C3 — Proteins Flashcards
Polypeptide
A linear sequence of amino acids covalently joined together by peptide bonds
Prosthetic group
An organic cofactor tightly bound to a protein
Primary structure of a protein
the unique number and linear sequence of amino acids that constitute the polypeptide chain
Tertiary structure
refers to the further bending, twisting and folding of the polypeptide chain with the secondary structures to give an overall specific 3D conformation of a protein.
Quaternary structure
is the overall protein structure that results from the association of two or more polypeptide chains to form a functional protein.
Denaturation
is the loss of the specific 3D conformation of a protein molecule
Describe the main features of the molecular structures of haemoglobin and collagen, visible in figure 3.1. [5]
Haemoglobin (max 3)
- Tetramer of 4 polypeptide chains/ 2 identical dimers forming a globular molecule
- each chain folded to give a specific overall 3D conformation
- each chain contains a Haem prosthetic group
Collagen (max 2):
- Single collagen molecule consists of 3 polypeptide chains that
- wound around each other to form a rope-like triple helix called tropocollagen
Some extra features of tropocollagen are:
-> Small R group of Gly is present at every third residue -> the three helical α-chains can pack tightly together, which provides high tensile strength.
-> The residues in the X and Y positions are located on the outside of the triple-helix, where there is room for the bulky R groups of proline and other residues.
-> Proline with its ring structure, stabilises the rigid three-stranded collagen helix
The tropocollagen is held together by an extensive network of hydrogen bonds.
-> Hydrogen bonds formed between the N-H group of Gly residue in one alpha-chain and the C=O group of another amino acid residue in a neighbouring alpha-chain help hold the three chains together.
-> The hydroxyl groups (–OH) of hydroxyproline and hydroxylysine residues also participate in interchain hydrogen bonding.
- In addition, covalent cross-links are also present within tropocollagen molecules to further impart the collagen fibre with high tensile strength.
- The increasingly rigid and brittle character of aging connective tissue results from accumulated covalent cross-links in collagen fibrils.
Haemoglobin (extra):
Function: Transports oxygen (O2) in the blood from the lungs to other tissues in the body to supply cells with the O2 required for aerobic respiration.
General structure: Multimeric protein comprising 4 polypeptide chains, namely 2 α-chains and 2 β-chains. It is a tetramer (α2β2) made up of two identical dimers (αβ).
alpha or beta polypeptide chain -> 8 alpha helices per pp chain -> folded pp (polypeptide) chain -> globular molecule
Haemoglobin is a transport protein. Collagen is a structural protein. Explain how the molecular structures of Haemoglobin and collagen are related to their functions. [5] (relate to chemical properties)
Haemoglobin (any 2 to 3)
- Hydrophilic amino acid residues located at surface of each subunit, making hydrophobic cleft soluble in cytosol of RBCs, facilitating oxygen transport
- Hydrophobic cleft, allows for Haem prosthetic group to bind to O2
- 4 subunits, increase haemoglobin’s overall capacity for oxygen transport
- Haem group bears an Fe2+ ion, which binds reversibly to oxygen facilitating its uptake and release
- Binding of oxygen to a subunit results in conformational changes in remaining subunits, which allow them to bind more readily to oxygen (cooperative binding)
- globular shape, so that many haemoglobin molecules can be packed into a red blood cell facilitating oxygen transport (weak point)
Collagen (any 2 to 3)
- Every third residue is glycine which is small enough to fit in centre of triple helix, to allow the 3 alpha-chains to pack tightly together providing high tensile strength
- the 3 alpha chains held together by extensive hydrogen bonds formed between the neighbouring alpha-chains, providing high tensile strength
- Covalent cross-links present within tropocollagen molecules, to further impart collagen fibre with high tensile strength (can also between different tropocollagen molecules)
- Tropocollagen molecules further assemble in a staggered manner linked by covalent cross-links, forming collagen fibres that has high tensile strength (covalent cross-links present due to interactions between R groups; the N and C terminus)
Describe the primary structure of collagen polypeptide chains. [2]
(primary structure -> address sequence and unit number)
- Amino acid sequence of a polypeptide chain consists of a repeating tripeptide sequence of glycine-X-Y, where X is often proline and Y is often hydroxyproline or hydroxylysine
- each polypeptide chain is about 1000 amino acid residues long
Explain how 3 collagen polypeptide chains are able to form a tightly coiled 3 stranded helix. [2]
- Every third residue is glycine which is small enough, to fit in centre of triple helix
- the three polypeptide chains held together, by extensive hydrogen bonds formed between -NH of Gly residue in one alpha-chain and C=O of another amino acid residue in a neighbouring alpha-chain OR between -OH of hydroxyproline and hydroxylysine residues in different alpha-chains (quaternary structure)
Some features of tropocollagen are:
-> Small R group of Gly is present at every third residue, fits in centre of triple helix -> the three helical α-chains can pack tightly together, which provides high tensile strength.
-> The residues in the X and Y positions are located on the outside of the triple-helix, where there is room for the bulky R groups of proline and other residues.
-> Proline with its ring structure, stabilises the rigid three-stranded collagen helix
The tropocollagen is held together by an extensive network of hydrogen bonds.
-> Hydrogen bonds formed between the N-H group of Gly residue in one alpha-chain and the C=O group of another amino acid residue in a neighbouring alpha-chain help hold the three chains together.
-> The hydroxyl groups (–OH) of hydroxyproline and hydroxylysine residues also participate in interchain hydrogen bonding.
- In addition, covalent cross-links are also present within tropocollagen molecules to further impart the collagen fibre with high tensile strength.
- (The increasingly rigid and brittle character of aging connective tissue results from accumulated covalent cross-links in collagen fibrils.)
The bonds found between the alpha and beta polypeptide chains in a haemoglobin are the same as those found holding the tertiary structure together, except that covalent bonds are absent. Describe the types of bond, other than covalent bonds, that help to maintain both the tertiary and quaternary structure of haemoglobin. [3] (Type of bond -> name of bond + how it forms)
Ref to R group interactions
- Ionic bonds, formed between oppositely-charged R groups
- hydrogen bonds, formed between hydrogen atom in a R group and strongly electronegative atom in another r group
- hydrophobic interactions, formed between hydrophobic r groups
Haemoglobin is a transport molecule and carries oxygen which binds to the non-protein haem group. In areas of the body where there is a lot of respiration and therefore carbon dioxide production, the haemoglobin releases oxygen. With reference to the information above and your knowledge of proteins, explain how Haemoglobin can release oxygen in these circumstances.
- CO2 produced binds haemoglobin
- which destabilises oxyhaemoglobin, lowering the affinity of haemoglobin for oxygen
- hence promoting release of oxygen by haemoglobin
- Reject: description of how oxygen is carried by haemoglobin
Carbon monoxide binds to haemoglobin at the oxygen-binding sites. When CO is present in the blood, at concentrations of 0.1% or above, the person will become unconscious due to lack of oxygen supply from haemoglobin. Treating this person with 100% oxygen may allow them to regain consciousness. Suggest how this treatment works. [2]
- Oxygen competes with carbon monoxide for binding site
- carbon monoxide less likely to bind to binding site in presence of 100% oxygen
With reference to figure 2.1, explain how the highest level of protein structure of one G-actin subunit is maintained. [3] (1 N terminus and 1 C terminus -> 1 pp)
- Tertiary structure
- one polypeptide/subunit as seen in figure 2.1, with one N terminus and 1 C terminus
- is folded and twisted/coiled to give specific 3D conformation/globular shape
- maintained by R-groups interactions between amino acid residues such as hydrophobic interactions, ionic bonds, hydrogen bonds, disulfide bonds
- within tertiary structure hydrophobic regions localised in interior and shielded from aqueous environment while hydrophilic regions exposed to exterior
- within tertiary structure secondary structures are observed (12 alpha-helices and 3 beta-pleated sheets)
- maintained by intra-chain hydrogen bonds between C=O and N-H groups of polypeptide backbone
Explain the changes that occur when F-actin is subjected to high temperatures. [2]
- Kinetic energy of protein increases/ thermal agitation occurs, resulting in disruption of intermolecular interactions such as hydrophobic interactions, ionic bonds, hydrogen bonds between G-actin subunits
- resulting in disassembly of F-actin /separation of G-actin subunits/ loss of quaternary structure of f-actin/loss of specific 3D conformation/denaturation of F-actin
Compare the structure of tropocollagen and F-actin [2]
Similarities: (any 1)
- Both have a fully extended/elongated/repeated structure
- both have a helical structure
- both have non-covalent interactions between monomers
- Both have a quaternary structure
Differences:
T: Consists of alpha-chains as the protein subunit
FA: Consists of G-actin as the protein subunit
T: Consists of protein subunits that are fibrous/lacking tertiary structure
FA: Consists of protein subunits that are globular/possessing tertiary structure
T: has alpha-chains
FA: contain alpha-helices and beta-pleated sheets
T: consists of 3 protein subunits
FA: consists of multiple/more than three/varying numbers of protein subunits
T: contains covalent cross-links present between alpha-chains/subunits
FA: does not contain covalent cross-links/ only non-covalent interactions
T: Contains a repeated tripeptide sequence of GlyX-Y in the protein subunit
FA: contains no repeating sequence in the protein subunit
T: is a triple helix
FA: is a double helix
Describe the molecular structure of haemoglobin. [4]
- tetramer of 4 polypeptide chains / 2 identical dimers forming a globular molecule, held by multiple non-covalent interactions ;
- each chain consists of eight α-helices, stabilized by hydrogen bonds ;
- each chain is folded such that amino acid residues located at surface are hydrophilic, while those buried in interior are hydrophobic ;
- each chain has a hydrophobic cleft, which contains a haem prosthetic group ;
- haem group consists of an iron ion (Fe2+), held in a porphyrin ring ;
Classification: shape of proteins:
Fibrous proteins vs globular proteins
FP: Pp chains are elongated and wound around each other to form rope-like structure.
GP: Polypeptide chains are folded, bent and twisted to form a compact and
spheroidal structure.
FP: Each polypeptide chain has a repetitive amino acid sequence.
GP: Each polypeptide chain has a specific and non-repetitive amino acid sequence.
FP: Each polypeptide chain is limited to a small, specific variety of amino acids.
GP: Each polypeptide chain is made up of a wide variety of amino acids.
FP: Amino acid sequence may vary slightly between two samples of the same fibrous protein.
GP: Amino acid sequence never varies between two samples of the same globular protein.
FP: The length of the polypeptide chain may vary in two samples of the same fibrous protein.
GP: The length of polypeptide is always identical in two samples of the same globular protein.
FP: Fibrous proteins have stable structures due to the numerous intra- and inter- molecular hydrogen and covalent bonds.
GP: Globular protein have relatively unstable structures due to the numerous intra- and inter-molecular non-covalent bonds, such as hydrogen bonds, ionic bonds and hydrophobic interactions.
FP: Fibrous proteins are generally insoluble in water.
GP: Globular protein are generally more soluble in water than fibrous proteins
FP: Fibrous proteins perform structural functions.
GP: Globular protein perform metabolic functions.
FP: Collagen, myosin, fibroin in silk, actin, keratin, elastin.
GP: Enzymes, hormones, antibodies and haemoglobin.
Structure and properties of amino acids
Structure: contains…a basic amine group (–NH2), an acidic carboxyl group (–COOH)
a hydrogen atom and a R group.
Properties:
- Insoluble in organic solvents but soluble in water where they form ions. The amine and carboxyl group of amino acids can readily ionise.
- Ability to form Zwitterions
Zwitterions are formed by:
the loss of a hydrogen ion (H+) from the carboxyl group (–COOH) making it negatively charged (–COO-).
This hydrogen ion (H+) associates with the amine group (–NH2), making it positively charged (–NH3+).
Because the resulting amino acid contains one positive charge and one negative charge, it is an electrically neutral, dipolar ion which is known as zwitterions
Ability to act as buffer
- AA are amphoteric as they exist as zwitterions in aqueous medium. They have both acidic and basic properties in aq solution.
- Acid added, an amino acid (+H3N–RCH–COO-) takes up a hydrogen ion (H+) and becomes +H3N–RCH–COOH, i.e. the carboxyl group accepts the hydrogen ion.
- Alkali added, an amino acid (+H3N–RCH–COO-) loses a hydrogen ion and becomes H2N–RCH–COO- i.e. the amine group loses a hydrogen ion which combines and neutralises the OH-.
- The presence of the free amine and carboxyl group confers the polypeptide the ability to buffer solutions, (although not to as great an extent as free amino acids.) The R groups of some amino acids are able to ionise as well, thus conferring additional buffering capacity on the polypeptide.
- The property of buffering solutions is essential in biological systems, where small changes in pH can affect the functioning of enzymes and other proteins.
Classification of AAs based on chemical properties of their R groups
- NON-POLAR amino acids (Hydrophobic),
9/20 AAs, are hydrocarbon in nature; unreactive, tend to become localised in the interior. - POLAR amino acids (Hydrophilic)
6/20 AAs, no overall net charge - ACIDIC amino acids: (Hydrophilic)
- have a net negative charge when ionised in water, owing to the presence of a carboxyl group in the R group. - BASIC amino acids (hydrophilic)
- have a net positive charge when ionised in water, owing to the presence of an amine group in the R group
Proteins definition
Proteins are molecules made up of one or more polypeptide chains that has attained a stable, specific 3D conformation and is biologically functional
Bonds present in primary structure, secondary, tertiary and quaternary structure.
Primary structure: Peptide bonds formed between the amine group (–NH2) of one amino acid and the carboxyl group (–COOH) of another.
Secondary structure: Hydrogen bonds formed between the O atom of the C=O group of one amino acid residue and the H atom or the N-H group of another amino acid residue of the polypeptide backbone.
Tertiary and quaternary structure:
- Ionic bonds
- Hydrogen bonds
- Hydrophobic interactions
- Disulfide bonds between R groups of different protein subunits.
BETWEEN AMINO ACID R GROUPS
Alpha-helix
Shape: extended spiral spring
Nature of bonds:
- Stabilised by intrachain (within the same polypeptide chain) hydrogen bonds. The hydrogen bond is formed between the O atom of the C=O group of an amino acid residue (nth) and the H atom of the N-H group of another amino acid that is situated four amino acid residues (nth + 4 residue) ahead in the linear
sequence.
- hydrogen bonds formed are parallel to the main axis of the helix + all C=O and N-H groups of the peptide backbone can participate in hydrogen bonding to bring maximum stability to the α-helix.
- The α-helix makes one complete turn for every 3.6 amino acids.
- The R groups of the amino acid residues project outside the helix, perpendicular to the main axis. -> helps to prevent steric interference with the polypeptide backbone and with each other.
- Proline and hydroxyproline insert a kink and disrupt the formation of the α-helix.
- Amino acids with bulky R groups, e.g. tryptophan, if present in large numbers can also interfere with the formation of the α-helix.
Examples of protein with predominantly alpha-helix structure: keratin
Beta-pleated sheet
Shape: extended zigzag, sheet-like conformation
Nature of bonds: - stabilised by intrachain or inter chain hydrogen bonds, which occur between C=O and N-H groups of the polypeptide backbone within the same polypeptide chain or between C=O and N-H groups of neighbouring polypeptide chains
Antiparallel beta-pleated sheet:
neighbouring hydrogen-bonded polypeptide segments run in opposite N-terminus to C-terminus directions (they alternate)
Parallel beta-pleated sheet:
hydrogen-bonded segments run in the same N-terminus to C-terminus direction.
amino acid residues in a β-pleated sheet usually have small R groups as Amino acids with bulky R groups interfere with the formation of the β-pleated sheet by causing steric hindrance.
