types of secondary structure in the same polypeptide chain 4. Structural diversity required for proteins to conduct a large range of biological functions 5. More common and fulfill many different functional roles in the cell 6. Normally soluble in water and present in the cytosol
96
What are the types of membrane proteins?
1. Integral (AKA as transmembrane or embedded) 2. Peripheral (associated loosely via ionic bonds and H-bonds with polar headgroups or other proteins) 3. Lipid-anchored
97
Label the membrane proteins
98
Hydrophobic amino acids are mainly located in the ___________ region of the lipid bilayer. They avoid contact with _________
hydrophobic region water
99
Trp and Tyr are ___________ amino acids, and they are normally locate at the interface of _______________ and the ___________________
amphipathic interface of polar headgroup apolar hydrocarbon region
100
Charged residues (Lys, Arg, Glu, Asp), are found in the __________ phase (intracellular or extracellular portions)
aqueous
101
What is the definition of protein denaturation
loss of 3D structure that causes loss of function
102
Denaturation can be induced by: (6 points)
1. Heat: it breaks intramolecular bonds, mainly H-bonds 2. Increase in salt concentration: it disrupts ionic interactions between charged amino acids 3. Extreme pH: it changes charges and therefore ionic interactions between charged amino acids and H-bonds between water and amino acids. 4. Organic solvents (e.g. alcohol or acetone) and detergents: disrupt van der Waals interactions and hydrophobic effect between apolar amino acids 5. Urea: disrupt of van der Waals interactions between apolar amino acids, and H-bonds between polar amino acids 6. Reduction agent (e.g. mercaptoethanol): it reduces disulfide bonds.
103
What does denaturation lead to?
Denaturation leads to protein precipitation, normally as a consequence of exposing hydrophobic surfaces (e.g. albumin in egg white precipitates after being subject to heat)
104
At low pH (acidic, lots of H + ) NH 3+ and COOH in termini, and side chains are __________
protonated
105
At high pH (basic pH, lots of OH -), NH 3+ , COOH in termini, and side chains...?
lose their protons
106
Define pI
isoelectric point of a protein, is the pH at which the net charge is 0
107
If pH in buffer is lower than pI, the protein charge is?
positively-charged
108
If pH in buffer is higher than pI, the protein is?
negatively-charged
109
T/F: denaturation agents are relatively mild and normally do not break peptide bonds in the primary sequence
True
110
Describe Renaturation
proteins can regain their native and active 3D structure once returned to conditions in which the conformation is stable
111
Denaturation agents that break peptide bonds affect...? Example?
the primary structure and the protein does not recover the original structure E.g: proteases
112
Name all 7 functions of proteins
1. Enzymes 2. Defensive 3. Storage 4. Transport 5. Signalling (receptor) 6. Structure 7. Mobility
113
What is the function of enzymatic proteins? Give an example
114
What is the function of defensive proteins? Give an exmaple
115
What is the function of storage proteins? Give example
116
What is the function of transport proteins? Give example
117
What is the function of Hormonal proteins? Give example
118
What is the function of receptor proteins? Give example
119
What is the function of contractile and motor proteins? Give example
120
What is the function of structural proteins? Give examples