Tutorial 1 proteins lecture 3 - 6 Flashcards
what are the common functions of proteins?
- catalyze reactions
- structure - collagen
- transport molecules - hemoglobin and myoglobin
- immune protection - antibodies
- replicate dna / rna - polymerase
- cell signal - insulin
label each circled part of amino acid
H2N - amino group
R - sidechain
COOH - carboxyl group
non polar uncharged
amino acid
Alanine
COO-
CH
H3N+
CH3
polar uncharged
amino acid
Asparagine
COO- CH H3N+ CH2 C H2N O
polar uncharged
amino acid
Serine
COO- CH H3N+ CH2 OH
polar -‘ve charge
amino acid
Glutamic acid
COO- CH H3N+ CH2 CH2 COO-
define each of the levels of protein structure
primary secondary super-secondary domain tertiary quaternary
define primary protein structure
amino acid sequence
define secondary protein structure
3D arrangement of a protein chain over a short region.
a-helices, b sheets / strands
define super-secondary protein structure
groups of secondary structures
define domain protein structure
super-secondary structure with a specific function
define tertiary protein structure
3D structure of a complete protein chain
define quaternary protein structure
interchain packing and structure for a protein that contains multiple protein chains
what type of bonds stabilise primary structure?
Peptide bond - covalent
what type of bonds stabilise secondary structure?
hydrogen bonding stabilises a-helices & b-structure
what types of bonds stabilise tertiary structure?
hydrogen bonding,
hydrophobic interactions,
disulfide bridges (covalent),
salt bridges / ionic bonds
what types of bonds stabilise quaternary structure?
same as tertiary
hydrogen bonding,
hydrophobic interactions,
disulfide bridges (covalent),
salt bridges / ionic bonds
describe the difference between a parallel and an antiparallel beta sheet
parallel
- 2 strands running in same direction (N - C)
- H bonds in zig zag
antiparallel
- 2 strands run in opposite direction (N - C)
- H bonds vertical
describe the properties of glycine and proline that make them suitable for turns, but unfavoured in alpha helices
helix breakers
small side chains make glycine very flexible. decrease steric hinderance.
proline is rigid, built in turn because of the bonding between the R group and the amino group.
describe in general terms , the process by which an unfolded polypeptide chain, folds into its native (normal) conformation (shape)
- formation of short 2° structure segments
- nucleic come together growing cooperatively to form a domain
- domains come together (but 3° structure still partly disordered
- small conformational adjustments to give compact native structure
what are the bonds that are broken when a protein becomes unfolded?
all except covalent bonds
- H bonds
- ionic interactions
- hydrophobic interactions
what effect does unfolded protein have on the function?
destroys function
unfolded no longer has the 3D shape to carry out function
the function is determined by shape
with an example describe how misfolding of a proteincan lead to a disease
cystic fibrosis
prion diseases - 1 misfold prion introduce to system and cause other proteins to misfold. this results in proteins aggregating together forming amyloid plaque eg kuru, mad cow (BSC). physically ingested.
alzheimers disease - misfold proteins aggregate to form plaque
what is a post-translational modification (PTM)
a chemical group that is added to an amino acid residue after translation has occurred
chemical groups are added covalently
eg phosphorylation, glycosylation, methylation, lipidation, acetylation
what is phosphorylation?
the addition of a phosphate group to an amino acid
how (in structure-function terms) does phosphorylation affect protein function?
activate / deactivate proteins
adds large -‘ve charge can cause conformational change within protein that will affect function of protein
