Lectures 13, 14, 15 - The Chemistry of Life in relation to proteins

describe the composition and biological significance of proteins; i.e. describe what proteins are

• Proteins account for more than 50% of the dry mass of most cells.


• The name derives from Greek proteios, meaning “primary.”


• Proteins are cellular building blocks and molecular tools, carrying out a broad range of functions through diverse shapes and sizes.


• A protein is a biologically functional molecule consisting of one or more polypeptides

• The lecture emphasizes that protein functions are central to life and presents proteins as more immediately important to cellular function than genes.

polypeptides

unbranched polymers built from the same set of 20 amino acids

enzymatic proteins

catalyze chemical reactions. Examples include digestive enzymes, elastase, pepsin, DNA polymerase, and alcohol/aldehyde dehydrogenase.

defensive proteins

these protect against disease; antibodies can inactivate and help destroy viruses and bacteria.

hormonal proteins

these coordinate organismal activities. Insulin, secreted by the pancreas, promotes glucose uptake by other tissues and helps regulate blood sugar.

receptor proteins

these enable cells to respond to chemical stimuli. For example, receptors on nerve-cell membranes detect signaling molecules released by other nerve cells.

contractile and motor proteins

these generate movement. Actin and myosin drive muscle contraction; motor proteins also contribute to cilia and flagella movement. Other examples include kinesin and dynein.

structural proteins

these provide support. Keratin occurs in hair, horns, feathers, and other skin appendages; collagen and elastin form fibrous frameworks in connective tissues; silk proteins are used by insects and spiders.

storage proteins

these store amino acids. Casein supplies amino acids to young mammals, plant seeds contain storage proteins, and ovalbumin in egg white supplies amino acids to the developing embryo.

transport proteins

move substances. Hemoglobin transports oxygen from the lungs to tissues; other proteins move molecules across membranes.

describe other protein functions

• signaling proteins

• regulatory proteins

• special-purpose proteins

• proteins involved in cellular recognition and reception

• Examples include nerve growth factor, rhodopsin, green fluorescent protein, antifreeze proteins, ferritin, myoglobin, and insulin receptors.

describe the amino acid structure

• Amino acids are organic molecules containing amino and carboxyl groups.

• Each amino acid has a central α carbon attached to an amino group, a carboxyl group, and a variable side chain (R group).


• The R group determines many of an amino acid’s chemical properties, including whether it is hydrophobic, hydrophilic, or charged.

for the 20 amino acids, ensure you have an idea as to what the structure looks like

non-polar, hydrophobic amino acids

• glycine (Gly, G)

• alanine (Ala, A)

• valine (Val, V)

• leucine (Leu, L)

• isoleucine (Ile, I)

• methionine (Met, M)

• phenylalanine (Phe, F)

• tryptophan (Trp, W)

• proline (Pro, P).

polar, hydrophilic amino acids

• serine (Ser, S)

• threonine (Thr, T)

• cysteine (Cys, C)

• tyrosine (Tyr, Y)

• asparagine (Asn, N)

• glutamine (Gln, Q).

charged, hydrophilic amino acids

these are basic, positively charged amino acids:

• lysine (Lys, K)

• arginine (Arg, R),

• histidine (His, H)

the acidic, negatively charged amino acids are:

• aspartic acid (Asp, D)

• glutamic acid (Glu, E).

polypeptides

• Amino acids are joined by covalent peptide bonds to form polypeptides.

• Polypeptides range from a few amino acids to more than 1,000 monomers.

• Each polypeptide has a unique, linear amino-acid sequence, with an amino end (N-terminus) and a carboxyl end (C-terminus).

what does peptide-bond formation involve?

the removal of water

describe the relationship between protein structure and protein function

• A protein’s specific activities arise from its intricate three-dimensional architecture.


• A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a particular shape.


• The amino-acid sequence determines the protein’s three-dimensional structure, and the structure determines how the protein works.

• Protein function commonly depends on the ability to recognize and bind another molecule.

• remember that there are 4 levels of protein structure

primary protein structure

the unique linear sequence of amino acids. It is determined by inherited genetic information

secondary protein structure

local coils and folds in the polypeptide backbone. Repeating backbone constituents form hydrogen bonds that stabilize common structures:


• α helix: a coiled structure.


• β pleated sheet: a folded structure formed from β strands.

tertiary protein structure

the overall three-dimensional shape of a single polypeptide, arising mainly from interactions among R groups rather than interactions between backbone constituents. The slides identify hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions. Covalent disulfide bridges can reinforce the structure.

quaternary protein structure

the arrangement formed when a protein contains multiple polypeptide chains. Examples include collagen, with three polypeptides coiled like a rope, and hemoglobin, with four subunits—two α and two β.

protein denaturation

the loss of a protein’s native structure; a denatured protein is biologically inactive.

what can cause protein denaturation?

Physical and chemical conditions, including changes in pH, salt concentration, and temperature, can cause a protein to lose its native structure.

why is it difficult to predict a protein’s structure from its primary sequence?

proteins may pass through several stages before reaching a stable structure.

what are misfolded proteins associated with?

diseases including Alzheimer’s disease, Parkinson’s disease, and mad cow disease. The lecture describes conformational diseases as a growing category

what is sickle-cell disease?

Sickle-cell disease is an inherited blood disorder caused by a single amino-acid substitution in hemoglobin

describe the primary-structure change in sickle-cell disease

the small change in primary structure (where there’s a single-amino-acid substitution in haemoglobin) alters hemoglobin’s behavior

• abnormal molecules aggregate into fibers, causing red blood cells to deform into a sickle shape.


• Normal hemoglobin molecules do not associate with one another, and each carries oxygen. In sickle-cell hemoglobin, aggregation reduces oxygen-carrying capacity.

describe the 6 structural models of proteins

• Space-filling models show the molecule’s overall occupied volume.


• Wire-frame models display structural details.


• Ribbon models emphasize the protein’s fold and secondary structures.


• Transparent shapes can show overall shape and some internal details.


• Solid shapes are useful when structural detail is unnecessary.


• Simplified diagrams may use a simple shape for a generic enzyme or a dot to represent a protein.

x-ray crystallography

used to determine protein structures and requires crystals. X-ray diffraction patterns are collected using an X-ray source, a crystal, and a digital detector.

nuclear magnetic resonance (NMR) spectroscopy

can determine molecular structures without protein crystallisation

bioinformatics

predicts protein structure from amino-acid sequences

how can the structural information of an enzyme be used?

to examine enzyme mechanisms, binding pockets, and interactions between proteins and inhibitors

applications of NMR

NMR is presented as a high-resolution, atomic-level method for determining chemical and biochemical structures.


Applications include studying proteins, nucleic acids, sugars, lipids, and drugs; determining three-dimensional biomolecular structures; elucidating nanoscale materials; supporting novel drug development (“SAR by NMR”); validating molecular identity, including biosimilars and protein aggregation; and profiling metabolites in cells, serum, and urine.

describe the function of enzymes. give an example

Enzymes are proteins that act as catalysts, speeding up chemical reactions.


• Enzymes can perform their functions repeatedly, acting as workhorses for processes of life.


• Digestive enzymes, for example, catalyze the hydrolysis of bonds in food molecules.


• Elastase is described as a serine protease. X-ray crystallographic snapshots of the enzyme in action show structural changes in its peptide-binding pocket during catalysis.

COPD - what is it?

COPD → chronic obstructive pulmonary disease

• defines emphysema as enlargement of the alveoli (tiny lung air sacs) accompanied by destruction of their cell walls.

• The presentation reports COPD as the third most common cause of death among middle-aged and elderly men in the Western world.

• caused by absence of normal inhibition of human neutrophil (leukocyte) elastase, a proteolytic enzyme in our bodies

⍺1-antitrypsin (AAT)

an inhibitor of elastase

what is elastase?

Human neutrophil (leukocyte) elastase is a proteolytic enzyme that breaks down elastin, a normal structural component of lung tissue. AAT helps protect the lung by inhibiting elastase.

describe elastase and AAT in relation to COPD

COPD material describes an imbalance between destructive elastase and protective AAT, contributing to ongoing inflammation and damage to the alveoli.
• Cigarette smoke is identified as the leading reason for uncontrolled circulating elastase levels. Hereditary AAT deficiency is also identified as a cause of familial emphysema

describe structure-guided inhibitor development in relation to biological drug design.

Atomic-level, three-dimensional structural information can be used to screen or synthesize inhibitors with tighter binding.
• The lecture illustrates human neutrophil elastase in complex with a dihydropyrimidone-based inhibitor (DHPI).

description of the drug-development funnel

The drug-development funnel is described as reducing the number of candidate drugs as studies reveal safety or effectiveness problems.