B1.2 Proteins

Structure of amino acid

Amino grp, R-grp, carboxyl grp

Peptide bond formation

What are non-essential amino acids

Amino acids that can be synthesized by our cells(11 amino acids)

What are essential amino acids

Amino acids that cannot be synthesized and are obtained from food(9 amino acids)

Why do vegans have to pay attention to their diets

Meat contains all 9 essential amino acids→vegan diet needs to be well balanced and ensured all essential amino acids

How many naturally occurring amino acids are there

20

Examples of polypeptides

1. Rubisco- enzyme catalyzing CO2 fixation from atmosphere during photosynthesis

2. Insulin(produced in pancreas)- absorbs glucose from blood

3. Immunoglobulin- antibodies(Y-shape)

4. Rhodopsin- pigment in retina of eye

5. Collagen- fibrous protein

6. Spider silk-spiders use it to suspend themselves

7. Haemoglobin

8. Keratin

9. Histones

What is denaturation

Irreversible change of protein conformation(bonds between R groups break easily)

Ionized amino acid structure

Types of R-groups

(Hydrophobic)Non-polar: neutral charge(hydrocarbon)

(Hydrophilic)Polar: forms polar cov bond(partial charge)

Polar ionised: can form +ve(basic) or -ve (acidic)charge

What is the primary structure of a protein?

The sequence of amino acids(the DNA determines this)

The precise position of each amino acid determines 3D shape of protein

The same sequence always gives rise to same 3D shape→proteins have precise, predictable and repeatable structures

What is the secondary structure of a protein?

Forms due to pleating and coiling of amino acid chain

Held tg by weak H-bonds(betw non adjacent amino acids→N-H and C- -O))

Forms alpha helix and beta pleated sheets

What is the tertiary structure?

Complex 3D shape into which secondary structure folds(gives protein specific shape)

Folding occurs due to interactions betw R groups

Bonding involved in tertiary structures of protein

1. H-bond: betw polar R-groups(different from location of H-bonds in secondary structure)

2. Disulfide linkage(S-S): cov bonds betw cysteine amino acids

3. Hydrophobic interactions: betw non-polar R groups and water→fold intro interior of polypeptide to avoid h2o

4. Ionic bond: betw ionised R-grps(carboxyl grp can become -ve while amino grp becomes +ve through ionic bonding)

Solubility of proteins(with polar and non polar amino acids)

Forms globular structure:

1. Hydrophilic amino acids on the outside(interacting with water)

2. Hydrophobic amino acids clustered in the centre

Where are polar amino acids proteins found

1. Surface of membranes→interacts with water

2. Interior pores within membrane→creates hydrophilic channels for polar molecules to pass in n out of cell

3. On outside of enzymes so enzymes r soluble

Where r non-polar amino acids found

In regions of proteins that don’t interact with aqueous solutions

Integral proteins have regions with hydrophobic amino acids, helping them embed in membranes

What is the quartenary structure of a protein

Multiple polypeptide chains(subunits) functioning tg as one protein

Difference between conjugated and non-conjugated protein

Conjugated- contains non-protein components(prosthetic grps)

eg: Haemoglobin(4 subunits with prosthetic haem grp each that contains iron ion)

Non-conjugated- contains only amino acids

eg: insulin(2 polypeptide subunits joined by disulfide bridges) and collagen(fibrous protein, consists of 3 subunits tg in helix shape)

NOS: Cryogenic electron microscopy

Cryo-EM: involves rapid freezing of protein solutions, exposing them to many electrons to produce image(can be used to recreate 3D shape of proteins)

NOS: crystallography

Until recently, proteins had to be crystallized to reconstruct and visualise them with X-ray crystallography. Had issues such as:

1. Time consuming, works on single pitied protein only

2. Some proteins don’t crystallize

3. Structure visualised out of cellular environment, removing contextual info

Globular proteins

Spherical(non polar inside, polar outside)

Soluble therefore easily transported

Eg: insulin: consists of 2 polypeptide chains(polypeptide A has 21 aa residues, B has 30) held tg by 3 disulfide bridges

Fibrous protein

Long strands of polypeptide chains, has cross linkages due to H-bonds

Little or no tertiary structure

Large number of hydrophobic R-grps therefore insoluble

Contains highly repetitive sequence along with insoluble property→makes it strong n suitable for structure

Other than polarity, what other chemical property of amino acids vary due to charge?

Solubility(non-polar r neutral, polar r charged)