M2 - 'The Central Dogma' Flashcards
How do atoms interact covalently?
Strong (150-1000kJ/mol)
Directional
Convey shape
How do atoms interact noncovalently?
Ionic interactions
Dipole interactions
Dipole ion interactions
Hydrogen bonds
Dispersion forces
Steric repulsion
Hydrophobic interactions.
Describe the structure of the atom.
Nucleus is dense, it consists of neutrons and protons. Almost all the mass is in the nucleus.
Are covalent bonds directional?
Yes
Describe bond rotation.
Single bonds have free rotation.
Double and triple bonds do not have free rotation.
These are different conformations, one is more stable that the other.
Describe isomers and conformation.
Isomers are molecules that have the same molecular formula but have a different arrangement of the atoms in space. Covalent bonds need to be rearranged. That excludes any different arrangements which are simply due to the molecule rotating as a whole, or rotating about particular bonds. We call structures that arise from bond rotation conformations and some are very stable due to noncovalent interactions.
Describe what structural isomers are and stereoisomers.
Structural Isomers: Same molecular formula but different arrangement of bonds.
- Different functional groups
- Different position of functional group
Stereoisomers: Same molecular formula and arrangement of bonds but orientation of bonds in space differs.
- Geometric such as cis/trans
- Optical isomers
Describe the Fisher projection and Haworth projection in relation to glucose ring and chain.
Fisher projection: Vertical bonds behind the plane; Horizontal bonds in front of the plane.
Haworth projection: Bonds pointing down correspond to right hand in Fisher, Thick bonds closet.
Describe cis/trans isomerism.
Must have a double bond, restricted rotation means that it can only exist in 2 forms.
Describe chirality.
A carbon with 4 different groups attached is a chiral carbon. 2 conformations are possible allowing them to be optical isomers.
Describe chirality in a ring structure.
It introduces a new chiral carbon - the anomeric carbon. It’s freely interchangeable in water, and other carbohydrates from similar ring structures. Glycosidic bonds lock the alpha and beta forms of the glucose molecules.
Why are noncovalent bonds important in biology?
They are individually weak, collectively strong and they give flexibility.
Describe how Van der Waal’s bonds are used for gecko feet.
Gecko feet have extended surfaces that make Van der Waal’s interactions with walls, ceilings and other surfaces.
How are metal ions sometimes important in proteins?
Metal ions often part of proteins, bind to charged and polar parts of the proteins.
What are dispersion forces?
Weak electrostatic interaction.
Interaction between atom close in space.
Important in macromolecular structures.
Describe the properties of water.
Excellent solvent.
Cause of hydrophobic interactions: bio-membranes, proteins.
High heat capacity: good heat transport
High vaporisation heat.
Freezes from the top downwards
Strong cohesion and adhesion.
Good solvent except for hydrophobic molecules.
Describe some general rules about drawing a Fisher projection.
The vertical lines are drawn away from you whereas the horizontal ones are drawn towards you.
Draw the general amino acid structure.
COOH
NH2 - C - H
R
What is a zwitterion?
This is the physiological form that it exists in normally.
What is the equation of pH?
pH = -log[H+]
What is the acid dissociation constant equation? What does it show?
Ka = ([H+][a-]) / [HA]
It describes how strong an acid is.
What is the Henderson-Hasselbalch equation?
pH = pKa + log([A-]/[HA])
How can we calculate the pH of buffers?
The Henderson Hasselbalch equation.
What is the ratio of bicarbonate/carbonic acid in blood?
There’s 10 times as much bicarbonate as carbonic acid in blood.
What are the two types of special amino acids.
Gly: smallest, gives flexibility in proteins, not considered either hydrophobic or hydrophilic.
Pro: Forms a 5 membered ring ‘Stiff’ in proteins due to ring hydrophobic.
How are amino acids joined?
They are joined by peptide bonds and are formed by condensation and cleaved by hydrolysis.
What are the four hierarchical levels of protein structure?
Primary structure: Sequence of amino acids linked by covalent bonds.
Secondary structure: Folding of the backbone through hydrogen bonding (e.g., α-helices, β-strands).
Tertiary structure: 3D arrangement of secondary structures and side chain interactions.
Quaternary structure: Assembly of multiple polypeptide chains (only in multimeric proteins).
What experimental methods are used to determine protein structures?
X-ray crystallography: Most widely used.
NMR spectroscopy: For small proteins.
Electron microscopy: Suitable for large structures and rapidly advancing.
What are the key features of secondary protein structures?
Formed by hydrogen bonds between backbone atoms.
α-helix: Right-handed helix, with side chains extending outward.
β-strand: Nearly extended chain; forms β-sheets in parallel or anti-parallel arrangements.
β-turns: Allow the chain to reverse direction sharply.
What is the role of Proline in secondary structures?
Proline introduces kinks in helices and disrupts hydrogen bonding.
It exists in cis and trans conformations due to its rigid ring structure, with enzymes catalysing the transition.
What is a Ramachandran plot, and why is it important?
A Ramachandran plot maps the allowed torsion angles (phi φ and psi ψ) of amino acids in protein structures, showing regions corresponding to α-helices, β-sheets, and other conformations.
How does the α-helix structure form?
Hydrogen bonds form between the C=O of residue i and the N-H of residue i+4.
Helices have a rise of 1.5 Å per residue and are typically right-handed.
What are the differences between parallel and anti-parallel β-sheets?
Parallel: Hydrogen bonds connect one amino acid to two in the adjacent strand.
Anti-parallel: Each amino acid pairs with one in the adjacent strand.
What stabilizes tertiary protein structures?
Tertiary structures are stabilized by:
Hydrogen bonds.
Hydrophobic interactions.
Salt bridges (ionic bonds).
Disulfide bonds (covalent).
Van der Waals interactions.
What are motifs in protein structures?
Motifs are combinations of secondary structure elements (10-30 amino acids) that form recognizable patterns, e.g.:
Helix-turn-helix: Binds DNA.
ββ motif: Anti-parallel β-strands.
βαβ motif: Parallel β-strands connected by α-helix.
What is the function of the zinc finger motif?
The zinc finger motif stabilizes a structure with a Zn²⁺ ion and binds DNA strongly and specifically, often acting as a transcription factor.
What is a protein domain?
Domains are compact, independently folding units of a protein, often containing specific functional elements or active sites.
How do α-helices and β-strands interact in tertiary structures?
They combine to form motifs and domains through noncovalent interactions like hydrogen bonds, ionic bonds, and hydrophobic effects.
What are the key features of globular, fibrous, and membrane proteins?
Globular proteins: Water-soluble with hydrophobic cores and hydrophilic surfaces.
Fibrous proteins: Rope-like structures (e.g., collagen, keratin).
Membrane proteins: Interact with hydrophobic membrane regions.
What is quaternary structure in proteins?
Quaternary structure describes how multiple polypeptide chains interact, found only in multimeric proteins. Examples include hemoglobin (α2β2) and GAPDH (homo-tetramer).
Why is the quaternary structure important?
It enables functions such as catalysis in GAPDH and oxygen transport in hemoglobin. Some proteins, like restriction enzymes, rely on quaternary structure for specific DNA binding.
What is the structure and significance of collagen?
Collagen forms a triple helix (Gly-X-Y sequence), requiring vitamin C for Proline hydroxylation. It’s the most abundant protein in humans and critical for the extracellular matrix.
What was Anfinsen’s experiment on protein folding?
Anfinsen demonstrated that proteins can fold spontaneously into their native structure after unfolding, showing that a protein’s sequence determines its 3D structure.
How do urea and β-mercaptoethanol disrupt protein folding?
Urea disrupts hydrogen bonds and hydrophobic interactions, while β-mercaptoethanol breaks disulfide bonds, leading to protein unfolding.
Why can’t proteins fold through random exploration?
The vast number of possible conformations would take billions of years to explore. Instead, folding is an ordered process guided by the hydrophobic collapse.
What role do chaperones play in protein folding?
Chaperones prevent aggregation of unfolded proteins and assist in proper folding, often requiring ATP for conformational changes and release.
What are chaperonins?
Chaperonins are a type of chaperone that provides an isolated environment for folding proteins, preventing aggregation in the crowded cellular environment.
What is Protein Disulfide Isomerase (PDI), and what does it do?
PDI catalyzes the formation and rearrangement of disulfide bonds, aiding protein folding and stability, especially in multi-domain proteins.
What causes protein misfolding diseases like vCJD?
Misfolding leads to abnormal β-sheet aggregates, forming amyloids and prions. In vCJD, these aggregates accumulate in the brain, causing neurodegeneration.
How does sickle cell anemia relate to protein misfolding?
A mutation in hemoglobin causes it to aggregate into chains, distorting red blood cells into a sickle shape, impairing oxygen transport.
How does the cellular environment affect protein folding?
The cell is crowded, making aggregation likely. Specialized machinery, like chaperones, ensures efficient folding despite these conditions.
What are the key messages about protein folding from this lecture?
Quaternary structures are vital for protein functions.
Folding is guided by hydrophobic collapse and sequence information.
The cell uses machinery to prevent misfolding and aggregation.
Misfolding can lead to severe diseases.
How is oxygen carried in the blood and why?
It has low solubility and only 5% or the oxygen in our blood is carried in solution. Transport: Need a protein that will bind oxygen at 100 torr and release it at 20 torr - Haemoglobin. In muscle: Needs a protein that will bind oxygen at 20 torr - Myoglobin.
Describe myoglobin and it’s saturation curve.
Myoglobin is well adapted to ensure good supply of oxygen to muscles.
Mb + O2 <–> MbO2
The curve is hyperbolic, characteristic of simple binding of ligand to a protein.
Describe haemoglobin and the type of binding it uses, and it’s curve.
It’s a sigmoidal binding curve. Lungs have 98% saturation. Tissues have 32% saturation. The tighter binding or higher affinity of myoglobin ensures efficient transfer of oxygen from haemoglobin.
What is a heme?
Heme: is a prosthetic group (a tightly bound cofactor).
A protein without its prosthetic group is an apoprotein. Heme contains an iron atom. The Fe binds to the four N atoms in the centre of the protoporphyrin ring. Sigmodial curve is a sign of cooperativity. That is the 4 binding sites aren’t independent but cooperate to bind and release oxygen.
Describe the relationship between 2,3 - bisphosphoglycerate and oxygen affinity.
2,3-BPG is made from 1,3-BPG (an intermediate in glycolysis). One molecule of BPG binds to the central cavity in Hb and the additional interactions stabilise deoxy-Hb (T form) and therefore haemoglobin has lower affinity for O2.
Describe the Bohr Effect.
Salt bridge formed by protonation of
histidine (pKa of side chain ~ 7)
This stabilises T state
CO2 release lowers pH and binding of CO2 also leads to formation
of salt bridges on the interface
stabilising the T state.
Both are allosteric effectors shifting
equilibrium between R and T state by
binding away from the heme.
