Protiens Flashcards
What elements do proteins contain ?
C, H, O, N, (sometimes) S
What are the monomers that make up proteins ?
Amino acids
What is the structure of an AA?
Consists of 1 central C atom bonded to a H atom, a Carboxylic group (-COOH), and amino group (-NH2) and a specific side chain/ R-group
What do R-groups determine ?
Property of AA
What are the four types of AA
Neutral and non-polar
Neutral and polar
Acidic and polar
Basic and polar
Which R groups are hydrophilic and which are hydrophobic ?
Polar forms H bond with water - hydrophilic
Non-polar cannot form H bonds - hydrophobic
How to categories the R groups into the four categories
Neutral and non-polar : no charge, no S,O,N
Neutral and polar : no charge, contains S O N
Acidic and polar : negative charge
Basic and polar : positive charge
What are the properties of AA?
Colourless
Crystalline solids
Generally soluble in water but insoluble in inorganic solvents
Dissolves in water to form ions : -NH2 to -NH3+ and -COOH to -COO-
Amphoteric : exhibits both acid and basic properties
Zwitterions formed when both amino and carboxyl group fully ionised
What are zwitterions ?
Molecules that bear charged groups of opposite polarities
What is the isoelectricc point ?
pH at which AA exists mainly in its zwitteroin form
What is electrophoresis ?
Separation technique based on the movement of charged ions under the influence of an electrical field
What type of AA move towards which end in electrophoresis ?
AA with net positive charge move towards the negative electrode (cathode)
AA with net negative charge move towards the positive electrode (anode)
What bond is formed between AAs?
Peptide bond (-CONH-)
What is the direction of a polypeptide ?
1st AA : amino end ( N terminus)
Last AA : carboxyl end ( C terminus)
What are the four levels of organisation ?
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
What does primary structure refer to ?
Type, number and sequence of AAs linked by peptide bonds
Why is primary structure important ?
Determines properties and 3D shape of polypeptide
Determine biological function of polypeptide
What does secondary structure refer to ?
Localised folds and coils that occur in the polypeptide chain
How are the folds and coils in secondary structure formed ?
Formed as a result of interchain H bond at reglar intervals along polypeptide backbone between AA lying close to each other
Is R group interaction involved in secondary structures ?
No
What are the two types of secondary structures ?
Alpha-helix (a-helix)
Beta-pleated sheet (ß-pleated sheet)
How is a-helix formed ?
The oxygen of the carbonyl group of residue n forms H bond with the H of the amino group of residue (n+4)
What is the structure of a-helix ?
The helix backbone winds around long axis resulting in right-hand coil with H bonds all aligned parallel to axis while the R groups project outward
Inter-chain H bonds stabilise the a-helix
How many AA (avg) are there per complete turn in the a-helix ?
3.6
What is a ß-pleated sheet ?
A structure comprising of 2 or more adjacent regions (ß strands) of a polypeptide chain held by multiple intracranial H bonds at regular intervals
What are the two types of ß-pleated sheets?
Parallel ß-pleated sheets : adjacent ß-strand run in same direction
Anti-parallel ß-pleated sheet : adjacent ß strand run in opposite direction
Where are the R groups projected in ß-pleated sheet?
Above and below the ß-pleated sheet
Usually which type of R groups (hydrophilic or hydrophobic) on AA makes up the ß strand ?
The composition of ß strands tend to favour AA with hydrophobic R-groups
What is tertiary structure ?
When polypeptide folds extensively upon itself to form a precise compact globular shape involving R group interactions between AA that are far away from one another
what are the types of R group interactions between AA in tertiary structure ?
Disulfide bond (covalent)
H bond
Ionic interaction
Hydrophobic interaction
Why is tertiary structure important ?
It allows important AA residues that are far away to be brought together into localised region
- these regions often act as proteins active site, binding site and functional site
What does tertiary structure look like ?
Globular shape of protein with distinct / 3D conformation
Are tertiary structures soluble in water ?
Yes
Why are tertiary structures soluble in water ?
Hydrophobic R groups are hidden in the interior of the protein molecule while the hydrophilic R groups are exposed to the aqueous external environment
Can proteins with tertiary structure also have secondary structure present ?
Yes
What is quaternary structure ?
Association of two or more polypeptide chains held together by hydrophobic interactions, H bonds and ionic interaction to form a precise structure
What are ionic bonds ?
Electrostatic attraction between oppositely changes R groups from different parts of the chain
Is formation of ionic bond dependent on pH ?
Very dependent
- ionisation of the R groups depend on the pH the AA is exposed to
Are ionic bonds weak or strong ?
Relatively weak (non-covalent)
- easily interrupted by change in pH and temperature
- ionisation of R groups depend on pH
When are H bonds formed ?
Formed when a H atom that is covalente bonded to an electronegative atom ( usually N, O) is simultaneously attracted to another electronegative atom
What are hydrophobic interactions ?
When non-polar (hydrophobic) R groups cluster together in water forming weak associations called hydrophobic interactions
What are disulfide linkages ?
Bond formed between two sulfur atoms on different R groups (cysteine residues - contain sulfur)
How is the 3D structure of a protein disrupted ?
Change in temperature
Change in pH
Concentration of salts and reducing agents
What is denaturation ?
Change to the specific 3D shape of polypeptide chains due to unfolding of chains, resulting in loss of function / biological activity
Does desaturation affect primary structure ?
No since it does not involve hydrolysis of peptide bonds
Which structure(s) does denaturation involve ?
Secondary
Tertiary
Quaternary
How does temperature affect protein ?
Heat can be used to disrupt H bonds, ionic bonds and non-polar hydrophobic interactions
Heat increases the kinetic energy of and causes the molecules to vibrate so rapidly and violently that the bonds are disrupted
How does pH affect the protein ?
Acids and bases disrupt ion in bonds between AA of a polypeptide
Additional H+ ions in acids combine with teh -COO- group on AA and form -COOH
Reduced number of H+ ions cause NH3+ groups to lose H+ ions and form NH2
How does metal salts and reducing agents affect protein ?
Heavy metal salts denature proteins in similar way as pH since these salts are charged
Reducing agents may disrupt disulfide bonds which are formed through oxidation
What is an example of a transport protein ?
Haemoglobin
What is haemoglobin ?
It is found in RBCs as an oxygen-carrying globular protein associated with a non-protein heme group which contains Fe2+
How many polypeptide chains are haemoglobin made of ?
4 - 2 are (a chains) and 2 are (ß chains)
What kind of secondary structure exists in haemoglobin ?
Only a-helixes
What is the primary structure in haemoglobin ?
Interactions between AA that are far away result in extensive folding and coiling of the polypeptide chain
- gives rise to specific 3D conformation where a hydrophobic cleft lined with hydrophobic AA is formed
- provides hydrophobic environment for heme group that is largely hydrophobic
How is haemoglobin a good transport protein - structure and function (tertiary structure) ?
Compact and globular : allows more to be packed into a RBC for transport of oxygen
The four polypeptide chains coils closely together, there hydrophobic side chains are pointing towards the center while the hydrophilic groups point outwards : making haemoglobin soluble in aqueous mediums thus a good transport protein
What is cooperative binding in haemoglobin ?
Where the binding of oxygen to one heme group facilitates the binding of oxygen to the other heme groups on the same molecule
What is a heme group made up of?
Porphyria rings and iron ion (Fe2+)
What is the structure of a heme group ?
The Fe2+ is at the centre of the porphyrin ring and the heme is orientated such that the Fe2+ on one face is complexed to an AA residue leading the other face for binding oxygen
How many heme groups are there in one haemoglobin ?
4
- 1 bonded to each polypeptide
What is the maximum number of oxygen that a haemoglobin can carry at one time ?
4 - 1 per each heme group
How is heme held in place in the haemoglobin ?
By weak bonds between heme and some of the R groups in the polypeptide
Are haemoglobin pH and temperature dependent ?
Yes
Presence of non-covalent bonds (ionic bond, hydrophobic interactions, H bonds) important in holding the enzyme in shape, thus sensitive to pH and temperature
What type of mutation occurs to result in sickle cell anemia ?
Gene mutation which leads to a change in primary structure
Which structure in haemoglobin is affected in sickle cell anemia ?
Primary structure
What is mutated in sickle cell anemia ?
Gene mutation in the R group chain of the haemoglobin causes a change of one AA : valine is coded for instead of glutamic acid
What is the mutated haemoglobin called ?
Haemoglobin S (HbS)
What is the difference between valine and glutamic acid that causes sickle cell anemia ?
Valine is hydrophobic while glutamic acid is hydrophilic : solubility of the deoxygenated HbS decreases
How does the change in primary structure due to mutation affect haemoglobin’s function ?
HbS molecules will aggregate (lock together) and become rigid, precipitating out of solution, causing RBC to collapse
HbS will chain together forming stiff rod-like structures within the el which changes the RBS into a sickle shape : sickle-shaped cells are not flexible and can stick to vessel walls, causing blockage that slows or stops the flow of blood thus oxygen is not able to reach nearby tissues
What is collagen ?
Main protein found in connectivity tissue in animals
Responsible for skin strength and elasticity together with soft keratin
Why is collagen important ?
It is an important structural protein essential to creating the body’s physical structure as an extracellular matrix acting as a supporting framework over which cells are arranged
Describe the primary structure of collagen
- rich in AA glycine and propine, every third AA is glycine which is the smallest AA
- contains modified AA hydroxyproline and hydroxylysine
- has a repeating sequence of gly-x-y where x is usually proline and y is often hydroxyproline
What makes up one tropocollagen ?
3 polypeptide chains (~1000 AA) wound tightly around each other to form a triple helix
Describe the secondary structure of collagen
Kinked helix formed by polypeptide chain where there is a sharp change in the direction of the helix axis
- kinks allow the 3 helix to wound around each other more tightly to form tropocollagen
- glycine fits nicely into the interior of the triple helix
As a whole, which level of structure does tropocollagen show ?
Quaternary
How is each tropocollagen stable ?
Interchain H bonds formed between the three polypeptide chains
- between the -NH group of glycine and the -CO group of residues on neighbouring chains
What is a collagen fibril ?
Where each complete tropocollagen interacts with other tropocollagen running parallel to it, forming covalent bonds between side chains (R groups) of the lysine residues which hold many tropocollagen molecules side by side
How are the tropocollagen arranged in a collagen fibril ? Why ?
Parallel chains of tropocollagen molecules are in staggered arrangement
- eliminated presence of weak area
- results in banded appearance of fibrils
What are collagen fibres ?
Collagen fibrils further aggregate into collagen fibres
Where does the assembly of collagen fibres occur ?
Outside the cell
What is the most important level of organisation in collagen ?
Secondary structure
How does the secondary structure of collagen relate to its function as a structural protein ?
Collagen is fibrous or strand-like
- allows for larger surface area for cross-linking (H bonds) so as to increase tensile strength
How does the primary structure of collagen relate to its function ?
AA sequence and length is not very specific
- depending on the AA sequence present, different types of collagen can result
Is collagen soluble in water ?
Insoluble due to large molecular size consisting of many hydrophobic AA ( glycine, proline)
Thus making it highly stable and fit for being a structural protein
Where does collagen exhibit high tensile strength ?
Within each subunit
Between tropocollagen
Aggregation into collagen fibrils
How does tropocollagen contribute to collagen tensile strength ?
Within each tropocollagen
-3 polypeptides tightly coiled together mean that more force is required to break the tropocollagen compared to it being made up of only one polypeptide
- strand-like structure of each polypeptide means greater surface area exposed for more cross-linking (interchain H bond) which will stabilise the structure
Between tropocollagen
- staggered arrangement of tropocollagen ensures that there are no weak areas
- covalent cross-links formed between tropocollagen further strengths the structure
What is a G-protein coupled receptor ?
The largest group of plasma membrane receptors (embedded in the membrane, sere to receive signals)
- integral palms membrane proteins that transduce signals from extracellular ligands to signals in intracellular relay proteins (G proteins)
What are G proteins ?
Function as molecular switch (inside cell) that are either on or off
When are G proteins active ?
When GTP (guanosine triphosphate) bound
When are G proteins inactive ?
When GDP (guanosine diphosphate) bound
What is the structure of G protein coupled receptor ?
Structural signature of 7 hydrophobic transmembrane a-helix segments with extracellular N terminus and intracellular C terminus
What is the secondary structure of the G-protein coupled receptor ?
Each of the transmembrane regionals contain an a-helix where r hydrophobic AA face outwards to the hydrophobic core of the plasma membrane
How does the secondary structure of the g-protein coupled receptor relate to its function as signalling protein ?
Allows for the receptor to be embedded within the plasma membrane
How are the specific binding sites on the G-protein coupled receptor formed ?
Specific loops between the helixes form specific 3D conformation for extracellular binding sites for signalling molecules and intracellular binding sites for G protein molecules
How does the specific binding sites on the g-protein receptor relate to its function as signalling protein ?
Allows for specific signalling ligands to bind to the receptor and activate receptor to interact with specific G proteins
