Protein structure, function, & mutations Flashcards
Which part of the amino acid has a positive charge?
amino group
Which part of the amino acid has a negative charge?
carboxyl group
Which amino acids have a negative charge?
aspartic and glutamic acid
What amino acids have a positive charge?
arginine, lysine and histidine
Which amino acid has a phenol ring?
Tyrosine
How is the hydrophobic core formed during folding?
from non polar side chains
How are polar side chains exhibited on proteins after folding?
Project outwards to form hydrogen bonds with water
polar molecule meaning
molecule with partial positive and negative charges - charged
non-polar meaning
no charge
Describe the effect of urea on proteins
Urea can denature proteins by direct interaction
is the effect of urea on proteins reversible or irreversible?
reversible
Describe Van der Waals
short range weak electrical attraction and repulsion
Describe non-covalent interactions
electrostatic attraction between positively and negatively charged ions
Types of secondary structure
alpha helix, beta sheet, random coil
Which type of beta sheets has a continuous structure
anti-parallel
describe the characteristics of protein domains
compact, stable, hydrophobic core
Describe Green Fluorescent protein as a domain
very stable, formed from beta sheet structure
What are the functions of GFP
biological research, labels specific proteins
What is the PDZ domain
common structural domain found in signalling proteins of bacteria, yeast, animals etc
Where is PDZ abundant?
brain and synapses
What is the function of PDZ
mediate protein-protein interactions, and act as protein scaffolds
Where does the PDZ mainly act as a protein scaffold
post synaptically
Describe src tyrosine kinase
multi protein domain
What are SH2 and SH3
Src tyrosine domains
What is the function of SH2
adds specificity to kinase
What does SH2 bind to
phosphorylated tyrosine residues
What is the function of SH3
adds specificity to kinase
What does SH3 bind to
proline rich regions in proteins
Describe quaternary structure
proteins in a multi protein complex
What do common structures in proteins indicate?
Common functions
What do tubulin subunits form
microtubules
What are the different structures of microtubules?
filaments, sheets, rings and tubes
What do protein-protein interactions require?
complementary surfaces
What drives coiled coil packing
hydrophobic interactions
Examples of proteins as molecular motors
myosin on actin, kinesin on microtubules, polymerases on DNA
What type of amino acids are in membrane spanning domains
non-polar
Describe the the terminals in single pass type 1 membrane proteins
N terminus is extracellular, C terminus is intracellular
Which domain is largest in single pass type 1 membrane proteins
Extracellular domain
Describe the relationship of tumour necrosis factor with the membrane
tethered to membrane by lipid modifications
Examples of post-translational modifications
phosphorylation, glycosylation, palmitoylation, ubiquitination and acetylation
Where do post-translational modifications occur?
on reactive side chains
Describe lipid modifications
variety of lipophilic covalent attachments
Examples of lipid modifications
Acylation, Prenylation, GPI anchors
Describe acylation
intracellular addition of long chain fatty acids to cysteine residues
Describe prenylation
intracellular addition of farnesyl groups
Where do GPI anchors occur
extracellularly
Is acylation reversible?
YES
Describe palmitoylation
covalent attachment of fatty acids usually to cysteine
TRUE or FALSE, palmitoylation is irreversible
FALSE
Describe the bonding in a farnesyl anchor
thioether linkage between cysteine and prenyl groups
Describe the bonding in palmitoyl anchors
thioester linkage between cysteine and palmitic group
What is the general function of lipid anchors?
target and stabilise association of proteins with the membrane
What is the function of GTPase Ras
transmit signals within cells
What lipid modifications can be performed on ras?
farnesylation and palmitoylation
What is the function of lipid modifications on RAS
regulate cycling of Ras between membranes
What is the function of depalmitoylation of Ras
allows cycling back to endomembranes
What is the function of GTP
signalling molecule
what is synaptosomal-associated protein 25
t-SNARE protein
How is synaptosomal associated protein 25 modified
palmitoylation
what is the function of palmitoylation on synaptosomal associated protein 25
allows recycling between PM, endosomes and golgi
Where are disulphide bonds typically found?
secreted proteins like anti-bodies
Describe proteolytic processing
active hormone or enzyme is post-translationally cleaved
what is the outcome of proteolytic processing
mature functional molecule
What does glycosylation modify
extracellular proteins (generally)
What are the two types of glycosylation
N-linked and O-linked
What is the function of N-linked glycosylation
cellular protection
example of N-linked glycosylation
mucins in mucous
describe O-linked glycosylation
attachment via hydroxyl group of serine
What type of proteins does O-linked glycosylation modify?
intracellular proteins
Example of glycosylation patterns
blood groups
What is released from the kinase following protein phosphorylation
ADP
What amino acids does protein phosphorylation usually occur on
serine, threonine and tyrosine
What does protein phosphorylation do
converts a hydroxyl group into negatively charged phosphate groups
Where on proteins does phosphorylation occur?
binding surface
What does protein phosphorylation prevent/promote?
protein interactions
What type of change is phosphorylation to the protein
conformational change can alters nature of binding surface
Describe GTP binding proteins
heterotrimers
What is the function of GTP binding proteins
Bind guanine nucleotides GDP and GTP
Where are GTP binding proteins located
inner surface of plasma membrane and transmembrane receptors
Describe ubiquitination
attachment of new protein by addition of chain of ubiquitin to lysine residues
What are the types of ubiquitination
mono-ubiquitylation, multi-ubiquitylation, and poly-ubiquitylation
Which type of ubiquitination is the most common?
poly-ubiquitylation
What is the function of mono-ubiquitylation
histone regulation
what is the function of multi-ubiquitylation
endocytosis
what is the function of poly-ubiquitylation
proteasomal degradation, DNA repair, and further modification
What is the function of sorting siganls
direct target proteins to correct destination
What happens if a protein has NO sorting signal
remains in the cytosol
What is a signal peptidase?
protease that chops off signal peptide
What is the function of a signal peptidase
allows release of mature protein into ER lumen
What type of proteins can cross the ER
water soluble proteins
What happens to transmembrane proteins in the ER
partially cross the ER and become embedded in the membrane
When does protein folding occur
translocation
What influences protein folding
primary structure of the protein
What type of bonding stabilises protein folding
covalent bonding
What type of bonding is mainly involved with protein folding
non-covalent bonding
What is the function of disulphide bonds in protein folding
aid folding and stabilisation of final structure
What is the function of molecular chaperones?
assist protein folding
What do molecular chaperones bind to
misfolded exposed hydrophobic regions
How do heat shock proteins assist protein folding?
hydrolyse ATP
When is protein misfolding common
at high temperatures
What is the difference between Hsp70 and Hsp60
Hsp60 acts on fully synthesised proteins, Hsp70 works during protein synthesis
How does Hsp70 work?
binds to regions of hydrophobic amino acids, applies mechanical force to aid correct folding
How does Hsp60 work?
Acts as an isolation chamber, applies mechanical force
Describe the Hsp60 chamber
lining that prevents protein binding
What can misfolding lead to
aggregation
Where do protein aggregations accumulate
extracellular matrix
Diseases associated with protein aggregations
Alzheimer’s and prion diseases
What is the effect of aggregation on neurons
neurons cant regenerate, so detrimental to brain function
Example of stable beta sheet aggregates
amyloid fibrils
what causes amyloid fibrils to aggregate
cross linking
What is the function of amyloid fibrils
store peptide hormones in secretory granules
Give examples of prion diseases
Creutzfeldt-jakob disease, bovine spongiform encephalopathy
Where are prion proteins located?
outside of PM, mainly in neurons
What is the function of prion proteins?
maintaining myelination of peripheral nervous system
What is different about abnormal prion proteins?
resist protease action, so aren’t degraded
Where does protein destruction occur?
proteasome
What proteins are targeted for destruction?
old and damaged, incorrectly assembled, proteins whose concentrations change depending on cell state
How are proteins marked for destruction?
covalent attachment of ubiquitin
What binds to ubiquitylated proteins
proteasome cap
What is the effect of proteases on proteins targeted for destruction?
cleave the protein into short peptides
What is ubiquitination mediated by?
ubiquitin conjugating enzymes and ubiquitin ligases (E2 & E3)
What is the function of ubiquitin ligases (E3)?
bind to degradation signals on proteins
What does ubiquitin ligases E3 enable ubiquitin conjugating enzymes E2 to do
Enables E2 to link a polyubiquitin chain to lysine on target protein
What type of DNA is conserved? (introns or exons)
Exons
Mutations in which cell type are inherited?
Germline
What type of mutations are dominant
gain of function
What type of mutations are recessive
loss of function
Describe an amorphic mutation
complete loss of function
Describe hypo-morphic mutations
reduction of function
Describe a hyper morphic mutation
increase in protein function
Describe an antimorphic mutation
Protein interferes with function of wild type protein
Describe a neo morphic mutation
acquisition of a new function or ectopic expression or function
Describe a synonymous mutation
does not disturb the protein sequence
Describe a non-synonymous mutation
structural change of protein
What is an indel
insertions of deletions of sequence
What is the effect of an indel
adds residues into protein sequences
What are the types of mutation (non-sense) etc
transition, transversion, mis-sense, non-sense, neutral, silent, frameshift
Describe a transition mutation
change of base from purine to purine
Describe a transversion mutation
substitution of purine to pyrimidine
Describe a missense mutation
change in amino acid
describe a non-sense mutation
change to code for a stop codon
What is the effect of a non-sense mutation
premature termination of translocation, incomplete polypeptide
What is a neutral mutation
changes from one AA to another with non functional effect
What does wobble base pairing cause
spontaneous mutation
describe deamination
chemical change - cytosine is deaminated into uracil
describe depurination
chemical change - adenine or guanine is lost from DNA backbone
What type of mutations do X-rays and gamma rays induce?
point mutations
Why does ionising radiation (x-rays) induce point mutations
high energy
What is the effect of UV on DNA
replication problems
Why does UV cause DNA replication problems
low energy so causes photochemical changes in DNA
What are the types of chemical induced mutations
base analogues, base modifiers, intercalating reagents
Example of a base analogue
5-bromouracil
What type of mutations do base analogues cause
transition mutations
What is the effect of base modifiers
chemically modify structure of bases
what is the effect of intercalating agents
insert themselves in-between bases in DNA
what type of mutations do base modifiers cause
transition mutations
What type of mutations do intercalating agents cause?
frameshift or deletion
What causes sickle cell anaemia?
recessive mutation
what mutation causes sickle cell anaemia
single point missense mutation at residue 6 in the beta chain
how can sickle cell anaemia mutation be identified?
electrophoresis
What is an advantage of being a heterozygous carrier for malaria
tolerance to malaria
what is the function of the cystic fibrosis transmembrane conductance regulator
transport chloride, regulate ion concentration in extracellular fluid
where are mutations in GTPase Ras normally found
cancer cells
What is the effect of mutations on ras
impairs the intrinsic GTPase activity
What are the types of chromosomal mutations
deletion, inversion, duplication, translocation
Describe the Philadelphia chromsome
translocation of a piece of chromosome 22 to chromosome 9 causing fusion of 2 genes
What is the function of lipid modifications
help to bind proteins to membranes
