proteins Flashcards
what are proteins
- polymers
- organic molecules containing C, H, O, N and sometimes S
- amino acids (monomers) join together via peptide bonds to form a polypeptide chain
- 20 different amino acids
describe the structure of amino acids
each amino acid consists of a central carbon atom (alpha carbon), bonded to a H atom, a carboxyl group (COOH), an amino group (NH2), as a specific side chain (R group)
when dissolved in aq env within the cell,
COOH -> COO-
NH2 -> NH3+
What are the properties of this AA
R group properties:
- contains only O & N
- uncharged
- hydrophilic
neutral and polar
O and N are more electronegative, can form H bond with H2O, so the R group is polar (thus hydrophilic)
cysteine contains Sulfur too
if a R group is non-polar, what does that imply?
hydrophobic, cannot form H bonds with H2O, uncharged, only contain C & H atoms
hydrOphObic = nOn pOlar
if R group is polar, what does that imply?
hydrophilic, can form H bonds with H2O due to electronegativity
(R group is either charged or contains N & O atoms if neutral)
hydrophiLic = poLar
properties of amino acids (color, state, solubility)
colorless, crystalline solids
generally soluble in water (even those with hydrophobic R groups as only the R group is hydrophobic, overall the whole AA is polar)
dissolves in water to form ions/ gets ionized
(amino group picks up H+ to form —NH3+,
carboxyl group loses H+ to form —COO-)
insoluble in organic solvents
are amino acids acidic or basic, how does this affect its function
amphoteric in nature (amino group basic, carboxylic group acidic)
ionized AA can act as pH buffers (solutions that can resist small changes in pH) because —COO- groups can accept small amounts of H+ added into solution, while —NH3+ groups can donate H+ to neutralise small amounts of OH- added
what are zwitterions
when both amino and carboxyl groups are ionised in solution, AA has charged groups of opposite polarities, exists as zwitterion
no net charge
amino acid exists in zwitterion form at isoelectric point (certain pH, varies from AA to AA based on R group. eg neutral R groups have an isoelectric point close to pH7)
what are peptide bonds
covalent bonds
formed via condensation reaction (removal of 1 H2O between 2AA)
broken via hydrolysis reaction (addition of 1 H2O)
do polypeptides show directionality?
yes, through a free amiNo end, N-terminus (start) and a free Carboxyl end, C-terminus (end)
what is the primary structure?
defined as the type, number, and sequence of AAs joined by PEPTIDE bonds that make up the polypeptide
determines how polypeptide is folded into a protein => determines 3D shape of protein => determines property and function of protein
each type of protein has a specific primary structure
are proteins and polypeptides the same?
no
polypeptide = unfolded chain of AA
protein = folded
what is the secondary structure? (extent of folding, bonds, 2 common types)
localised folds and coils within a polypeptide chain (only a segment of polypeptide chain is folded)
result of formation of intrachain HYDROGEN bonds (between OXYGEN OF CARBONYL GROUP C=O and HYDROGEN ATTACHED TO AMINO GROUP N-H) at regular intervals along polypeptide chain between AAs that are close together
hydrogen bonds are weak individually but collectively stabilise the secondary structure
2 types commonly seen in proteins : alpha helix, beta pleated sheets
alpha helix (structure, bonds, aa per turn, r group projected where)
polypeptide backbone forms right-handed coil along long axis, with H bonds aligned parallel to the x-axis, all R groups projected outwards
H bonds between oxygen of carbonyl group C=O of an AA residue (n) and the hydrogen attached to the amino group (N-H) of another AA residue (n+4)
eg 10th AA bonds with 10+4=14th AA
3.6 amino acid residues per complete turn of alpha helix
eg fibrous protein keratin and globular protein haemoglobin
beta pleated sheet (structure, bonds, r group projected where, 2 types)
polypeptide is folded into 2 or more adjacent regions (beta strands), held by multiple INTRACHAIN (between adjacent beta strands) H bonds (oxygen of carbonyl group C=O and hydrogen of amino group N-H)
R groups are projected above and below the beta-pleated sheet, so beta pleated sheets tend to be found in interior of proteins if R groups are hydrophobic (shield R groups from aqueous env)
parallel : adjacent beta strand runs in same direction
antiparallel : adjacent beta strand runs in opposite direction
what is the tertiary structure (extent of folding, shape, bonds, solubility)
extensive folding of polypeptide chain into a precise, compact, and globular 3D shape
formation of H bonds, ionic bonds, disulfide bonds, and hydrophobic interactions between R groups of AAs that are far away (bring them together into localised regions to form functional parts of protein eg active/binding sites)
hydrophilic R groups on exterior of protein, hydrophobic R groups in interior of protein, so protein is soluble in aq env
what is the quarternary structure (how many polypeptide chains, bonds, which proteins)
association of 2 or more polypeptide chains
held together by H bonds, ionic bonds, disulphide bonds, and hydrophobic interactions between the R GROUPS OF AAs on adjacent polypeptides
eg keratin, collagen, haemoglobin
what are ionic bonds
charged R group in one part of polypeptide attracts oppositely charged R group in another part of chain
electrostatic attraction between oppositely charged R groups
non covalent
what are hydrogen bonds
when H atom is covalently bonded to electronegative atom (eg O or N), O or N tends to “pull” electrons to itself, so H atom has a slightly positive charge
thus O & N atom has a slight negative charge + contain lone pair(s) of electrons
attraction between these positive H and negative O/N atoms results in hydrogen bonds
non covalent
what are hydrophobic interactions
in aq env, non-polar R groups tend to cluster together
when polypeptide chain is exposed to water, will fold such that hydrophobic R groups are in interior (shielded), hydrophilic R groups are on exterior
non covalent, major driving force in protein folding
