Module 01: Amino Acids Flashcards
These are the building blocks of proteins. And all have the same basic structure.
Amino acids
What comprises an amino acid?
(1) Amino group
(2) Carboxyl group
(3) Alpha H
(4) Side Chain (R)
This gives identity to amino acid.
R group
There are two (2) stereoisomers:
L and D
Where is the amino acid in D-stereoisomers?
Right
Where is the amino acid in L-stereoisomers?
Left
These are characterized to be non super imposable and pertains to two amino acids that are not the same but hold mirror-like images.
Enantiomers
if the side chain is hydrogen, it is called “_________________”.
Glycine
if the side chain is methyl (CH3), it is called “_________________”.
Alanine
The amino group and the carboxyl group are bonded to the same carbon atom called “__________________.”
Alpha Carbon Atom
How many alpha amino acids are encoded by the genetic code share the generic structure?
20
When carbon has four different groups attached to it, it is called “_____________” or “_________________”
Chiral or Asymmetric
This is cyclic amino acid, is the exception to the basic structure of amino acids.
Proline
Where are L isomers found?
Proteins
Where are D isomers found?
Cell wall of bacteria and peptide antibiotics
This pertains to amino acids with side chains that do not like to reside in an aqueous environment; hence, prompting them to reside in the core of the protein.
Hydrophobic
This is a hydrophobic group that contains only carbon or hydrogen atoms.
Aliphatic
This is the simplest amino acid, although placed under nonpolar and aliphatic its small H do not contribute much to hydrophobic interactions.
Glycine
These amino acids are those with side-chains that prefer to reside in an aqueous environment and hence can be generally found exposed on the surface of a protein.
Polar amino acids
what is the ph of non-polar, aliphatic groups?
7
What are the types of nonpolar aliphatic r groups? (GAVILM)
(1) Glycine
(2) Alanine
(3) Proline
(4) Valine
(5) Isoleucine
(6) Leucine
(7) Methionine
What are the types of Aromatic r groups? (PTT)
(1) Phenylalanine
(2) Tyrosine
(3) Tryptophan
What is the side chain of phenylalanine?
Benzene Ring (nonpolar)
What is the side chain of tyrosine?
Phenolic OH group (polar and ionizable, has pK3
What is the side chain Tryptophan?
Indole Ring
What are the types of Polar, uncharged r groups? (STACG)
(1) Serine
(2) Threonine
(3) Cysteine
(4) Asparagine
(5) Glutamine
The side chains do not ionize at pH 7 but are capable of hydrogen bonding with water.
Polar, uncharged r groups
These polar, uncharged r groups contain the polar hydroxyl group.
(1) Serine
(2) Threonine
This polar, uncharged r groups contains thiol/sulfhydryl group
Cysteine
What are the types of positively charged r groups? (LAH)
(1) Lysine
(2) Arginine
(3) Histidine
What amino group does lysine contain?
epsilon
What amino group does arginine contain?
guanidino
These can display ionic interactions with basic AA (+) or H – bond with OH containing amino acids
Negatively Charged r groups
What are the types of negatively charged r groups?
(1) Aspartate
(2) Glutamate
This is a fibrous protein of connective tissues.
Collagen
These are found mainly in collagen and gelatin proteins.
Hydroxyproline and Hydroxylysine
This is iodinated AA found only in thyroglobulin in the thyroid gland.
Thyroxine
This Is found in proteins involved in blood clotting.
y-carboxyglutamic acid
These are residues created by modification of AA residues already incorporated into a polypeptide
Uncommon Amino acids
This is an important chemical messenger involved in reward, motivation, memory, attention and even regulating body movements.
Dopamine
It is the inactive form and most of it is converted to an active form called _______________by organs such as the liver and kidneys.
triiodothyronine
This is a neurotransmitter or chemical messenger in the brains that blocks specific signals in the central nervous system; thus slowing down the brain and providing protective or calming effect.
Gamma-aminobutyric acid
This pertains to the oxidation of 2 cysteine to form cystine (Cys). These are used to stabilize the structures of many proteins.
Disulfide Bond Formation
This is used to convert pro and lys to OH-pro and OH-lys
Hydroxylation
This is synthesized by decarboxylation of histidine
Histamine
This is derived from tryptophan, that similarly functions as neurotransmitters and regulators.
Serotonin
This is found in nature in the peptides carnosine and anserine and is a component of pantothenic acid (vitamin a).
B-alanine
This is derived from tyrosine.
Epinephrine (Adrenaline)
This is a constituent of the penicillin antibiotics.
Penicillamine
These are known to be important metabolic intermediates (BOHOMOHOMO)
(1) Betaine
(2) Ornithine
(2) Homocysteine
(4) Homoserine
This is a derivative of 4 lysine residues found in the fibrous protein elastin.(con tissue prot)
Desmosine
This is a rare amino acid derived from serine. It is introduced during protein synthesis and not a product of modification. It contains selenium and not sulfur
Selenocysteine
These are two amino acids not found in proteins, are intermediates in the biosynthesis of arginine and in the urea cycle
Ornithine and citrulline
This is produced by the pineal gland, a small endocrine gland found outside of the BBB. This is a part of a system that regulates sleep and wake cycle by chemically causing drowsiness and lowering the body.
Melatonin
What are the functions of amino acids?
(1) Components of proteins
(2) Formation of glucose (glucogenic AA)
(3) Precursors of nitrogen containing compounds
(4) Transport and storage form of ammonia (glN)
(5) Buffer
(6) Chemical messengers/neurotransmitters
(7) Detoxification reactions
These are neurotransmitters derived from tyrosine. Include dopamine, epinephrine and norepinephrine.
Catecholamines
Where is gamma-aminobutyric derived from?
Glutamate
What are the essential amino acids?
(1) Arginine
(2) Histidine
(3) Isoleucine
(4) Leucine
(5) Lysine
(6) Methionine
(7) Phenylalanine
(8) Threonine
(9) Tryptophan
(10) Valine
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What are the non-essential amino acids?
(1) Alanine
(2) Asparagine
(3) Aspartate
(4) Cysteine
(5) Glutamate
(6) Glutamine
(7) Glycine
(8) Proline
(9) Serine
(10) Tyrosine
This is known as a potent vasodilator released as part of the immune response. Moreover, this increases localized blood volume for white blood cells
Histamine
This includes a description of all covalent bonds (peptide and disulfide bonds) linking amino acids in the polypeptide chain.
Primary Structure
This refers to the sequence of amino acid residues from the N –terminal to the C- terminal. This determines how a protein folds into a unique 3-d structure.
Primary Structure
This refers to stable arrangements of AA residues giving rise to recurring structural patterns.
Secondary structure
This describes all aspects of 3- dimensional folding of a polypeptide
Tertiary structure
This describes the arrangement in space of a protein consisting of 2 or more subunits.
Quaternary structure
This is the sequence of amino acids in a polypeptide chain, read from the N-terminal end to the C-terminal end
Primary Structure
This pertains to the ordered 3-dimensional arrangements (conformations) in localized regions of a polypeptide chain; refers only to interactions of the peptide backbone
Secondary structure
This is the arrangement of monomer subunits with respect to each other
Quaternary structure
This refers to spatial arrangement of amino acids that are adjacent in a segment of a polypeptide chains, They do not consider the side chains
Secondary structure
How many amino acids are generated per turn in an alpha helix?
3.6 (5.4)
Side chains of AA residues ________________from the helical backbone.
Protrude outwards
The hydrogen-bonds are ___________to the helical axis
Parallel
Alpha Helixes are stabilized by what?
Stabilized by H-bond between NH and C=O of the peptide bonds. All peptide bond components participate in H- bonding.
Alpha helixes are destabilized by what?
Proline (helix breaker) and glycine (which tends to form coiled structures different from an a-helix)
In this, the polypeptide backbone is tightly wound around an imaginary axis
Alpha helix
Which alpha helix is more stable, right or left?
Right alpha helix
These organizes polypeptides into sheets. An extended zigzag conformation of protein backbones. In this, the protein backbones are arranged side-by-side through H-bonds.
B-pleated sheet
In beta pleated sheets, h-bonds are _____________to the backbone direction
perpendicular
In beta pleated sheets, the side chains of adjacent AAs protrude in _____________.
opposite directions (parallel or anti-parallel)
These are like silk fibroin and fibroin of spider webs
B-keratin
These beta pleated sheets run in an opposite direction of its neighbor (A)
Anti-parallel
These beta pleated sheets run in the same direction with longer looping sections between them (B)
Parallel
These beta sheets reverses the direction of a polypeptide chain and connect the ends of two adjacent segments of antiparallel - sheet.
Beta Turns
How are beta turns generated?
The structure is a 180o turn involving four amino acid residues, where the carbonyl group of the first residue forms an H –bond with the amino group of the fourth
These residues often occur in b-turns
Glycine and Proline
This type of beta turns usually involves proline as the 2nd amino acid residue
Type I
This type of beta turns usually have glycine as the 3rd residue
Type II
This three dimensional globular structure formed by bending and twisting of the polypeptide chain. This is also known as the highest order for monomeric protein
Tertiary Structure
What are the interactions included for tertiary structures?
(1) Hydrophobic interactions hydrophobic amino acid side chains into the interior of the protein shielding them from water
(2) Disulfide bonds
(3) Hydrogen bonds
(4) Electrostatic interactions between charged amino acid side chains
This structure is known as the association of the polypeptide chains
Quaternary Structure
In the quaternary structure, each polypeptide chain in the protein is called ________________.
Subunit (homo or hetero)
This is a pancreatic hormone consisting of 2 polypeptide chains
Insulin
This is a pancreatic hormone that opposes insulin
Glucagon
This is a local hormone produced by the stomach, stimulates the secretion of gastric juice
Gastrin
This is a a tripeptide of glutamate, cysteine and glycine, it is found in all mammalian cells except neurons.
Glutathione
