BIOC 192 - Module 1 (Protein structure and function)

Central dogma

This explains how genetic information flows across a cell. From DNA, to RNA and finally to proteins.

ATP

energy currency of the cell

What are the 4 groups attached to the central alpha carbon of an amino acid?

Amino group, acid group, hydrogen and R group

Which amino acid is the only exception to having a chiral center?

Glycine (its R-group is just a Hydrogen atom, meaning the central carbon is not chiral).

How is a peptide bond formed, and what are its key structural characteristics?

Formed via a condensation/dehydration reaction between the alpha-carboxyl group of one amino acid and the alpha-amino group of the next. Characteristics: It has partial double-bond character due to resonance, making it planar and rigid (restricting rotation around the C-N bond).

How many different amino acids are there?

20

Enzymes which break down proteins

Proteases

Protein which breaks starch down into sugars

Amylase

Enzyme which helps metabolise alcohol

Alcohol dehydrogenase

Hormone in cell signalling to take up glucose

Insulin

Protein which binds oxygen in the lungs and carries it in the blood to tissues for use in metabolism

Hemoglobin

Membrane protein which generates ATP for use in cellular functions

ATP synthase

Protein for DNA replication that binds to one strand of DNA and adds the complementary strand to it

DNA polymerase

Protein that creates a single strand of RNA that is complementary to one of the strands of duplex DNA

RNA polymerase

What is the main experimental technique used to determine protein structure?

Protein crystallography

Imino acid which does not have a protonated side chain

Proline (P), Pro

4 classifications of amino acids

Non-polar side chains, Polar side chains uncharged, Polar side chains charged acidic and basic

Two types of amino acid abbreviations

3 letter and 1 letter

pKa value

The pH at which the amino acid or protein is 50% ionised

Isoelectric point (pI)

The pH at which the net chrage of an amino acid or protein is zero

When an amino acid is modified after it has been added to a protein

Post translational modification

Bond that forms when two cysteines for a covalent bond

Disulfide bond

What does a hydrophobic core help with in a protein

Stability of the protein structure

What is the alpha domain family?

Amphipathic helices with side-chains packed closely together with a hydrophobic core

What is the alpha/beta family?

A mixture of alpha and beta structure, creates barrel shape which is hydrophobic in the core.

What is the antiparallel family?

Mostly antiparallel structure

What are the key steps involved in folding a protein?

Primary, secondary and tertiary

What is a chaperone and what role do they play in protein folding?

Molecular chaperones arehelperproteins that bind to unstable polypeptide chains to ensure they achieve the correct three-dimensional shape without becoming stuck or clumped together.

What is the role of enzymes

Catalyse thermodynamically favourable reactions by lowering activation energy

Three properties of coenzymes

Small organic molecules, carriers of electrons, atoms or functional groups and are often derived from vitamins.

What do isomerases do?

Transfer of atoms/groups within a molecule to yield and isomeric form

What do ligases do?

Join two molecules together and form a new bond

Two classes of cofactors

Inorganic and organic

How do enzymes lower Gibbs free energy?

Ground state destabilization and/or stabilize transition state, making it happier.

4 types of enzyme-substrate bonds

Ionic bonds, hydrogen bonds, Van der Waals interactions and covalent bonds

What do enzymes bind most effectively with?

The transition state of the reaction

Three properties of metal ion catalysis

Act as Lewis acids to polarize water or other functional groups, good sites for electron transfer (redox) and substrate orientation due to specific coordination geometry

What does an acid-base catalysis involve?

H+ transfer

What does covalent catalysis involve?

Formation of a reactive, short-lived intermediate which is covalently attached to the enzyme

What does Kcat mean?

The number of substrate molecules converted to product, per unit of time, when E is saturated with substrate.

What does ground state destabilization do?

Reduces activation energy by destabilising the substrate.

What does transition state stabilization do?

Lowers free energy of the transition state which makes the reaction faster.

Why does the rate of an enzyme substrate reaction stop increasing linearly after some time when enzyme amount is fixed and [S] is increased?

Because all the active sites are occupied.

What order kinetics is the linear part of a substrate - enzyme graph and why?

First order as the rate depends on substrate concentration

What order kinetics is the non-linear part of a substrate - enzyme graph and why?

Zero order as the rate does not depend on substrate concentration.

Define Vmax

The maximum velocity possible when [S] = infinity and [E] is constant.

Define Km

The [S] at which V = ½ Vmax.

What does a low Km suggest?

A high affinity of E and S.

What does a high Kcat suggest?

A high turn over of substrate into product per second.

What are the two main classes of enzyme inhibitors based on the nature of their binding?

Reversible inhibitors and irreversible inhibitors.

How do reversible inhibitors bind to an enzyme?

They bind via non-covalent interactions (e.g., hydrogen bonds, ionic bonds, hydrophobic interactions) and can readily dissociate from the enzyme.

How do irreversible inhibitors bind to an enzyme?

They bind covalently to essential functional groups in the active site, permanently inactivating the enzyme.

Where on an enzyme does a competitive inhibitor bind?

It binds directly to the active site of the enzyme, competing directly with the substrate for binding.

What effect does a competitive inhibitor have on Km and Vmax?

Increases Km and Vmax remains unchanged

What effect does a non-competitive inhibitor have on Km and Vmax?

Km stays the same and Vmax decreases.

Where on an enzyme does a non-competitive inhibitor bind?

It binds to an allosteric site (a site other than the active site), regardless of whether the substrate is bound or not.

On a Lineweaver-Burk plot, what visual pattern indicates pure non-competitive inhibition?

A shift on the Y axis (Vmax) but not on the X axis (Km).

What enzyme class reverses phosphorylation?

Phosphatases

What does haem refer to?

Four pyrrole rings linked together in a plane. This is where Fe is bound.

What 6 things are the Fe2+ ion in hemoglobin bound to?

4 Nitrogen atoms of the haem, one N of histidine F8 and one to O2.

What happens to the binding of Fe2+ when O2 is bound?

This bond brings the Fe into the plane so it is no longer dished.

Why does hemoglobin have four globin and 4 heme subunits?

Because this allows cooperative binding of O2 and therefore delivery to tissue is also more efficient.

What is allostery?

Binding of molecules to additional sites away from the active site.

What causes the hemoglobin to have a sigmoidal binding curve?

Due to the cooperativity of the heme, when one O2 binds, the other three follow soon after

What is the T-state of hemoglobin?

Tense state, with a low affinity for oxygen. This is the state it will be in when returning to the lungs.

What is the R-state of hemoglobin?

Relaxed state, with a high affinity for oxygen. This is the state it will be in when leaving the lungs to deliver O2 to the tissues.

How does the binding of myoglobin and hemoglobin differ?

Myoglobin binds the O2 tighter.

What does BPG do for hemoglobin?

It stabilizes Hb in the T-state so promotes correct oxygen release where it is needed.

What does CO2 do for hemoglobin?

Reduces oxygen affinity by binding to the amino terminal group which stabilises the T-state.

Why does foetal hemoglobin have a higher affinity for O2?

It is less sensitive to BPG as it does not have as strongly positive pocket.

What causes sickle cell anemia?

An E6V variant in the beta subunits.

How is sickle cell anemia treated?

With a hemoglobin oxygen-affinity modulator which stabilizes the oxygenated state so that oxygen affinity is increases which pushes towards the R-state.

What determines if a substance acts as a drug or poison?

Dose and route of administration

What is the name of a cellular protein that controls chemical signalling between and within cells?

Receptor

Three main types of receptor classes

Ligand - Gated Ion Channels, G Protein Coupled Receptors and Receptor Tyrosine Kinases.

Substance that binds to a receptor

Ligand

Ligand that is produced in the body

Endogenous ligand

Ligand that is produced outside of the body

Exogenous ligand

Where are most receptors found?

On the outer cell membrane

What is the point of a ligand binding to a receptor?

Causes an activation or inhibition leading to a cellular response.

A ligand that binds to a receptor and activates it

Agonist

A ligand that binds to a receptor and inactivates it

Antagonist

What is a second messenger?

A molecule inside the cell which amplifies signals from outside the cell

What is the role of phosphorylation and dephosphorylation in signal transduction pathways?

They act as an on/off switch that transmit, amplify and turn off signals inside a cell.

What is the role of GLP-1?

It is a vital messenger to control blood sugar levels, digestion and appetite.

What signal transduction method is the fastest?

Ligand-gated ion channels.