BIOCHEM TEST 1 (amino acids, peptides & proteins)

what is physiological pH

7.4

What is the zwitterionic form of an amino acid?

It is the dipolar ionic form where the carboxyl group is deprotonated (-COO⁻) and the amino group is protonated (-NH₃⁺), resulting in no net charge.

What is the isoelectric point (pI) of an amino acid?

It is the pH at which the amino acid has no net charge and does not migrate in an electric field.

How is the isoelectric point of a neutral amino acid calculated?

By averaging the pKa of the carboxyl group and the pKa of the α-amino group.

At what pH is an amino acid in its cationic form?

At low pH (≤ 1.0), where both the amino and carboxylic acid groups are protonated.

At what pH is an amino acid in its anionic form?

At high pH (≥ 12.0), when both the carboxyl and amino groups are deprotonated.

What happens to functional groups as pH rises?

≤ 1.0 - All groups protonated.

1.0<pH<pI - Protonated R (if ionizable) and amino group, deprotonated carboxyl group

pI<pH<12.0 - Protonated amino group, deprotonated carboxyl, and R group (if ionizable)

≥ 12.0 - All groups deprotonated

aromatic amino acids

tryptophan, tyrosine, and phenylalanine

properties of aromatic amino acids

absorbs light in the ultraviolet region of the spectrum (helps in detecting + quantifying proteins without destroying them)

amino acids that are sulfur containing

cysteine and methionine

amino acids with a chiral carbon in their structure

not glycine

R/S vs D/L

• In R/S, calculate the left or right by rating functional groups

• D/L by comparing to D or L glyceraldehyde, from most oxidized to least oxidized 

• 99.9% of what we label as R is D, and the same for L and S

peptide bond is formed in a _____ reaction

condensation

peptide bond is formed between the ____

The carbon of the carboxyl group of one amino acid and the nitrogen of the amino group of the second. The oxygen of the carboxyl group and two hydrogens of the amino group leave as water.

when are proteins/proteins at their isoelectric point

when the solution is not migrating towards an electric field

when are peptides/proteins in cationic form

when the protein move towards the cathode

when are peptides/proteins in anionic form

when the protein moves toward the anode

peptide size

12 or fewer amino acid residues are present

oligopeptides size

between 12 and <20 amino acid residues

polypeptides size

20 or more amino acid residues present

monomeric proteins

contain a single correctly folded polypeptide chain

multimeric proteins

contain two or more polypeptide chains

homomultimeric proteins

composed of polypeptides with the same amino acid sequence/primary structure

heteromultimeric proteins

composed of different polypeptides- can have their own primary stucture

subunits

individual polypeptide chains that comprise a multimeric protein

amino (N) terminus is located

on the end of a free amino group (not involved in peptide bond formation) LEFT

carboxy (C) terminus is located

on the end of a free carboxylic acid group (not involved in peptide bond formation) RIGHT

enzymes

biological catalysts, most diverse group

regulatory proteins

regulate cell activity and other protein abilities

Regulatory protein examples (3)

1. peptide and protein hormones

2. allosteric enzymes

3. initiation factors

transport proteins

carry substances from one place to another

Transport protein examples (3)

1. membrane transporters

2. hemoglobin

3. serum albumin

storage proteins

provide a reservoir of essential nutrients

Storage protein examples

1. myoglobin

2. ferritin

3. ovalbumin

4. casein

structural proteins

provide strength, support, and form to cells, tissues, and organisms

Structural protein examples (5)

1. collagen

2. alpha keratin

3. beta keratin

4. cytoskeletal protein fibers

5. tubulin, actin, and spectrin

contractile and motile proteins

provide cell/organism with motion

contractile and motile proteins examples (3)

1. actin and myosin

2. tubulin

3. dynein and kinesin

scaffold proteins

act as bridges to form supramolecular complexes

protective proteins

work as cell or organism defense

Protective protein examples (4)

1. antibodies

2. hemostatis cascasde

3. toxins

4. keratins

stress proteins

allow abiotic survival

Stress protein examples (3)

1. cytochrome P450

2. metallothionein

3. heath shock proteins (HSP)

exotic proteins

don't fit in any other classifications

exotic proteins example

glue proteins