Module 1: From Polypeptide to Protein

Question 1

Polypeptide

Answer 1

primary structure of the protein comprised of a linear array of amino acids

Question 2

What are the two ends of a polypeptide?

Answer 2

Amino end (N-terminus) and Carboxyl end (C-terminus)

Question 3

Parts of an amino acid. Which of these parts make the amino acids unqiue?

Answer 3

Hydrogen atom, carboxyl group, amino group and R group. R group is what gives the amino acids its unique properties

Question 4

Two ways in which amino acids are classified?

Answer 4

solubility in water & polarity of side chain

Question 5

Solubility

Answer 5

refers to a physical property of a molecule that can bond with water through HB

Question 6

Hydrophillic

Answer 6

solube; HB can form with water; charge-polarized

Question 7

Hydrophobic

Answer 7

insoluble; HB cannot form with water; water repels HB in favour of forming bonds with itself

Question 8

Two catergories of hydrophobic amino acids

Answer 8

aromatic amino acids and aliphatic amino acids

Question 9

Which amino acid can act as an aromatic amino acid and an aliphatic amino acid?

Answer 9

tyrosine

Question 10

Prime contributors to overall charge of protein

Answer 10

postively charged (lysine and arginine) and negatively charged (aspartic acid and glutamic acid)

Question 11

Cysteine

Answer 11

can form covalent bonds with other cysteine residues forming disulphide bridges

Question 12

Glycine

Answer 12

very small and can allow bends in polypeptides

Question 13

Proline

Answer 13

side chain can form bond back with amine sidechain of amino acid producing a kink in the chain

Question 14

Histidine

Answer 14

has a sidechain that allows it to shift from positive to neutral charge depending on pH of the environment

Question 15

Peptide bonds

Answer 15

formed by condensation reactions (-water) between the amino group of one amino acid and the carboxyl group of another amino acid

Question 16

mRNA

Answer 16

carries gene’s message from DNA out of nuclues to a ribosome for production of a specific protein this gene codes for

Question 17

Primary structure of protein

Answer 17

linear arrangement of amino acid and the sequence is determined by nucleotide sequence of encoding gene
double stranded DNA is transcribed into single stranded mRNA, once its introns are removed it becomes a mature RNA containing only the codons for that specific protein, and then it is a translated in a ribosome

Question 18

Statistical coil

Answer 18

idea that proteins may not have a single, stable structure but rather switch between a collection of related structures

Question 19

local interactions that maintain protein shape

Answer 19

ionic bonds, hydrogen bonds, van der Waal forces, hydrophobic effect

Question 20

Secondary structure of a protein

Answer 20

consists of local chemical interactions that fold a protein

Question 21

Motifs

Answer 21

combinations of secondary structures

Question 22

three basic secondary structures

Answer 22

alpha-helix, beta sheet, and turn loops

Question 23

alpha helix

Answer 23

sprial, rod-like structures

Question 24

beta sheet

Answer 24

planar structure, composed of alignments of two or more strands

Question 25

turns/loops

Answer 25

connectors; bends in the polypeptide backbone that lie between the alpha helcies and beta strands

Question 26

Coiled-coil motif

Answer 26

two alpha helices are wrapped around one another

favoured in the cytosol

Question 27

zinc-finger motif

Answer 27

alpha helix and two beta strands held in position by interaction of precisely position Cys and His residues with a zinc atom
usually found within DNA binding proteins

Question 28

beta-barrel motif

Answer 28

large beta-sheet that loops back around itself
first strand and last strand of sheet forms HBs with each other
useful for forming a channel or pore across hydrophobic membrane

Question 29

helix-loop-helix motif

Answer 29

two small alpha helicies joined but are held together in specific orientation relative to one another by noncovalent interactions between specific amino acid residues and a cofactor, calcium

Question 30

Tertiary structure of protein

Answer 30

overall 3D confirmation of single protein

fundamental unit of tertiary structure is the domain

Question 31

Domain

Answer 31

substructure produced by any part of a polypeptide chain that can fold independently into a compact, stable structure

Question 32

two types of domain

Answer 32

functional and structural

Question 33

Functional domain

Answer 33

regions of protein that perform a specific activity

Question 34

Structural domain

Answer 34

regions of protein that form compact, largely independent globular domains

Question 35

Quaternary structure of a protein

Answer 35

number and organization of subunits in a multimeric protein

Question 36

Intrinsically unstructured proteins

Answer 36

proteins that lack a tertiary structure as isolated subunits
when they interact with one another they may form a structured complex

Question 37

Native state

Answer 37

refers to the most thermodynamically stable conformation of a protein

Question 38

Reversible denaturation experiment

Answer 38

Christian Anfinsen used denaturation and dialysis to unfold the protein and bring it back to its native state. He used urea and beta mercaptoethanol to unfold the protein. It was observed that as soon as it was brought back to its native state, it reassembled spontaneously into its folded condition.

Question 39

Sickle cell anemia

Answer 39

occurs due to misfolded haemoglobin

there is a single amino acid change in beta-globin sequence from glutamine to valine at position 6.

Question 40

Emphysema

Answer 40

condition when individual has diffculty breathing
alpha-1-antitrypsin -> protein found in lungs to maintain elasticity of the tissue
aspatic acid is replaced with valine at position 256

Question 41

What are prion diseases?

Answer 41

fatal transmissable neurodegenerative diseases.
it has a lengthy incubutation period in which it has a compromised immune system preventing the cells from notifying the body that something wrong is taking place

Question 42

modes of acquisition for prion disease

Answer 42

spontaneous, heritability, infectious

Question 43

Prion

Answer 43

abnormal form of a normal prion protein (PrPc is the normal form, and the PrPSc)

Question 44

Charactersitics of normal vs. abnormal prion protein

Answer 44

rich in alpha helicies vs. rich in beta sheets
soluble vs. insoluble
PK sensitive vs. PK insensitive
no aggregation vs. aggregation

Question 45

What gene codes for prion protein?

Answer 45

PRNP gene is located on the short arm of chromosome 20

Question 46

Missense mutations

Answer 46

changes in single amino acids

Question 47

insertions or deletions

Answer 47

insertions or deletions of additional amino acids

Question 48

nonsense mutations

Answer 48

truncated forms of proteins

Question 49

What are the clinical features of prion disease?

Answer 49

progressive neurological decline (rapidly progressive dementia, ataxia, visual problems, akinetic mutism)

Question 50

What is the suspected method of infection in prion proteins?

Answer 50

It is easier for the PrPSc to infect the PrPc when it is in its transient unfolded state (more suspectible to transitioning into abnormal prion)
then these PrPSc clump together through nucleation to form amyloid fibrils which then breaks out multiple seeds that can go on coverting PrPc into PrPSc

Question 51

Where does the infection of PrPc occur?

Answer 51

usually occurs in ER, but can also occur in lysosomes and endosomes

Question 52

What technique can be used to observe the conversion of prion proteins in the body?

Answer 52

immunofluorscence

Question 53

Are prion aggregates always bad?

Answer 53

No, Mod5 is a yeast prion that takes advantage of aggregation and uses it during stressful situations