M2 - 'The Central Dogma' Flashcards

Question

What are the two types of special amino acids.

Answer 1

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.

Answer 2

They are joined by peptide bonds and are formed by condensation and cleaved by hydrolysis.

Answer 3

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).

Answer 4

X-ray crystallography: Most widely used. NMR spectroscopy: For small proteins. Electron microscopy: Suitable for large structures and rapidly advancing.

Answer 5

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.

Answer 6

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.

Answer 7

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.

Answer 8

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.

Answer 9

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.

Answer 10

Tertiary structures are stabilized by: Hydrogen bonds. Hydrophobic interactions. Salt bridges (ionic bonds). Disulfide bonds (covalent). Van der Waals interactions.

Answer 11

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.

Answer 12

The zinc finger motif stabilizes a structure with a Zn²⁺ ion and binds DNA strongly and specifically, often acting as a transcription factor.

Answer 13

Domains are compact, independently folding units of a protein, often containing specific functional elements or active sites.

Answer 14

They combine to form motifs and domains through noncovalent interactions like hydrogen bonds, ionic bonds, and hydrophobic effects.

Answer 15

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.

Answer 16

Quaternary structure describes how multiple polypeptide chains interact, found only in multimeric proteins. Examples include hemoglobin (α2β2) and GAPDH (homo-tetramer).

Answer 17

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.

Answer 18

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.

Answer 19

Anfinsen demonstrated that proteins can fold spontaneously into their native structure after unfolding, showing that a protein's sequence determines its 3D structure.

Answer 20

Urea disrupts hydrogen bonds and hydrophobic interactions, while β-mercaptoethanol breaks disulfide bonds, leading to protein unfolding.

Answer 21

The vast number of possible conformations would take billions of years to explore. Instead, folding is an ordered process guided by the hydrophobic collapse.

Answer 22

Chaperones prevent aggregation of unfolded proteins and assist in proper folding, often requiring ATP for conformational changes and release.

Answer 23

Chaperonins are a type of chaperone that provides an isolated environment for folding proteins, preventing aggregation in the crowded cellular environment.

Answer 24

PDI catalyzes the formation and rearrangement of disulfide bonds, aiding protein folding and stability, especially in multi-domain proteins.

Answer 25

Misfolding leads to abnormal β-sheet aggregates, forming amyloids and prions. In vCJD, these aggregates accumulate in the brain, causing neurodegeneration.

Answer 26

A mutation in hemoglobin causes it to aggregate into chains, distorting red blood cells into a sickle shape, impairing oxygen transport.

Answer 27

The cell is crowded, making aggregation likely. Specialized machinery, like chaperones, ensures efficient folding despite these conditions.

Answer 28

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.

Answer 29

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.

Answer 30

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.

Answer 31

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.

Answer 32

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.

Answer 33

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.

Answer 34

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.

M2 - 'The Central Dogma' Flashcards

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