Lecture 5 - Proteins Flashcards
what are polymeric proteins?
chain like molecule made of monomers
what are the 8 types of protein?
structural, storage, O2 transport, metabolism, cellular response, movement, protection, catalysis
what are proteinogenic amino acids?
the 20 standard amino acids, each have an L and d form
what form do most amino acids in the body exist in ?
Zwitterionic form
what are essential amino acids?
Amino acids that the body cant make which must be gained through diet
which amino acids are polar?
serine, threonine, asparagine, glutamine, cysteine, tyrosine
which amino acids are acidic?
glutamic acid and aspartic acid
which amino acids are basic ?
histidine, arginine and lysine
which amino acids are non-polar ?
glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan and proline
Describe the peptide backbone formation of a protein
rigid and planar bonds which initially form a partial double bond - usually trans and rotation at chiral is limited with bulky R groups + space availability
Describe the primary structure
Amino acid sequence from N-terminus to C-terminus in which a genetic mutation can result in primary structure being changed therefore change in protein function
Describe the alpha helix
flexible, coiled, proline is a helix breaker, stabilised by extensive intra chain hydrogen bonding, 3.6 amino acids per chain, R groups project outwards to avoid sterile hindrance, distance between amino acids = 1.5 A (with circle on top)
Describe the beta pleated sheet
5-10 amino acids - parallel to antiparallel or mixed, strong + resilient, distance between amino acids = 3.5 A (with circle on top), frequently a part of enzyme active sites
what is an amphipathic alpha helix?
proteins that have hydrophilic and hydrophobic parts which are important in helix formation
what are the 6 super secondary structures?
Beta hairpin motif, helix-loop-helix, greek key, coiled coil, zinc finger and beta barrel
Describe the beta hairpin
two adjacent antiparallel beta strands joined by a hairpin loop
Describe helix loop helix
two alpha helices joined by a loop
Describe the greek key motif
three antiparallel beta strands connected by hairpins
4th adjacent to the first and connected to first via longer loop
Describe the coiled coil
repeats of 7 residues which results in an amphipathic alpha helices with a strip of hydrophobic residues which coil around similar helices
Describe the zinc finger motif
two antiparallel beta sheets followed by an alpha helix stabilised by a zinc ion
describe the beta barrel motif and the 3 types
multiple antiparallel beta sheets that twist to form a closed structure
- up to down - 8 antiparallel beta sheets connected by hairpin loops
- jellyroll barrel - 8 beta strands arranged as 2 four stranded antiparallel beta sheets wrapped around a hydrophobic interface
- pore forming- 2 4 stranded antiparallel sheets with polar side chains facing inwards to create a channel for hydrophilic molecules
Describe a domain
polypeptide chain that folds independently into a stable structure with its own hydrophobic core
proteins can have several different domains- each one associated with a specific function
Describe fibrous proteins
insoluble in water, important in providing support and strength
Describe collagen
superhelices of gly-rich triple alpha helices that assemble into fibrils, main protein in connective tissues,, strong and elastic
can produce less due to connective tissue disorder forming hyper-flexibility of joints and fragile skin
Describe alpha keratins
coiled coils of two alpha helices that assemble into larger fibres, strong and inextensible, insoluble and chemically inert, disulphide bridges across coiled coils
Describe beta keratins
fibroin found in the silk of spider webs - layers of antiparallel beta sheets rich in ala and glycolic residues, small side chains interdigitate allowing close packing
Describe globular proteins
mix of irregular folded secondary elements to form a compact 3D shape, soluble in water with inner hydrophobic core, transported easily in body fluids
Describe haemoglobin
tetramer - 4 polypeptide chains and 4 ahem groups +myoglobin, transports O2, carbon monoxide poisoning as CO binds more easily
Describe sickle cell disease
caused by a single gene defect in beta globing gene changing primary structure of protein, spleen produces red blood cells and filters misshaped cells so because there are lots of misshaped cells with this genetic disorder the spleen has to work harder therefore causing damage
- being a carrier makes you susceptible to malaria
Describe immunoglobulins
Y shaped proteins that identify and combat invading foreign organisms
4 chains lined by a disulphide bridge - 2 heavy chains and 2 short chains which can have a variable structure
Describe denaturation
proteins lose structure in native state due to changes in environment
Describe PH denaturation
change in PH changes interaction with bonds therefore adding pressure and causing bond breakage
Describe heat denaturation
increase in vibrations which breaks hydrogen bonds and render proteins insoluble in water,
what is pyrexia?
ancient anti viral defence mechanism where some bacteria can survive in extreme environments e.g. thermos aquatics lives in hot springs and produces DNA polymerase at these high temperatures
Describe denaturation with solvents
forms new hydrogen bond with R chains therefore breaks intra and inter chain bonds and protein unfolds
