Proteins Flashcards
acidic basic and polar uncharged and non polar egs
glutamic acid aspartic acid
lysine histidine arginine
tyrosine
glycine alanine phenylalanine
importance of AA chirality
(not glycine)
amino acids make up proteins, proteins specific 3D structure depends on primary structure, sequence of amino acids. Amino acids make up enzymes, with specific binding sites, such that only one enantiomer of the reagent is able to bind to the active site
zwitterion definition
molecule that contains both a region of positive charge and negative charge
solubility of AA in low and high pH
low and high pH : protonated and deprotonated, increased hydrogen bonding with water, more soluble
physiological pH of 7.3 –> isoelectric point where 99.9% of amino acids are zwitterions
ionic bonding with other zwitterions increases, diminished interactions with water, less soluble
at physiological pH, acidic AA are deprotonated (-1) and basic AA are protonated (+1)
peptide bond definition
covalent bond formed between the carbonyl group C atom of 1 amino acid and amino group N atom of another amino acid, condensation reaction
peptide bonds, AA residues
characteristics of peptides
rigid, unrotatable peptide bond
flexible bonds between carbonyl C and alpha carbon, amide N and alpha carbon –> peptides are flexible
disulphide bonds structure
oxidisation of sulphydryl groups on 2 cysteine molecules, forming disulphide bonds
primary structure significance of proteins
sequence of amino acids determines secondary tertiary quaternary structure, determines final 3D structure, which determines function
changes in amino acid sequence could lead to small inter-species mutation(insulin across animals) or disease causing mutations (sickle cell anaemia)
function of disulphide bonds
stabilises protein conformation
define secondary structure
repeating patterns formed due to folding of AA close to each other, hydrogen bonding between the carbonyl group and amide group in the protein backbone
alpha helix structure and function
coils formed due to hydrogen bonding between carbonyl O and amide group H 4 AA residues away
often used as transmembrane channel proteins
no proline (no sharp turns possible) and no glycine (too flexible)
describe beta pleated sheets
run parallel or anti parallel, give proteins rigid cores
tertiary structure defition
3D structure of protein due to interactions between amino acid side groups especially for amino acids further apart from each other
quaternary structure
arrangement of 2 or more protein subunits and contacts
hydrophobic interactions
water and hydrophobic effect drives the folding of the protein in aq env
to increase entropy, more energetically favourable to decrease the contact area between the water molecules and non polar amino acid side chains, causing non polar side chains to be found inside the protein molecule, polar on the outside
simple protein definition
a protein made up of only amino acids and no other chemical components
conjugate protein definition
protein made of other chemical components in addition to amino acids
prosthetic group definition
non AA group of conjugated proteins
describe protein families
proteins with the same evolutionary origin that have a similar sequence of amino acids and similar functions
denatured proteins
denaturation: protein’s conformation is altered or destroyed, unable to perform normal function
changes proteins secondary tertiary quaternary structures, does not alter primary structure
native protein
protein that has the correct conformation (folding and stabilisation of 3D shape) and is functional
what causes denaturation
- apply heat (breaks H bonds)
- acids bases salts (salt bridges and H bonds)
- chemicals eg reducing agents (break disulphide bonds)
- detergents (open up hydrophobic regions)
- heavy metals (sulphydryl groups)
types of protein function
- transport (haemoglobin)
- protection (antibodies)
- movement (actin)
- storage (ferritin)
- regulatory proteins (insulin)
- structural proteins (collagen)
- enzymes (amylase)
- others (elastic proteins)
fibrous vs globular
more structural eg keratin
more functional eg enzymes, often contain specific 3D binding site
proteins and ligands
ligands: ions, small molecules, macromolecules
bind to protein in specific ways, more than 1 ligand can bind simultaneously
e.g. antibodies and antigens
enzyme function
biological catalysts that increase rate of metabolic reactions by decreasing activation energy without itself being altered in the reaction
enzyme activity
series of catalysed reactions are called a metabolic pathway,
activity must be regulated through phosphorylation (adding and removing P)
enzyme classes
polymerases - polymerisation
kinases - adding phosphate
phosphotases - removing phosphate
ligase - formation of bonds
protease - hydrolyse peptide bonds
oxidoreductase - redox
redox partial shift
eg polar covalent bonds, one electron has stronger electron affinity
C-O, C has less electrons, oxidised
C-H, C has more electrons, reduced
redox and enzymes
sometimes involves transfer of both H+ and electrons (eg reduction of NAD+ to NADH)
dehydrogenase/oxidoreductase
