Protein And Protein Structure

Question 1

What are some functions of proteins?

Answer 1

-enzymes
-storage
-structural
-transport
-defence (antibodies)
-regulatory
-receptors
-contractile

Question 2

How many proteins are roughly in humans

Answer 2

100,000

Question 3

what shapes can proteins appear in?

Answer 3

-globular
-fibrous (elongated)
-membrane spanning (need to be hydrophobic)

Question 4

what are the different protein structures?

Answer 4

-primary - sequence of amino acids
-secondary - local regions formed into regular structures
-tertiary - folding of polypeptide into 3D conformation
-quaternary - multiple subunits

Question 5

describe amino acids

Answer 5

-chiral molecules
-only 20 naturally occurring aa
-only L forms of the aa are used by cells (left-handed)
-consist of tetrahedral alpha carbon w amine and carboxyl groups and organic side chain

Question 6

what is the ionisation state at different pHs?

Answer 6

-low pH -amide group is +ve
-high pH - carboxyl group is -ve
-neutral pH - both groups are charged

Question 7

what are some drivers of the shape of proteins?

Answer 7

-amino acid sequence
-chaperones
-water (will cause hydrophilic R group amino acids to be on outside)
-disulfide bonds
-H bonds
-flexibility

Question 8

what kind of buffer are aa?

Answer 8

weak buffer

Question 9

What is the isoelectric point?

Answer 9

-the pH at which the molecule is electrically neutral
-avg of pK values on both side of neutral

Question 10

describe peptide bonds

Answer 10

-rigid
-planar
-stable and covalent
-physiologically broken by proteases
-avg protein has 300 peptide bonds

Question 11

what is post-translational modification?

Answer 11

-enzyme mediated modification of proteins after synthesis
-this changes properties of proteins

Question 12

what are examples of post-translational modifications?

Answer 12

-glycosylation - addition of carb
-cleavage
-lipid addition
-oxidation, carboxylation, acetylation
-phosphorylation

Question 13

what does phosphorylation of proteins do?

Answer 13

• changes shape
  -changes charge
  -activates protein
  -switches kinases on
  -switched phosphatases off

Question 14

what does side chain (R group) affect?

Answer 14

-size
-charge
-shape
-reactivity
-H bonding
-Determines protein shape & function

Question 15

how can aa be classified chemically?

Answer 15

-polar/non-polar
-acidic/basic

Question 16

how can aa be classified structurally?

Answer 16

-aliphatic/aromatic
-sulphur containing
-charged

Question 17

how can aa be classified structurally?

Answer 17

-aliphatic/aromatic
-sulphur containing
-charged

Question 18

describe dentin phosphoryns

Answer 18

-made up of aspartic acid (35-45%) and serine (40-55%)
-highly negatively charge and acidic
-regulate bio-mineralisation
-binds to collagen I and Ca2+

Question 19

how does aa structure relate to function?

Answer 19

Overall conformation gives protein its function
Binding specificity, flexibility, solubility, degradability
Position of amino acid side chains in 3D space

Question 20

what are the different protein structures?

Answer 20

-primary - linear sequence of amino acids
-secondary - local regions formed into regular structures
-tertiary - folding of polypeptide into 3D conformation
-quaternary - multiple subunits

Question 21

describe Secondary protein structure

Answer 21

Polypeptide chains can fold into regular structures
α helix
β pleated sheet
Structural motifs e.g. turns
Non regular coils & loops- more flexible e.g. hinges

Question 22

Describe the alpha helix

Answer 22

-tightly coiled rod
-globular, DNA binding, membrane spanning proteins
-H bonds bw NH and CO groups
-some amino acids form alpha helices more than other e.g. met, ala, glu, lys
-major structural motif for haemoglobin
-two or more alpha helices can entwine to form a cable e.g. keratin

Question 23

describe b pleated sheets

Answer 23

-H bonds form bw two parts of the protein that can be far apart
-H bonds are optimal when pleated
-can occur in same or opposite direction

Question 24

describe Haemoglobin

Answer 24

α helices: major structural motif
Two or more α helices can entwine to form a cable eg keratin

Question 25

describe b turns

Answer 25

-non regular
-4 amino acids
-hairpin loop
-H bonds formed
-v stable

Question 26

describe structural motifs

Answer 26

Grouping of a few secondary structural elements e.g. helix-turn-helix
Can occur in several proteins and carries out same function

Question 27

how are zinc finger proteins an example of structural motifs?

Answer 27

α helix, antiparallel β pleated sheet, Zinc coordinated by two His & two Cys residues
Mediates DNA/RNA binding

Question 28

describe the tertiary structure of proteins

Answer 28

-folding pattern of secondary structure
-3D structure provides binding sites for ligands
-maintains appropriate residue on surface - polar for aqueous, hydrophobic for membranes
-physically independent regions called domains

Question 29

describe chaperones

Answer 29

-use energy from ATP
-is a protein
-assists protein folding
-excludes water so it doesn’t affect protein shape
-heat shock proteins:
produced by cell sunder stress
many members are chaperones
-barrel shaped

Question 30

describe quaternary structure

Answer 30

Association of individual polypeptide subunits (dimers, tetramers, oligomers e.g. F-actin)
Forms one functional protein (non-covalent)
Subunits can be the same (homo) or different (hetero)
Increases stability

Question 31

describe the changing structure of Hb

Answer 31

-allosteric so binding site changes
-conformation change occurs in response to oxygen binding
-cooperative binding of oxygen

Question 32

describe protein ‘switches’

Answer 32

-GTPase family: guanine nucleotide dependent regulatory switches e.g. Ras, G proteins
-Active conformation when bound to GTP
-When bound to GDP activity turned off
Ras:
Controls cell growth
Commonly mutated in cancer

Question 33

why is shape important for enzymes ?

Answer 33

-active site of enzyme is specific to shape of substrate and bonds that can be formed
-antibodies have to bind to specific antigens

Question 34

why do most enzymes need a metal ion?

Answer 34

so electrostatic forces of attraction can form

Question 35

what is protein denaturation?

Answer 35

conformation of a protein changing bc the bonds have been disrupted and thus it has lost its function

Question 36

what are causes of denaturation?

Answer 36

-change in pH
-change in temp
-acids
-bases
-high salt conc
-solvent

Question 37

how can protein folding cause disease?

Answer 37

-aggregation of misfolded proteins
-amyloid related diseases are Alzheimer’s, Parkinson’s and Huntington’s -tightly packed layers of stable beta sheets

Question 38

what is a therapeutic approach for diseases caused by protein misfolding?

Answer 38

pharmaceutical chaperones that can fold proteins back into original shape

Question 39

what are prions?

Answer 39

misfolded proteins that can transmit their misfolded shape on to normal variants of the same protein

Question 40

what are diseases related to prions?

Answer 40

-CJD (Creutzfeldt-Jakob disease)
-BSE (Bovine Spongiform Encephalopathy)

Question 41

why can prions not be sterilised?

Answer 41

because they are not organisms so they will not be killed

Question 42

how do prions lead to neurodegeneration?

Answer 42

form deposits in the brain

Question 43

how do prions induce misfolding?

Answer 43

they act as templates and increase b pleated sheets

Question 44

describe the acidic amino acids

Answer 44

-carboxyl group is deprotonated
-negatively charged at neutral pH
-forms electrostatic interactions
-e.g. aspartate, glutamate

Question 45

describe basic amino acids

Answer 45

-positively charged at neutral pH
-hydrophilic nitrogenous bases
-e.g. histidine, lysine, arginine