M2 (Biochemistry) - Amino acids and Proteins

amino acid

organic compound containing both an amino group and carboxyl group

amino group, carboxyl group

amino acids contains what two distinct groups

a-amino acids

amino acids found in PROTEINS are ALWAYS ___

a-amino acid

amino acid which the amino group and carboxyl group is attached to the a-carbon atom

proline

only amino acid that is not an a-amino acid

a-imino acid

proline is an ___

20

how many standard amino acids do we have

nonpolar, polar neutral, polar basic, polar acidic

classifications of amino acids based on side chain polarity

glycine (gly, G)

simplest and only achiral amino acid which contains hydrogen as the side chain

alanine (ala, A)

amino acid containing methyl as the side chain

valine (val, V)

amino acid containing isopropyl as the side chain

leucine (leu, L)

amino acid containing isobutyl as the side chain

isoleucine (ile, I)

amino acid containing sec-butyl as the side chain

proline (pro, P)

amino acid containing pyrrolidine as the side chain

phenylalanine (phe, F)

amino acid containing a benzyl ring as the side chain

methionine (met, M)

amino acid containing thioether as the side chain

tryptophan (trp, W)

amino acid containing an indole ring as the side chain

serine (ser, S)

amino acid containing primary alcohol (hydroxymethyl) as the side chain

cysteine (cys, C)

amino acid containing thiol as the side chain

threonine (thr, T)

amino acid containing secondary alcohol (1-hydroxyethyl) as the side chain

asparagine (asn, N)

amino acid containing methyl + carbamoyl as the side chain

amide

carbamoyl is an ___, acting as a substituent

glutamine (gln, Q)

amino acid containing ethyl + carbamoyl as the side chain

tyrosine (tyr, Y)

amino acid containing phenol as the side chain

aspartic acid (asp, D)

amino acid containing methyl + carboxy as the side chain

glutamic acid (glu, E)

amino acid containing ethyl + carboxy as the side chain

histidine (his, H)

amino acid containing an imidazole ring as the side chain

lysine (lys, K)

amino acid containing aminobutyl (epsilon amino group) as the side chain

arginine (arg, R)

amino acid containing a guanidopropyl group (guanidino/guanido/guanidine) as the side chain

leucine, isoleucine, valine (LIV)

branched chain amino acids

methionine, cysteine (MC)

sulfur containing amino acids

serine, threonine (ST)

alcohol containing amino acids

asparagine, glutamine (NQ)

amidic amino acids

tryptophan, tyrosine, phenylalanine (WYF)

aromatic amino acids

essential, non-essential

amino acids can also be grouped according to whether the body can produce them or not

essential

amino acids that cannot be produced in the body, hence, important in diet

non-essential

amino acids that can be produced in the body

semi-essential

only becomes essential in specific conditions

arginine

semi-essential amino acid

growing children, post-surgery

when does arginine becomes fully essential

fvt wim hrlk

mnemonic for essential amino acids (single letter abbreviations)

glucogenic, ketogenic

another groupings of amino acids based on potential to be converted into glucose or ketone bodies

LL

mnemonic for purely ketogenic

FITTT

mnemonic for both glucogenic and ketogenic

the rest

purely glucogenic amino acids

acetone, acetoacetate, beta-hydroxybutirate

3 ketone bodies that can be produced in the body

chirality

property of amino acids that let them exist as enantiomers

L-isomer

preferred isomerism for amino acids

amphoteric

property of amino acids due to the presence of both acidic and basic groups in the structure

peptide

a chain of covalently linked amino acids is called a ___

unbranched

a peptide is an ___ chain of amino acids

dipeptide

compound containing 2 amino acids

tripeptide

compound containing 3 amino acids joined together in a chain

oligopeptide

term used to refer to peptides with 10 to 20 amino acid residues

polypeptide

refers to longer peptides of >20 amino acids

peptide bonds

bonds that link amino acids togetheri in a peptide chain

condensation reaction

the formation of a peptide bond is an example of what reaction

dehydration reaction

condensation reaction is also known as ___

carboxyl, amino

two amino acids can fuse together by combining the ___ group of one amino acid + ___ group of the next amino acid

primary, secondary, tertiary, quaternary

levels of protein structure

function

the level of protein structure determines the protein's ___

primary

order in which amino acids are linked together through its own unique amino acid sequence

peptide bonds

primary protein structure is stabilized by ___

secondary

arrangement in space adopted by the backbone portion of the protein

secondary

local folding or 2D folding

alpha helix, beta pleated sheets

two most common types of secondary structure

hydrogen bonds

secondary protein structure is stabilized by ___

tertiary

overall three-dimensional shape of a protein resulting from the interactions between amino acid side chains that are widely separated from each other within a peptide chain

covalent disulfide, electrostatic attraction, hydrogen bonds, hydrophobic interactions

tertiary protein structure are stabilized by multiple types of bonds such as

quarternary

highest level of protein organization

true

t or f: bonds that stabilize tertiary proteins also stabilize quaternary proteins

multimeric

quaternary protein structure can only be found in ___ proteins

hydrolysis, denaturation

two processes of protein breakdown

hydrolysis

process of breaking down a compound by adding water

denaturation

process of altering a protein's structure without breaking the peptide bonds using denaturing agents

broken

peptide bonds during hydrolysis

intact

peptide bonds during denaturation

destroyed

protein structure during hydrolysis

primary structure maintained

protein structure during denaturation

lost

function of protein during hydrolysis

lost

function of protein during denaturation

irreversible

reversibility during hydrolysis

reversible under certain conditions

reversibility during denaturation

insoluble

fibrous proteins are water ___

soluble

globular proteins are water ___

single

fibrous proteins usually have a ___ type of secondary structure

several

globular proteins have ___ types of secondary structure

support, external protection

function of fibrous proteins

metabolism, catalysis, transport, regulation

function of globular proteins

fibrous proteins

most abundant type of protein (by mass) in the human body

globular proteins

most abundant type of protein (by number) in the human body

fibrous

examples of this type of proteins are collagen, keratin, etc

globular

examples of this type of proteins are enzymes, buffer proteins, transport proteins, etc

structural proteins

functional protein responsible for providing support and shape to cells and tissues

collagen, elastin, keratin

examples of structural proteins

enzymatic proteins

functional protein responsible for catalyzing biochemical reactions

amylase, lipase, protease

examples of enzymatic proteins

transport proteins

functional protein responsible for carrying substances within the body or across cell membranes

hemoglobin, albumin, transferrin

examples of transport proteins

albumin

most abundant plasma protein that is a general transporter