SESSION 5 Flashcards
What are the functions of proteins?
Proteins play crucial role in virtually all biochemical processes:
- catalysts
- transporters
- structural support
- muscular contraction and motion
- immune protection
- ion channels
- receptors
- ligands in cell signalling
Describe the direct link between the DNA sequence and the protein sequence
DNA replication
Transcription
Translation
The nucleotide sequence of a gene determines the amino acid sequence of a protein
What do amino acids consist of?
Amino acids consist of a central carbon atom covalently bonded to:
- an amino group (-NH2)
- a carboxyl group (-COOH)
- a hydrogen atom (-H)
- a distinctive R group (side chain)
What are the ionised states of amino acids?
Both the carboxyl group and the amino group can ionise
BASE: NH2 + H+ NH3
ACID: COOH COO- + H+
Define amino acid residue
An amino acid residue is what remains of an amino acid after it has been joined by a peptide bond to form a protein
Classify amino acids by physical and chemical properties
Physical properties:
- aliphatic
- aromatic
Chemical properties:
- hydrophobic
- hydrophilic
- polar
- non- polar
- acidic
- base
- neutral
Explain Pk values of ionisable side chains
An aid dissociation constant Ka is a quantitative measure of the strength of an acid in solution
Pk -> how likely is it to ionise
The lower the value, the more likely it is to be acidic, lose a proton
Describe peptide formation
The linking of two amino acids is accompanied by the abstraction of a water molecule
Peptide bonds are created by enzyme catalysed condensation reactions
And broken down by enzyme catalysed hydrolysis reactions
Describe the properties of peptide bonds
Peptide bonds are planar- all lie in the same place
Peptide bonds are rigid:
- partial double bond characteristics- less flexible and shorter
- unable to rotate
Bonds on either side of the peptide bond are free to rotate
Peptide bonds exhibit a tran’s conformation
Cannot form cis formation as it results in steric clashes
Define conjugated proteins
Some proteins contain covalently linked chemical components in addition to amino acids
What is the importance of amino acids in proteins?
The amino acid sequence of a protein determines:
- the way in which the polypeptide chain folds
- the physical characteristics of the protein
Define the isoelectric point
The isoelectric point of a protein is the pH at which there is no overall net charge
PI > 7 - contain many positively charged amino acids
PI < 7 - contain many negatively charged amino acids
If the pH of the solution < the pK value then the group will be protonated
If the pH of the solution > the pK value then the group will be deprotonated
Define peptide
A few amino acids in length
Define polypeptide
Many amino acids
Describe what is meant by primary, secondary, tertiary and quaternary structure of proteins
Primary structure- the amino acid sequence of a protein
Secondary structure-
stretches of the polypeptide chain that form a-helical and B- sheets.
Bonds on either side of the peptide bond can rotate freely
When these angles remain the same throughout a segment of polypeptide the protein adopts a regular secondary structure
Tertiary structure- The full 3D structure of the protein Involves the folding up of the secondary structures Improper folding (amyloidosis) may cause disease Most proteins fold spontaneously, but some require help of molecular chaperones
Quaternary structure-
Interaction between and arrangement of different polypeptide chains (subunits) within the same protein
The polypeptide chains may be identical (homomeric) or different (heteromeric)
Define both globular proteins and fibrous and their roles
Globular- several types of 2 structure Compact shape Role: Enzyme and regulatory proteins E.g. Carbonic anhydride
Fibrous
Single type of repeating secondary structure
Long strands or sheets
Role: Structure, support, protection
Describe the type of bonds and forces involved in protein structure
Primary structure- covalent bonds (peptide)
Secondary structure - hydrogen bonds
Tertiary structure- hydrogen bonds/ van der waals/hydrophobic interactions/ covalent (disulphide)/ ionic interaction
Quaternary structure- same as tertiary
Explain the key features of the two major secondary structure elements of proteins (a-helix and B- sheets)
B-sheet:
- extended conformation
- parallel or antiparallel
- multiple inter- strand H- bonds
- e.g. Fatty acid binding protein
A- helix:
- right- handed helix
- 3.6 amino acids per turn
- small hydrophobic AA’s such as Ala + Leu are strong helix formers
- pro acts as a helix breaker because the rotation around N- Ca bond is impossible
- Gly acts as a helix breaker because the tiny R- group supports other conformations. E.g. Iron storage protein ferritin
Explain the physiological roles of myoglobin and haemoglobin
Myoglobin-
a single subunit protein that contains one haem group for the binding and transport of oxygen. It can bind one molecule of oxygen. Mb exhibits hyperbolic O2 binding - no cooperativity
Haemoglobin-
A tetrameric protein (2xa, 2xB subunits) containing four haem groups.
It can bind our molecules of oxygen
Hb exhibits sigmoidal O2 biding
Contrast the oxygen- binding properties of myoglobin and haemoglobin and explain why haemoglobin is most suited to its role of an oxygen transporter
Mb has a very high affinity for O2, thus will only release O2 when pO2 is extremely low
Hb however can exist in two states- a low affinity T- state and a high affinity R- state
Transition between these two states gives Hb it’s sigmoidal binding curve- Hb’s affinity to O2 increases as more O2 binds
Describe the major structural differences between oxygenated ad deoxygenated haemoglobin and the molecular basis of cooperativity
Deoxyhaemoglobin can exist in a low affinity T-state or a high affinity R state
The binding of O2 promotes the stabilisation of the R state- cooperatively
Describe the effects of CO2, H+ and 2-3- bisphosphoglycerate and CO on the binding of O2 by haemoglobin, and the physiological significance of these effects
CO2 and H+ decrease the affinity of Hb for O2. At sites of low pH and increased CO2, e.g. Muscle tissue during exercise, more oxygen is required and will be released. This is called the Bohr effect
2-3- bisphosphoglycerate (BPG) decreases the affinity of Hb four O2. Curve shifts right
BPG concentration increases at high altitudes, promoting O2 release at tissues.
BPG is also produces during metabolism, so O2 is released more readily in areas performing high amounts of metabolism
CO binds to Hb 250X more readily than oxygen. It is fatal when COHb is > 50%. The binding of CO also acts to increase the affinity of unaffected subunits for oxygen
Appreciate that mutations in Globin can give rise to diseases such as sickle cell anaemia or thalasaemia
Sickle cell anaemia
SSA is an autosomal recessive genetic blood disorder.
It is caused by a single nucleotide polymorphism resulting in the substitution of (hydrophilic) Glutamate -> Valine (hydrophobic) in the B- subunit of Hb
A sticky hydrophobic pocket formed by Val allows deoxygenated Hbs to polymerise
This leads to the distortion of RBCs into the sickle cell shape.
This distortion causes stress to the cell membrane and causes premature cell lysis
The sickle cell also blacks microvasculature
Thalassaemias
Thalassamias are a group of genetic disorders where there is an imbalance between a and B subunits
B- thalassamias- decreased or absent B- chains. A- chains are noble to form stable tetrameters. Symptoms appear after birth
A- thalassamias- decreased or absent a- chains. There are several different levels of severity as there are multiple copies of the a- chain gene present. B- chains can form stable tetrameters with increased affinity for oxygen. Onset before birth
Explain why some amino acid side chains are charged at physiological pH
If the pH of the solution < the pK value then the group will be protonated
If the pH of the solution > the pK value then the group will be deprotonated
What does the pKa value of an amino acid side chain tell you about that chemical group?
PKa value - log of the acid dissociation constant
Negatively charged R groups have a lower pK value
Positively charged R groups have a higher pK value
The lower the pK value the more likely it is for the R group to loose a proton and be in an acidic form
The higher the pK value the more likely it is for something to be basic
Why do you think histones have a positive charge?
DNA backbone is negatively charged due to the presence of phosphate groups and this is to allow tight association between the histone and he DNA backbone in order to control packaging and transcription
