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381 - Biochemistry (COMPLETED) > Tutorial - Week 4 - Amino acids, protein structure & function > Flashcards

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

1
Q

Key concept: describe the structure and properties of amino acids

A
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2
Q

Key concept: describe the primary structure of proteins

A
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3
Q

Key concept: Describe polymerisation of amino acids

A
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4
Q

Key concept: Describe peptide bonds

A
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5
Q

Key concept: Describe intramolecular bonds

A
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6
Q

Key concept: Describe secondary structure of proteins

A
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7
Q

Key concept: Describe tertiary structure of proteins

A
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8
Q

Key concept: Describe quaternary structure of protein

A
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9
Q

Key concept: Describe proteins associated with membranes

A
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10
Q

Key concept: Describe denaturation

A
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11
Q

Key concept: Describe isoelectric point

A
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12
Q

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

A

20

Classified based on the chemistry of the side chain

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13
Q

What are the different side chain groups?

A
  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?

A

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)?

A

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?

A

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

A

True

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23
Q

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

A
  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
Q

Phenylalynine is an aromatic AA but is ________ therefore often classes as a ___________ AA

A

Non-polar

Hydrophobic

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26
Q

What effect can aromatic amino acids contribute to?

A

The hydrophobic effect

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27
Q

Tyr and Trp are __________, meaning?

A

amphipathic

they have hydrophilic and
hydrophobic properties

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28
Q

Tyr – has an _____________ group that can form ________. Often classes as?

A

(-OH) hydroxyl

H-bonds

(often classified as polar uncharged)

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29
Q

Trp has what in the indole ring?

What does it form?

A

Nitrogen in the indole ring, forms pi-bonds and H-bonds

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30
Q

What is an indole ring?

A

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

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31
Q

What do aromatic residues absorb?

A

UV Light

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32
Q

What do these AAs all have in common in terms of what they absorb?

A

UV Light

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33
Q

Why are Tyr and Trp often used in spectrophotometry in the lab?

Why is Phe not used?

A

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

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34
Q

What is the molar coefficient of trp?

A

e280 (Trp) = 5.500 M-1 .cm-1

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35
Q

Label

A
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36
Q

Why is cysteine a unique AA?

Why is it important?

A

because it can make a disulfide bond (covalent bond between 2 sulfur atoms (S-S))

Very important for the structure of proteins

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37
Q

Why are disulfide bonds important?

A
  • Disulfide bonds play an important role
    in the 3D structure of many proteins
  • Disulfide bonds stabilise the structure
    and are important for the function
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38
Q

What is important about polar charged amino acids?

A

Form ionic bonds (electrotactic interactions, salt bridge)

They have charge and the charges can establish electrostatic interactions which are very important for structure

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39
Q

Whats the difference between a peptide, a polypeptide, and a protein?

A
  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
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40
Q

What is an example of a peptide?

A
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41
Q

What is an example of a polypeptide chain?

A
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42
Q

What is an example of a protein?

A
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43
Q

What is the key difference between polypeptides and proteins?

A

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

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44
Q

When is a newly synthesised polypeptide (chain of
amino acids) is obtained?

A

At the end of translation

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45
Q

To achieve its biological active form, the new polypeptide must…?

A

Fold into its proper 3D structure

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46
Q

The polypeptide might have ________________________ by having
other molecules/groups added

Examples?

A

post-translational modifications

(Phosphorylation) or
intramolecular covalent bonds (e.g. disulfide bonds)

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47
Q

What might protein folding also involve but not necessarily?

A

It might undergo enzymatic processing (e.g. cleavage)

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48
Q

Name the levels of protein structure and describe them

A
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49
Q

What kind of bonds are peptide bonds and where do they form?

A

They are stable covalent bonds and form between the amino group and carbonyl group of amino acids

50
Q

Amino acids ________ to form _________ & ________ via ________ bonds

A

polymerise

peptides

proteins

peptide

51
Q

What is released during the formation of the peptide bond? What is this process called?

A

1 molecule of water is released during
the formation of the peptide bond
(condensation, or dehydration)

52
Q

T/F: Peptide bonds are ionic bonds
that link amino acids together to
form proteins only

A

False

Peptide bonds are covalent bonds
that link amino acids together to
form peptides, and proteins

53
Q

What is the process of 1 water molecule being released when peptide bonds are formed called?

A

Dehydration

54
Q

What is the process of 1 water molecule being added when peptide bonds are broken called?

A

Condensation

55
Q

What is this called?

A

A dipeptide

56
Q

What is important about the structure of the peptide bond?

A

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
Q

Is there any flexibility between covalent bonds?

A

No - no movement and is very strong in structure

58
Q

Why is the peptide bond so strong?

A

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
Q

Describe Peptide bond resonance:

A

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
Q

T/F: Peptide bond has H-bond donor and H-bond acceptor.

Explain

A

True

NH group is a H-bond donor, the C-O group is a H-bond
receptor

61
Q

T/F: Peptide bond in the polypeptide sequence can establish H-bonds and be involved in…?

A

True

Secondary structure

62
Q

Chemical groups in the peptide bond and side chains of amino acids are involved in ___________________

Name them

A

intramolecular interactions

  1. Ionic bonds
  2. Hydrogen bonds
  3. Disulfide bonds
  4. van der Waals Forces
63
Q

What are ionic bonds referred to as?

Where do they occur?

A

Also referred to as electrostatic interactions and salt bridges): between side chains of basic and an acidic amino acid

64
Q

Hydrogen bonds also known as?

Where do they occur?

A

(H-bonds): between peptide bonds and/or
between side chains of polar amino acids

65
Q

Disulfide bonds also known as?

Where do they occur?

A

(also referred to as disulfide bridges, or disulfide linkages):

a covalent bond between two Cys

66
Q

van der Waals forces also referred to as?

Where do they occur?

A

Sometimes referred to as hydrophobic interactions, or London dispersion forces): between two hydrophobic amino acids

67
Q

The sequence of amino acids (primary structure) determines ___________ bonds

A

Intramolecular

68
Q

Why are chemical interactions that stabilise higher levels of
protein structure imporant?

A

These interactions are important to fold the polypeptide chain into a 3D shape, which is essential
to obtain a functional peptide/protein.

69
Q

What are the two types of secondary structures?

Label these

A

𝛼-helices

β-sheets
* Antiparallel
* Parallel

Turns or loops
(connecting 𝛼-helices
or β-sheets)

70
Q

What is a secondary structure?

A

Secondary structure: portions of the polypeptide
chain that fold into a local spatial arrangement

71
Q

Describe the a-helix secondary structure (3 points)

A
  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
Q

What level of structures are these?

A

Secondary structures

73
Q

What are helix breakers?

What are examples of helix breakers?

A

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
Q

What kind of shape is the beta pleated sheet?

A

Zigzag structure

75
Q

In a beta pleated sheet, The side chains of adjacent amino acids protrude from…?

A

protrude from the zigzag
structure in opposite directions, creating the alternating pattern
seen in the side view

76
Q

_________ are formed between the peptide bonds of adjacent β-
strands to form a β-sheet

A

H-bonds

77
Q

The individual β-strands that form a β sheet are usually __________
on the polypeptide chain but can also be quite _______

A

nearby

distant

78
Q

T/F: β sheets can be antiparallel (formed with nearby sequences). β sheets can be parallel (formed with more distant portions of
the polypeptide).

A

True

79
Q

What is shown here?

A

Turns or loops connect segments of α helix or of β strands.

80
Q

What do B turns often contain? What do they connect?

A

β turns, which often contain Gly or Pro residues,
connect segments of antiparallel or parallel β sheets.

81
Q

Tertiary structure is the overall _____ structure

A

3D

82
Q

Proteins fold to achieve the most stable structure, which contains: (5 points)

A
  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
Q

Proteins typically contain a mixture of polar and hydrophobic AAs: (2 points)

A
  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
Q

Generally based on the 3D shape, proteins can be classified as? (3 points)

A
  1. Fibrous proteins
  2. Globular proteins
  3. Disordered proteins
85
Q

What do the blue dashes indicate?

A

Hydrogen bonding between oxygen and hydrogen

86
Q

Define Quaternary structure:

A

proteins with more
than one polypeptide

87
Q

Do the polypeptide chains that form protein have to be identical?

A

No, they can be identical or different too

88
Q

What does the arrangement of polypeptide chains into a 3D structure constitute?

A

Quarternary structure

89
Q

Are individual subunits normally functional?

A

No

90
Q

T/F: The active protein requires the quaternary structure (made of
two of more subunits)

A

True

91
Q

What is this protein? Describe

A

Hemoglobin: 2 alpha-subunits (in
grey) and 2 beta-subunits (in blue)

92
Q

What is this protein? Describe

A

Lactate Dehydrogenase-5 (LDH5):
Homotetramer made of 4 identical
subunits (LDHA); each subunit is
here shown with a different colour

93
Q

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…?
A
  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
Q

Give examples of tertiary and quaternary structure, fibrous proteins

A
  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
Q

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?
A
  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
Q

What are the types of membrane proteins?

A
  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
Q

Label the membrane proteins

A
98
Q

Hydrophobic amino acids are mainly located in the ___________ region of the lipid bilayer. They avoid contact with _________

A

hydrophobic region

water

99
Q

Trp and Tyr are ___________ amino acids, and they are normally locate at the interface of _______________ and the ___________________

A

amphipathic

interface of polar headgroup

apolar hydrocarbon region

100
Q

Charged residues (Lys, Arg, Glu, Asp), are found in the __________ phase (intracellular or extracellular portions)

A

aqueous

101
Q

What is the definition of protein denaturation

A

loss of 3D structure that
causes loss of function

102
Q

Denaturation can be induced by: (6 points)

A
  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
Q

What does denaturation lead to?

A

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
Q

At low pH (acidic, lots of H + ) NH 3+ and COOH in termini, and side chains are __________

A

protonated

105
Q

At high pH (basic pH, lots of OH -), NH 3+ , COOH in termini, and side chains…?

A

lose their protons

106
Q

Define pI

A

isoelectric point of a protein, is the pH at which the
net charge is 0

107
Q

If pH in buffer is lower than pI, the protein charge is?

A

positively-charged

108
Q

If pH in buffer is higher than pI, the protein is?

A

negatively-charged

109
Q

T/F: denaturation agents are relatively mild and normally do not
break peptide bonds in the primary sequence

A

True

110
Q

Describe Renaturation

A

proteins can regain their native and active 3D structure
once returned to conditions in which the conformation is stable

111
Q

Denaturation agents that break peptide bonds affect…? Example?

A

the primary structure and the protein does not recover the original structure

E.g: proteases

112
Q

Name all 7 functions of proteins

A
  1. Enzymes
  2. Defensive
  3. Storage
  4. Transport
  5. Signalling (receptor)
  6. Structure
  7. Mobility
113
Q

What is the function of enzymatic proteins?

Give an example

A
114
Q

What is the function of defensive proteins? Give an exmaple

A
115
Q

What is the function of storage proteins?

Give example

A
116
Q

What is the function of transport proteins?

Give example

A
117
Q

What is the function of Hormonal proteins?

Give example

A
118
Q

What is the function of receptor proteins?

Give example

A
119
Q

What is the function of contractile and motor proteins?

Give example

A
120
Q

What is the function of structural proteins?

Give examples

A

381 - Biochemistry (COMPLETED) (47 decks)

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