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
what are disulfide bonds
strong covalent bond
only formed between the R groups of the AA cysteine (contains S)
2 of cysteine’s R group = S-S
not easily broken by heat/changes in pH
what does denaturing of proteins refer to, and what causes it?
denaturation refers to the loss of specific 3D conformation of a protein due to unfolding of polypeptide, resulting in loss of biological activity or function of protein. does not affect primary structure
caused by :
- changes in temp
- changes in pH
- changes in salt concentration
- presence of reducing agents
- places in organic solvents instead of aq env
effect of temperature on proteins
disrupts H bonds, ionic bonds, and hydrophobic interactions between R groups
heat increases KE of protein, molecule vibrates so rapidly and violently that bonds are disrupted
effect of pH on protein
disrupt the H bonds and ionic bonds between R groups
addition of H+ / OH- may result in neutralisation of charged R groups, or affect electrostatic attractions involved in H bonds and ionic bonds
effect of metal salts on proteins
heavy metal salts are charged, so disrupt ionic bonds between AAs
effect of reducing agents on proteins
disrupt disulfide bonds, as disulfide bonds are formed by oxidation of sulfhydryl groups on cysteine, so RA can act on bonds to break it
effect of organic solvents on proteins
changes the way a polypeptide folds (folding is largely dependent on hydrophobic interactions)
what is haemoglobin (where, function, shape, structure, subunits, sickle cell anaemia)
found in RBCs, oxygen carrying protein (metabolic function)
globular protein with a quarternary structure
- consists of 4 polypeptide chains forming 4 subunits (globin)
- 2 alpha chains/globins , 2 beta chains/globins (each chain has a tertiary globular structure)
each polypeptide forms localised coils of alpha helices (secondary structure). polypeptide is also extensively folded into a tertiary structure.
each subunit contains a NON-PROTEIN HAEM GROUP (reversible binds to O2), which consists of a porphyrin ring (hydrophobic, interior of subunit) with a Fe2+ ion
4 haem group = 4 O2 molecules per haemoglobin
when 1 O2 molecules bonds to 1 of the haem groups, causes a SLIGHT CONFORMATION CHANGE in haemoglobin, which INCREASES AFFINITY of the other subunits to oxygen (COOPERATIVITY)
mutation that causes a change in AA sequence (thus pri structure) of beta chains results in sickle cell anaemia
most important level of organisation in terms of function for haemoglobin?
tertiary
- globular shape
- soluble in water
- contains clefts for haem groups to embedded
haemoglobin structure to function (solubility)
haemoglobin is a globular protein with hydrophilic R groups exposed on exterior and hydrophobic R groups shielded in interior
soluble in water, allows haemoglobin to react with O2 in aqueous environment in cytoplasm of RBC
haemoglobin structure to function (size, extent of folding)
haemoglobin is extensively folded and compact
allows more haemoglobin to be found in the cytoplasm of the RBCs, more efficient O2 transport
haemoglobin structure to function (clefts)
haemoglobin has a specific 3D conformation with clefts lined with hydrophobic R groups found in interior
allows a haem group to be embedded in each subunit
haemoglobin structure to function (haem group)
haemoglobin contains 4 haem groups with Fe2+
Fe2+ in haem group allows oxygen bonding
each haemoglobin is able to bind to 4 O2 molecules
haemoglobin structure to function (affinity)
haemoglobin consist of 4 subunits, each with a haem group
allows cooperativity after O2 binding to 1 subunit to increase affinity of O2 to other subunits
→ curve has sigmoidal shape
what is collagen (function, shape, structure, subunits)
structural protein, support function, has high tensile strength
found in connective tissues (ligaments, cartilage, tendons, bone, teeth), contributes to skin strength and elasticity. important component of extracellular matrix
fibrous protein, quarternary structure, long and strand like
consists of recurring subunits known as tropocollagen
primary structure of collagen
polypeptide chains found in collagen exhibit a repeating sequence of glycine-X-Y, X is usually proline, Y is usually hydroxyproline (modified AA, proline + OH) or hydroxylysine
every 3rd AA in the polypeptide is glycine (most abundant), AA sequence also rich in proline
secondary structure of collagen
each polypeptide found in collagen forms a KINKED helix (not alpha helix)
quarternary structure of tropocollagen
each tropocollagen subunit is made of up 3 polypeptides wound around each other tightly, forming a triple helix
3 polypeptides form interchain hydrogen bonds between OXYGEN OF THE CARBONYL GROUP (C=O) and HYDROGEN OF THE AMINO GROUP (N-H) of AA residues found in adjacent polypeptides
glycine, smallest AA, in interior of triple helix
what is collagen fibril
covalent bonds/cross linkages are formed between the R groups of lysine residues found on adjacent parallel tropocollagens , forming a collagen fibril when many molecules of tropocollagen are held side by side
tropocollagen molecules in parallel chains are arranged in staggered arrangement to eliminate lines of weaknesses in collagen fibril
what is collagen fibre
collagen fibrils are further aggregated (bundled together) outside the cell to form collagen fibres.
collagen structure to function (solubility)
collagen is a fibrous protein in which hydrophobic R groups present are not shielded in the interior but point outward
insoluble in water to allow collagen to perform structural support function
collagen structure to function (sequence)
in collagen, every 3rd amino acid is glycine
allows triple helix to be coiled more tightly, increase stability of tropocollagen, increase tensile strength of collagen
collagen structure to function (shape)
each polypeptide forms a kinked helix that is long and strand like
more H bonds can be formed between the 3 polypeptides along their length, increase stability of tropocollagen, increase tensile strength of collagen
collagen structure to function (bonds)
covalent cross linkages between tropocollagens
allows tropocollagens to form collagen fibril, increase stability of collagen fibril, increase tensile strength of collagen
collagen structure to function (arrangement)
staggered arrangement of tropocollagens in a collagen fibril
eliminates lines of weaknesses in collagen fibril, increase stability of collagen fibril, increase tensile strength of collagen
collagen structure to function (bundling)
aggregation of collagen fibrils into collagen fibre
increase tensile strength of collagen
most important level of organisation in terms of function for collagen
secondary
- long strand-like shape as a fibrous protein
- insoluble in water
- structural support function
portion of G-protein linked receptor that is on surface of cell is the ?
extracellular domain of protein
forms a ligand (signalling molecule eg glucagon) binding site, folded into specific 3D conformation that is complementary to shape of ligand
portion of the G protein linked receptor that is within the cell surface membrane is the?
transmembrane domain
consists of 7 alpha helices that span the width of the membrane
amino acid residues in the 7 transmembrane alpha helices contain hydrophobic R groups that are projected outwards, allowing the protein to interact with the hydrophobic fatty acid tails of the phospholipids in the membrane
portion of the G protein linked receptor that is in the cytoplasm is the?
intracellular domain
forms a binding site for G protein
folded into a specific 3D conformation that is complementary in shape to the G protein
G protein is activated upon ligand binding to receptor, and will then transmit signal within cell
