4 Protein structure and function 2 Flashcards
Describe and explain Quarternary Structure
Most cellular proteins are oligomeric (>1 polypeptide chain)
- if an oligomer contains identical polypeptides, it is a homo-oligomer
- if an oligomer contains non-identical polypeptides, it is a hetero-oligomer
A protomer is the smallest distinct unit in a complex (e.g. haemoglobin is a dimer of aß protomer)
Describe inter-protein interactions
Subunits normally interact non-covalently (e.g. disulphide bonds)
Protein-protein interfaces:
- contain closely packed non-polar side chains and H-bonds (both main-chain and sidechain)
- are less hydrophilic than solvent-facing protein surfaces, but more hydrophilic than protein interiors
> lower interface-hydrophobicity is associated with transient oligomers
- certain residues found more frequently than at the surface (Arg, Trp, Tyr)
> buried salt-bridges increase oligomerisation specificity
- protein-protein interaction is a pattern-recognition process
Describe spatial arrangements in terms of proteins and polypeptide subunits
Polypeptide subunits in oligomers associate with a specific geometry (quarternary)
- in many cases, subunits are symmertrically arranged
- they can show rotational symmetry
Describe 2 reasons why proteins form complexes
- Efficiency/ease of construction
- can expand function
- easier repair (and control)
- can assemble at selected site (s)
- can reduce genome size (can use subints in more than one complex) - Oligomers can make better enzymes
- size increase can stabilise individual subints
- multiple binding/active sites
- subunits permit regulation and cooperativity
Describe the 3 main protein types (briefly)
- Fibrous
- normally display a single secondary structure
- e.g. a-keratin from wool + hair - Globular
- exhibit secondary structure elements inter-spaced with loops devoid of regular structure
- e.g. most cytoplasmic proteins - Membrane
- integral membrane proteins contain one or more hydrophobic domains that span the lipid bilayer
Describe globular proteins (using Haemoglobin as an example)
Haemoglobin: The oxygen carrier of blood
- 4 globin subunits (i.e. tetrameric protein)
- Adult form (HbA) contains two alpha (a) and two beta (ß) subunits: a2ß2
- Foetal form (HbF) contain two alpha (a) and two gamma (y) subunits: a2y2
The single haem group per subunit binds O2
- Contains protoporphyrin and iron (II) (Fe2+)
Describe the relationship between cooperativity and O2 affinity in haemoglobin
- deoxy-Hb aß dimers are held together by salt bridges and H-bonds
- these weaken when oxygen binds
- the two forms of T (taut) and R (relaxed) respectively
Describe haemoglobin, and how it works to bind with oxygen cooperatively
Haemoglobin must bind efficiently in the lungs and release oxygen to tissues
[can’t do this with constant oxygen affinity]
- Instead, Hb binds oxygen cooperatively
> binding of one oxygen makes the affinity at the other sites higher
> release of an oxygen reduces the affinity at the other sites
A sigmoidal surve is the signature of cooperativity
Describe how a structure of a protein can suggest the location where it functions
Secreted proteins, like Insulin
- contain an N-terminal leader or Signal peptide that interacts with the export machinery in the cell
- it can be exported + inserted into the membrane
- this signal peptide is recognised and directed to rough ER (different acidic/basic residue)
Membrane proteins with external N-termini also have signal peptides
- and they have hyrophobic regions (around 20aa) called transmembrane domains that span the membrane
Describe protein modifications that can occur to proteins
Proteins in eukaryotes often undergo covalent modification, usually following ribosomal synthesis (termed Post Translational Modification - PTM):
- these changes occur at specific sequences
- they can regulate protein activity:
> reversible changes include phosphorylation, methylation, and acylation
> irreversible changes can include cleavage
- they can regulate destination:
> e.g. lipidation and glycosylation
> the effect depends on the context (e.g. ubiquitination)
Describe glycosylation as a Post-translational modification that can be done to proteins
Glycosylation - attachment of carbohydrates
(common PTM)
- found particularly in extracellular + cell-surface proteins (protects against digestion)
- sugars attached to asparagine (N), serine (S), and threonine (T) residues
It can form two types of proteins:
- Glycoprotein: where carbohydrate is attached as a minor component
- Proteoglycan: where carbohydrate is attached as a major component
Glycosylation has a number of roles:
- aids protein folding and can influence targeting of newly synthesised protein to its destination
- glycosylation is involved in cell-to-cell recognition
Two types of glycosylation can occur:
- N-linked (occurs at N-X sequence) in residue
- O-linked (occurs at O-H of a -OH group)
Give an example of glycosylation in a protein
Glycosylation attachments determine blood group
ABO blood groups antigens are O-linked oligosaccharides on RBC proteins and lipids:
- all antigens share the O carbohydrate foundation
- A + B have an extra monosaccharide:
> A: N-acetylgalactaminose
> B: galactose
Describe hydroxylation as a Post-translational modification that can be done to proteins
Hydroxylations is the addition of an -OH in proline or lysine
- collagen is a fibrous protein of connective tissue
- collagen polypeptides consist of several hundred repeats of (Gly-Pro-OH-Pro)
Hydroxylated lysine residues are involved in collagen cross-linking
Give an example of glycosylation in a protein
e.g. Vitamin C
Vitamin C is required for Pro and Lys hydroxylation
- deficiency leads to scurvy (minor haemorrhages, fatigue, eventual heart failure)
- humans (and other primates) have lost the last enzyme within the ascorbic acid synthesis pathway
Describe genetic mutations, and how they can affect protein synthesis
Evolution has optimised proteins for their roles
- Mutations causing amino sequence changes are therefore often deleterious
NB
- if a protein is absent or dysfunctional, the other allele may produce sufficient protein for the effect to be a recessive trait (IF heterozygous)
List some effects of genetic mutations
- Disruption to a metabolic pathway
- Impairment or loss of defence against infection
- Protein aggregation
- Dysfunction of a regulatory protein or receptor
Describe disruption to a metabolic pathway as a side effect of genetic mutations
Disruption to a metabolic pathway
- loss of products(s) and accumulation of precursor
- e.g. The hereditary disease phenylketonuria, resulting from the loss of the phenylalanine hydroxylase enzyme
Describe impairment or loss of defence against infection as an effect of genetic mutations
Mutations within the innate or adaptive immune system
- can compromise their effectiveness/lead to inappropriate activation
Describe protein aggregation as an effect of genetic mutations
Protein aggregation
- can lead to disease such as Alzheimer’s and Huntingdon’s
Describe sickle cell anaemia as an example of genetic mutation
The mutation present is a single change in a base in DNA - a single change in an amino acid - which changes the B subunit in haemoglobin
- if 1 or the mutated Bs allele is present = asymptomatic
- if both mutated BsBs alleles are present = symptomatic
These mutated sickle haemoglobin molecules associate to form fibres under low O2 levels
These distort the erythrocytes into sickle shapes, which causes them to blocks capillary flow
Describe the relation of folding of proteins, and how mistakes can lead to disease
A protein’s function depends on it having a specific 3D structure
- this can be lost during a protein’s ‘lifecycle’
- problems can arise during protein folding (which has to occur rapidly in a highly concentrated environment)
Cells have developed extensive mechanisms to prevent or remove misfolded proteins, e.g.
- chaperones - to mediate folding
- proteasome (via ubiquitin) and lysosome (in autophagy) to mediate breakdown
Clues to a protein’s folded state may come from the exposure of hydrophobic residues
Describe protein misfolding disorders (PMDs)
Despite these control measures, proteins can fold into non-native ‘conformers’
- above a certain threshold, these act as seeds for aggregation
- leads to protein-misfolding disorders (50 examples, including Alzheimer’s, Parkinson’s, and Huntington’s diseases)
- they don’t just occur in the CNS (e.g. amyloidosis in liver, spleen and PNS)
- cytotoxic effects come from hydrophobic regions interacting with cellular components like lipids
- many of these disorders appear to be age-related (also genetic factors)
