Proteins Flashcards
(111 cards)
1
Q
What are proteins made of?
A
Carbon, hydrogen, oxygen, nitrogen
Sometimes Sulfur
2
Q
How can proteins be classified based on?
A
Shape, function and composition
3
Q
What are the two main shapes proteins can take?
A
Fibrous and globular
4
Q
What is the difference in 3d conformation between a fibrous protein and a globular protein?
A
Fibrous protein: polypeptide chains are elongated and wound around each other to form a rope-like structure
Globular protein: polypeptide chains are folded, bent and twisted to form a compact and spheroidal structure
5
Q
Do fibrous proteins or globular proteins have a repetitive amino acid sequence for each polypeptide chain?
A
Fibrous!
6
Q
Each polypeptide chain in a fibrous protein is made of a wide variety of amino acids. True or false?
A
FALSE!
each polypeptide chain in a fibrous protein is limited to a small, specific variety!
Globular proteins have polypeptide chains made of a large variety of amino acids
7
Q
Does the amino sequence vary slightly for fibrous or globular proteins?
A
Fibrous! The amino sequence may vary slightly between 2 samples of the same fibrous protein!
Globular protein: amino acid sequence never varies
8
Q
How does the length of the polypeptide differ in fibrous proteins and globular proteins?
A
Fibrous: length of polypeptide chain may vary in 2 samples of the same fibrous protein
Globular: length of polypeptide chain is always identical
9
Q
Do fibrous or globular proteins have a more stable structure?
A
Fibrous! Due to the numerous intra and inter molecular hydrogen and covalent bonds!
Globular: relatively unstable due to numerous inter and intra molecular NON-COVALENT bonds (hydrogen bonds, ionic bonds and hydrophobic interactions)
10
Q
Solubility in water for fibrous and globular proteins?
A
Fibrous: generally insoluble
Globular: generally more soluble
11
Q
Function of fibrous protein vs function of globular protein
A
Fibrous: structural functions
Globular: metabolic functions
12
Q
What is a simple protein made of?
A
Only amino acids
13
Q
What are conjugated proteins made of?
A
A protein combined with a non-protein component (a cofactor)
14
Q
What is the purpose of a cofactor? Is it organic or inorganic in nature?
A
Aids protein function. Can be both organic and inorganic.
Organic: a prosthetic group
15
Q
How many amino acids are fundamental animo acids used in protein synthesis?
A
20
16
Q
What is the difference between essential and non-essential amino acids?
A
Essential: cannot be synthesised by the body, obtained from diet
Non-essential amino acids: can be synthesised by the body
BOTH ARE EQUALLY IMPORTANT
17
Q
What are rare amino acids called? What are they made of?
A
Derivatives
DNA does not code for these rare amino acids, created via modification after incorporation into a polypeptide chain
Examples: hydroxyprolime from proline (found in collagen), hydroxylysine from from lysine (also found in collagen)
18
Q
What is the structure of an amino acid?
A
Central carbon
Basic amine group (-NH2)
Acidic carboxyl group (-COOH)
hydrogen atom
Variable R group (side chain)
19
Q
Physical property of amino acids?
A
Colourless, Crystalline solids
Relatively high melting points
20
Q
3 properties of amino acids?
A
- Able to act as zwitterions
- Ability to act as a buffer
- Unique properties of R groups
21
Q
Why do amino acids form ions?
A
Insoluble in organic solvents but soluble in water due to the amine and carboxyl group that can readily ionise
22
Q
How are zwitterions formed?
A
Loss of hydrogen ion from carboxyl group to form -COO- (negatively charged)
Hydrogen ion lost by carboxyl group associates with the amine group to for, -NH3+ (positively charged)
23
Q
What is a zwitterion?
A
Electrically neutral, dipolar ion
24
Q
Are amino acids amphoteric?
A
YES!
Reason: they exist as zwitterions in aqueous medium
25
What does amphoteric mean?
Having Both basic and acidic properties in aqueous solution, can act as buffers
26
Define the term ‘buffer’
A substance that can resist changes in ph in a solution when small amounts of acid or alkali are added to it
27
What happens when acid is added to a solution with amino acids?
Reminder: amino acid is already in zwitterion form!
-COO- part of the Amino acid takes up a hydrogen ion to form -COOH
CARBOXYL GROUP ACCEPTS HYDROGEN ION
28
What happens when an alkali is added to a solution with amino acids?
Reminder: amino acid is already in zwitterion form!
-NH3+ group loses a hydrogen ion to form -NH2
AMINO GROUP LOSES A HYDROGEN ION WHICH NEUTRALISES THE OH- IN THE ALKALINE SOLUTION
29
What are the 3 categories amino acids can be classified into based on their chemical properties of their R-groups?
Amino acids with NON-POLAR R groups
Amino acids with POLAR R groups
Amino acids with CHARGED R groups
30
R groups of non-polar amino acids are hydrocarbon in nature. True or false?
TRUE! many C-C and C-H bonds
31
How many amino acids have non-polar R groups?
9!
32
Characteristics of non-polar amino acids?
Hydrophobic and unreactive
33
Where do non-polar amino acids tend to be located in a protein?
Localised in the interior
Shielded from aqueous medium as the polypeptide folds into its specific 3d conformation
34
How many amino acids are polar?
6!
35
What are polar R groups?
-OH and -NH
36
Do polar R groups have a net charge?
NO
37
Are polar amino acids hydrophobic or hydrophilic in nature?
HYDROPHILLIC
38
How many charged amino acids are there?
5!
39
What bonds can polar R groups form with other polar R groups?
Hydrogen bonds!
Due to the lone pair of electrons
40
What bonds do charged amino acids form with other charged amino acids?
Ionic bonds!
41
What type of bonds do non-polar amino acids form with non-polar amino acids?
Hydrophobic interactions!
42
What is the net charge of acidic amino acids when ionised in water?
Net NEGATIVE charge
Due to carboxyl group in the R group (loss of hydrogen ion)
43
What is the net charge of basic amino acids when ionised in water?
Net POSITIVE charge
Due to presence of an amine group (gain hydrogen ion)
44
How are peptide bonds formed?
Between amine group (-NH2) group of one amino acid and the carboxyl group (-COOH) of the other
Condensation / dehydration reaction
45
What is a polypeptide?
Many amino acids joined together by peptide bonds in a specific linear amino acid sequence
46
What is each amino acid in a polypeptide called?
Amino acid residue
47
What are the 3 features of a polypeptide?
N TERMINUS: Free amine group (beginning of the polypeptide)
C TERMINUS: Free carboxyl group (end of the polypeptide)
R GROUP: Side chain, each amino acid projects its R group from the backbone of the polypeptide
48
Properties of polypeptide?
1. Ability to buffer (not as good as free amino acids)
- some R groups of amino acids are able to ionise (additional buffering capacity)
2. Variations in the length and the amino acid sequence of polypeptides, leads to diversity in the shape and biological functions
- molecules made of one of more polypeptide chains has attained a stable specific 3d conformation, and biologically functional
49
Importance of polypeptides and amino acids acting as buffers?
Essential in BIOLOGICAL SYSTEMS, where small changes in pH can affect the functioning of enzymes and other proteins
50
What is the primary structure of a protein?
Defined as the unique number and linear sequence of amino acids that constitute the polypeptide chain
51
The sequence of the primary structure is specified by DNA. True or false?
True! Proteins are synthesised from the N TO C TERMINUS by stepwise polymerisation of amino acids in the order specified by the sequence of nucleotides in a gene.
52
What does the primary structure determine?
Protein’s Structure and function!
How the proteins folds and coils into the specific 3d conformation and how each polypeptide chain will interact with another is inherent in the amino acid sequence
53
Does amino acid sequence or composition influence the characteristics of the protein more?
SEQUENCE
54
What determines the type and location of bonds present at higher levels of organisation in the protein?
Amino acid R-groups
Size, charge, polarity, hydrophobicity
55
Definition of secondary structure?
Regular coiling and folding of regions of the polypeptide chain give rise to repeated patterns
Result from hydrogen bonds at regular intervals along the polypeptide backbone
56
Where are the hydrogen bonds in the secondary structure located?
Between the N-H group of one amino acid and the C=O group of another amino acid
DOES NOT INVOLVE R GROUPS!
57
What are the 2 most common secondary structures?
a-helix and b-pleated sheet
58
Can a-helix and b-pleated sheet occur within the same polypeptide?
YES
59
What is the shape of the a-helix?
The a-helix takes the form of an extended spiral spring
60
What stabilizes the a-helix structure?
Intrachain hydrogen bonds between C=O and N-H groups of the peptide backbone
## Footnote
These bonds are formed between the O atom of the C=O group of an amino acid residue and the H atom of the N-H group of another amino acid situated four residues ahead.
61
How many residues are there per turn in an a-helix?
3.6 residues per turn
## Footnote
This regular spacing contributes to the stability of the a-helix.
62
What is the orientation of the R groups in an a-helix?
R groups project outside the helix, perpendicular to the main axis
## Footnote
This orientation helps prevent steric interference with the polypeptide backbone.
63
Name two amino acids that disrupt the formation of the a-helix.
Proline and hydroxyproline
## Footnote
These amino acids insert a kink in the helix structure.
64
What is an example of a protein with a predominately a-helical structure?
Keratin
## Footnote
Keratin is known for its structural role in hair and nails.
65
What is the shape of the B-pleated sheet?
Extended zigzag, sheet-like conformation
## Footnote
This unique shape allows for efficient hydrogen bonding.
66
How are hydrogen bonds formed in B-pleated sheets?
Between C=O and N-H groups of the polypeptide backbone
## Footnote
Hydrogen bonds can occur within the same polypeptide chain or between neighboring chains.
67
What types of hydrogen bonding can occur in B-pleated sheets?
Intrachain and interchain hydrogen bonding
## Footnote
Intrachain bonding occurs within the same polypeptide chain, while interchain bonding occurs between different chains.
68
What are 2 varieties of B-pleated sheets?
Anti-parallel B-pleated sheet (neighbouring hydrogen-bonded polypeptide segments run in opposite N-terminus to C-terminus directions)
Parallel B-pleated sheet (hydrogen bonded segments run in the same N-terminus to C-terminus direction)
69
Amino acids residues in B-pleated sheets usually have small R-groups. True or false?
TRUE!
Amino acids with bulky R-groups interfere with the formation of the B-pleated sheet by causing steric hindrance
70
What is an example of a protein which predominantly B-pleated sheets?
Silk fibroin
71
Define tertiary structure
Further bending, twisting and folding of the polypeptide chain with the secondary structure to give an overall specific 3d conformation of a protein
72
What bonds and interactions are in the tertiary and quantenary structure? Where are they located?
Disulfide, ionic, hydrogen bonds
Hydrophobic interactions
Between R groups of different amino acids within the SAME polypeptide chain for tertiary and between DIFFERENT polypeptide chains for quanternary
73
What is an example of a protein that has its tertiary structure as the final structure of a functional protein?
Ribonuclease
74
How do disulfide bonds form and break? (Covalent)
Form: Oxidation of sulfhydryl groups (-SH) of any two cysteine residues (removal of 2 hydrogens)
Break: reduction
75
How do hydrogen bonds form?
Between an electro positive hydrogen atom (attached to N, O or F) (H atom in -NH and -OH) and another electronegative atom (N, O or F) within the same polypeptide chain
Rationale: H atoms have a partial positive charge, N/O/F have a partial negative charge, oppositely charged atoms are attracted to each other to form a Hydrogen bond
76
Are hydrogen bonds weak?
Weak individually but a large number of hydrogen bonds confer stability to the protein
77
How are ionic bonds formed?
Between oppositely charged R GROUPS
78
Are ionic bonds strong in aqueous cellular environments?
NO!
relatively weak, may be broken by changes in pH of the surrounding medium
79
How do hydrophobic interactions occur?
Polypeptide folds so as to shield hydrophobic R -groups from the aqueous environment, hydrophobic interactions occur between hydrophobic R groups of amino acid residues
80
Definition of quantenary structure?
Overall protein structure that results from the association of 2 of more polypeptide chains to form a functional protein
81
What is a protein subunit?
The tertiary structure that each individual polypeptide adopts
82
What are multimeric proteins?
Proteins with more than one polypeptide/subunit
Subunits may be identical or different polypeptides
83
Function of haemoglobin?
Oxygen-binding protein
Transport O2
84
Where is haemoglobin found?
Found in blood within the red blood cells (erythrocytes)
85
Structure of haemoglobin?
Multimeric: 4 polypeptide chains, 2 a-chains and 2 B-chains
Tetramer (a2B2), made of 2 identical dimmers
86
Primary structure of haemoglobin?
Each an dimer made of 2 polypeptide chains (subunits)
1. a-chain (141 amino acids)
2. B-chain (146 amino acids)
87
Secondary structure of haemoglobin?
Each polypeptide chain: 8 a-helices stabilised by hydrogen bonds
88
Tertiary structure of haemoglobin?
Folded such that amino acid residues located at the surface of a subunit are generally hydrophilic so those buried in the interior are mostly hydrophobic, Makes haemoglobin soluble in aqueous medium, a good transport protein for oxygen in blood
Forms a hydrophobic cleft (lined with hydrophobic amino acid residues) to allow for the haem prosthetic group to bind, each polypeptide/haem group binds to a haem prosthetic group, each haemoglobin molecule can bind 4 molecules of O2
89
What is the haem prosthetic group in haemoglobin? (In tertiary structure)
Consists of an iron ion held in a porphyrin ring, binds to one of the oxygen atoms in a molecule of O2, Fe2+ binds reversible to O2 and enhances the release of O2 in metabolically active tissues (muscles)
90
Quanternary structure of haemoglobin?
2 subunits in each dimer held together primarily by hydrophobic interactions (ionic and hydrogen bonds also present)
Forms a globular molecule held by multiple NON-COVALENT interactions
91
How does haemoglobin bind to oxygen?
ALLOSTERIC PROTEIN! Cooperative binding!!
1. Fe2+ in the first haemoglobin subunit binds to 1 molecule of O2, pulls F helix closer to haem group
2. Creates a strain on the other haemoglobin subunits (previously obscured haem groups of the other subunits are revealed)
3. Remaining subunits changed their 3d conformation slightly, allowing respective haem groups to bind to O2 more readily (increases the remaining subunits’ affinities for O2 molecules)
How this relates to function: allows haemoglobin to be an efficient oxygen carrier
haemoglobin loses oxygen quickly in an environment with low oxygen concentration (muscles) and vice versa (lungs)
92
What is the shape of haemoglobin’s oxygen-dissociation curve? What is the significance?
Sigmoidal shape due to subunit cooperativity
Significance: high partial pressure where oxygen is loaded onto haemoglobin the lungs, low partial pressure where oxygen is unloaded from the haemoglobin in the rest of the body tissues
When partial pressure of oxygen is high: more haemoglobin subunits are bound to O2, haemoglobin more started with O2 (reverse occurs at low partial pressure of oxygen)
93
What is the shape of the oxygen-dissociation curve of myoglobin? Why?
HYPERBOLIC
Myoglobin: Made of only ONE polypeptide
Higher affinity binding to oxygen than haemoglobin at the same partial pressure
94
Properties of collagen
Strong
Insoluble
Great tensile strength
95
Primary structure of collagen (amino acid sequence? How long is each molecule?)
Each collagen molecule consists of 3 polypeptide chains
Repeating tripeptide sequence of Glycine - X - Y
X: often proline (prevents collagen from forming an a-helix)
Y: hydroxyproline / hydroxylysine
Each of the 3 polypeptide chains is about 1000 amino acid residues long
96
Secondary structure of collagen?
Collagen helix (regular, repeated structure)
Each collagen polypeptide: left handed helical conformation (3 amino acid residues per turn)
97
What makes up tropocollagen? (Quantenary structure)
3 parallel a-chains with a gentle, right-handed triple helix
Responsible for its characteristic high tensile strength
98
Why must glycine be at every third residue in the amino acid sequence?
Every third residue of the polypeptide passes through the centre of the triple-helix
Centre is so crowded that only the small R group of glycine can fit in
Allows the 3 helical a-chains to pack tightly together, provides high tensile strength
99
Are the X and Y residues of collagen located inside or outside of the triple helix?
Outside!
More room for bulky R groups of proline or other residues
100
Proline’s ring structure helps to stabilise the rigid 3 stranded collagen helix. True or false?
True!
101
How does bonding in tropocollagen give it its high tensile strength?
Extensive network of hydrogen bonds (interchain)
- between N-H group of Gly residue in one a-chain and C=O group of another amino acid residue in a neighbouring a-chain
- between hydroxyl (-OH) groups of hydroxyproline and hydroxylysine residues
Covalent cross links
102
How to form a collagen fibril?
Tropocollagen lay side by side, linked by covalent cross links between carboxyl end of one molecule and amino end of another
103
Why are tropocollagen molecules arranged in a staggered manner?
Sabilised by hydrophobic interactions between tropocollagen molecules
Confers greater strength
104
What is a result of accumulated covalent cross links in collagen fibrils?
Increasingly rigid and brittle character of aging connective tissues
105
How do collagen fibres form?
Aggregation of collagen fibrils
106
What feature of collagen structure could explain the banded appearance of the fibril?
Longitudinal displacement of collagen molecules
Each collagen molecule is displaced longitudinally by about 1/4 of its length from its nearest neighbour
Not linked, gap of around 40nm between the end of one triple helix and the beginning of the next
107
What is denaturation?
Loss of the specific 3d conformation of a protein molecule
Occurs when the bonds that maintain the conformation of the protein is broken and the protein unfolds so it can no longer perform its normal biological function (can be temporary and permanent)
108
In denaturation, only the primary structure remains unaffected. True or false?
TRUE
109
What bonds are disrupted to cause denaturation?
Disruptions in R group interactions (disulfide, ionic, hydrogen, hydrophobic interactions)
Disruptions in hydrogen bonds (between N-H and C=O groups of the polypeptide backbone)
110
How does heat cause denaturation?
Increases vibration of atms, disruptions of hydrogen, ionic and hydrophobic interactions
Eg egg whites become opaque during heating as denatured proteins are insoluble and solidify
111
How do changes in pH cause denaturation?
Changes the charges in acidic and basic R groups, leading to disruption of ionic and hydrogen bonds
