AMINO ACID AND PROTEINS 1 Flashcards
what is amino acid
the basic unit of a protein
what are the groups in amino acid
chiral carbon attached to
1. hydrogen
2. alpha amino group
3. carboxyl group
4. R-group / side chain
in stereoisomerism, difference between L-amino acid and D-amino acid?
L-amino acid: amino group is located at the left side of the fischer projection
D-amino acid : amino group is located at the right side of the fischer projection
what is the classification of amino acid based on
the chemical properties of the “R” group of the amino acid.
can be :
-hydrophobic + non polar
-polar + uncharged
-polar + negatively charged
-polar + positively charged
what other method can u classify amino acid
according to the R group of the amino acid :
1. aliphatic (leu,ile,ala,val)
2. aromatic (phe, trp, tyr)
3. AA containing sulphur (cys, met)
4. AA containing a hydroxyl group (thr, ser)
5. acidic AA (asp, glu)
6. basic AA (lys, arg, his)
7. Imino AA (pro ; has cyclic R group)
8. Amides (Gln, Asn)
Examples of nonpolar AA
-LEU
-PRO
-ALA
-VAL
-MET
-PHE
-TRP
-ILE
Examples of polar uncharged AA
-GLY
-SER
-THR
-CYS
-TYR
-HIS
-GLN
-ASN
Examples of polar negatively charged AA
-GLU
-ASP
Examples of polar positively charged AA
-LYS
-ARG
solubility of AA?
-generally soluble in polar solvent & insoluble in organic solvents bcs contain polar group
-aliphatic AA soluble in organic solvents
melting point of AA
-high MP.
-have crystalline structure, highly charged, polar groups
AA absorbance of UV?
-aromatic AA absorbs UV light bcs of the conjugated double bonds in their R group
-proteins containing aromatic AA can be detected in colourless solution
why is AA considered amphoteric?
-considered amphoteric & called zwitterions bcs contain both +ve & -ve charges depending on the functional groups present in molecules
are AA affected by pH?
-they are affected by the pH of their surrounding environment and can become more positively / negatively charged due to the loss / gain of protons (H+)
- AA which make up proteins may be positive, negative, neutral or polar in nature n together give a protein its overall charge
how is peptide bond form
via condensation (elimination of water)
describe protein structure
-protein = biopolymers of amino acis
-vary in size
-divided into 2 classes : globular & fibrous
-f(x) : as enzymes / structure / transport / hormones etc
-conjugated proteins : those that posses a non protein moeity
what are the organizational levels in protein structure?
primary, secondary, super secondary, tertiary, quaternary
describe the primary structure of protein
the linear sequence of amino acids
describe the secondary structure of protein
local conformations of the
polypeptide chain formed as a result of the regular folding of
backbone atoms without participation of side chain groups
OR common folding patterns in protein structure OR
structure of the polypeptide chain resulting from a lot of H
bonding between neighboring peptide bonds.
describe the super secondary structure of protein
the arrangement of
secondary structures in a specific manner
describe the tertiary structure of protein
the 3-dimensional structure of
the protein formed as a result of interactions between amino
acids far away from each other in the primary sequence.
describe the quaternary structure of protein
the association or arrangement of
polypeptide chains (subunits) in an oligomeric protein.
describe the alpha helix of secondary structure
-A lot of hydrogen bonding between C=Oand
-N-H groups of neighboring peptide bonds
-Helix is Right Handed
-In a globular protein, on average there are ~11 amino acid
(aa) in one helix (can be up to 53aa).
describe the beta pleated sheet of secondary structure
-like the alpha helix, has many hydrogen bonds between
neighboring peptide bonds of the same or different chain.
-2 types; Parallel (chains in same direction) or Anti-parallel
(chain in different directions).
-Forms the -pleated sheet structure.
-In a globular protein there are 2-15 aa in this structure
(average = 6).
-the anti-parallel is more commonly found.
-there is a slight right-handed twist.
-usually found in the central core of globular proteins.
what is tertiary structure
-The 3-D structure of a particular protein /polypeptide.
-Some include the arrangement of secondary structures –
Super secondary structures or motifs
-On average 27% are in alpha helix and 23% beta structures
-But there are exceptions – there is 75-80% alpha helix in
Myoglobin and Hemoglobin
-Concanavalin A has only beta structures and no alpha
helices. It is a lectin protein that binds selectively to
carbohydrates (sugars, glycoproteins) found in plants, human
etc.
-Usually all hydrophobic aa are found in the protein interior
(val, leu, met)
-Polar and charged aa (glu, asp, his, lys) are found on the
surface of the proteins – meets water molecules
-Polar aa with no charge can be found inside or on the surface
of globular proteins (ser, asn, tyr)
-Usually globular proteins that are large (>200aa) have
DOMAINs – for example, domain A & B (ex. Theenzyme
glyceraldehyde 3-P DH, phosphoglycerate kinase)
what are the forces that influences protein structure?
-the peptide bond - its geometry
-the hydrogen bond
-hydrophobic interactions
-electrostatic interactions
-van der waals interactions
-disulphide bond
why does the geometry of peptide bond influences protein structure?
-The C=O, C-N atoms are planar.
-Degree of rotation depends on the size of the R groups
of the amino acids in the peptide bond
-It has a double bond characteristic.
-The structure and geometry of the peptide bond limits
the degree of rotation or conformational coiling that
can take place.
why does hydrophobic interactions influences protein structure?
-Occurs between side chains (R) that are hydrophobic in
nature
-Automatically/spontaneously avoids interaction with water
(more stable)
-Usually in the core of globular proteins
why does electrostatic interactions influences protein structure?
Occurs between side chains that are charged (ex: between –
COO- with –NH+ groups)
why does van der waals interactions (dipole-dipole) influences protein structure?
-Transient weak electrical attractions; electron clouds around
molecule fluctuate and forms temporary electric dipoles
-(ex: between two methyl groups, –CH3
)
why does disulphide bond influences protein structure?
Between side chains of cysteine residues linking together
polypeptide chains (same or different chains)
what is the quaternary structure?
-The fourth level of protein structure is concerned
with the interaction of 2 or more polypeptide
chains to associate to form a larger protein
molecule.
-Proteins with more than one polypeptide chain are
said to be oligomeric, and the individual chains are
called subunits or monomers of the oligomer.
-The geometry of the molecule is its quaternary
structure. Two subunits forms a dimer, three a
trimer, four a tetramer etc.
-The subunits (polypeptide chains) may be identical
(homogeneous) e.g. muscle creatine kinase is a
dimer of 2 identical subunits or non-identical e.g.
haemoglobin is a tetramer and contains 2 alpha + 2
beta subunits (heterogeneous).
what is the central dogma of protein?
-The central dogma of protein folding – “The primary structure determines the tertiary structure”
-Protein folding is spontaneous and probably starts with a local secondary (α-helix or β-structure) structure, which forms the nucleus/centre, around which the rest of the coil folds around.
-Recently proteins called molecular chaperone or chaperone proteins have been discovered (originally called heat shocked proteins) which help in protein folding – although exactly how not known.
-Probably protect certain exposed non-polar regions of developing polypeptide
what is the structure of fibrous protein
keratin and collagen
what is the globular protein
myoglobin and hemoglobin
what is fibrous protein
formed from parallel polypeptide chains held together by cross links. these form long, rope-like fibres, with high tensile strength and are generally insoluble in water
what is collagen
the main component of connective tissue such as ligaments, tendons, cartilage
what is keratin
the main component of hard structures such as hair, nails, claws and hooves
what is silk
forms spiders’ webs and silkworms cocoons
explain keratin in depth
-Main structural component of hair (also nail, skin and horns etc).
-Its basic unit is the a-helix polypeptide.
-Two a-helices are twisted together to form a coiled-coil.
-Two coiled-coils twist together to form a protofilament/protofibril.
-Protofilaments are arranged in 9+2 fashion to form a microfibril
-Many microfibrils are packed together form a macrofibril
-Many macrofibrils pack together to form a fiber (a single hair)
what are the characteristics of the a-keratin polypeptide
-Rich in hydrophobic amino acids that promote a-helix formation.
-Because R-groups are directed toward the outside of the helix,
keratins are highly insoluble in water.
-Lack helix-breaking proline residues.
-Structure of protofilaments is stabilized by intermolecular hydrogen bonds and disulfide bridges.
-The disulphide bonds can be reductively cleaved by
mercaptans (ex. Ethyl or methyl mercaptans).
-Hair so treated can be curled and set in a “permanent wave” by an oxidizing agent which reestablishes the disulphide bonds and the hair in a new conformation.
explain collagen in depth
-Most abundant protein in vertebrates – 25% of all protein in body
-Structural component of extracellular matrix, bone, teeth, tendons and blood vessels.
-Basic structural unit is a collagen polypeptide that
forms a left-handed helix
-No α-helix or β-pleated sheet structure possible
-The collagen molecule is a triple helix of three
collagen polypeptides – ~ 3000A long
what is the example of fibrous protein
-structural protein with tensile strength
-glycine-proline-alanine
-3 polypeptide chains, each in the shape of helix
-3rd amino acid is glycine (allows the coils to lie close to e/o)
-triple strands wind around each other forming fibres
-molecules within the fibre are joined by cross linkages
what is globular proteins
-usually have a spherical shape caused by tightly folded polypeptide chains
-the chains are usually folded so that hydrophobic groups are on the inside, while the hydrophilic groups are on the outside. this makes many globular proteins soluble in water
what is the examples of globular proteins
-transport proteins ( haemoglobin, myoglobin, those embedded in membranes)
-enzymes (lipase, DNA polymerase)
-hormones (oestrogen, insulin)
what is myoglobin
-Myoglobin structure was elucidated by John Kendrew & Max
Perutz (late 50s) using x-ray crystallography techniques.
-Small in size (153 amino acid residues) and crystallizes easily
– easy to study.
-Has the ability to carry oxygen because it has a prosthetic
group – haem (a tetrapyrrole – see below).
-Myoglobin is extremely compact.
-75% of polypeptide is in alpha helix – 8 helix segments, A, B, C, D, E, F, G & H.
what is hemoglobin
-Hemoglobin (or haemoglobin, frequently abbreviated as Hb), which is contained in red blood cells, serves as the oxygen carrier in blood.
-Hemoglobin also plays a major role in the transport of carbon
dioxide from the tissues back to the lungs.
-Each heme group contains an iron atom, and this is responsible for the binding of oxygen.
-Has 4 polypeptide chains; 2 α chains (141aa – minus D helix); 2 β chains (146aa – shortened H helix) chains (i.e. has 4 subunits; 574 aa; M.Wt. 63,500)
-Each subunit almost spherical.
-Each subunit can carry 1 oxygen molecule
-Thus the capacity to carry oxygen is high:
Hb4 + 4O2 → Hb4(O2)4 oxy-hemoglobin
-Fe2+ in the protohaem can bind to 6 atoms (like myoglobin).
-The β subunits has 8 helical segments (A,B,C ….H) – just like myoglobin. The α subunits have 7 helical segments (minus the D segment).
