Sept 8 Protein Structure

Question 1

what are the bonds linking amino acids together?

Answer 1

peptide bonds

Question 2

what is the basic biological point of DNA and RNA?

Answer 2

to allow the synthesis of specific proteins which carry out the chemical and physical functions of cells

Question 3

what is the size of the smallest proteins?

Answer 3

~40 amino acids in length

Question 4

what is the average size of a protein?

Answer 4

~300-400 amino acids

Question 5

what is the largest known protein and how many amino acids long?

Answer 5

titin, muscle protein
~30,000 amino acids

Question 6

what is the primary structure of proteins?

Answer 6

the specific sequence of amino acids

Question 7

what kinds of shapes are created?

Answer 7

definite 3-D structures depending on the sequence of amino acids

Question 8

what determines the function of a protein?

Answer 8

its overall shape (specific folding pattern) and the distribution of amino acids with distinctive chemical properties throughout the overall shape

Question 9

what are the two major classes of amino acid side chains?

Answer 9

hydrophilic
water loving
polar electronic charge distribution
interact well with water

hydrophobic
non polar charge distribution
do not interact well with water

Question 10

what is the hydrophobic effect?

Answer 10

water molecules surrounding hydrophobic molecules dispersed in water adopt a constrained, cage like organisation, which has low entropy (stable)

Question 11

what happens if hydrophobic molecules coalesce? (come together to form one mass or whole)

Answer 11

total number of low entropy constrained water molecules is reduced
net increase in entropy
separate hydrophobic and aqueous phases

Question 12

what favours the coalescence of hydrophobic molecules?

Answer 12

weak non covalent van der waals intermolecular interactions

Question 13

what is the secondary structure of proteins?

Answer 13

local folding and hydrogen bonding
(alpha helix or beta sheets)

Question 14

what is the tertiary structure of proteins?

Answer 14

overall conformation
spatial organization of the multiple secondary structure elements

Question 15

what is the quaternary structure of proteins?

Answer 15

multimeric structure (when multiple proteins come together)

Question 16

what are supramolecular structures?

Answer 16

large scale assembly of proteins

Question 17

what are the different functions of proteins? (8)

Answer 17

structure
movement
molecular transformation
signalling
transport
binding
catalysis
regulation

Question 18

what dictates the protein structure and function?

Answer 18

the amino acid sequence (primary structure)
indirectly determined by DNA

Question 19

what proportion of a polypeptide do alpha helix and beta sheets occupy? and what is the rest?

Answer 19

60%
the rest is made of irregular structures, coils and turns, or is disordered.

Question 20

where does the bonding occur to create those structures?

Answer 20

peptide bond carbonyl O atoms on one amino acid and amino group hydrogens on a different amino acid residue

Question 21

what is the gross structure of an alpha helix?

Answer 21

a straight rod

Question 22

what is an important covalent bond interaction that is important in an amino acid?

Answer 22

side chain of amino acid cysteine contains sulfhydryl group that can form covalent S-S (disulfide) bonds with other cysteine side chains

Question 23

where can those disulfide bonds be found and what do they contribute to?

Answer 23

intrachain, contributing to the tertiary structure
interchain, contributing to the quaternary structure

Question 24

what is a “motif” in protein structure?

Answer 24

combination of secondary structures forming distinct local 3D structure
do not contain enough bonds to maintain shape if it is cut away from the rest of the protein
rest of protein also contributes to its stability
motifs are not structurally independent entities

Question 25

what are protein domains?

Answer 25

larger than motifs (less than 40 AA long) compactly folded can be made of various motifs characteristic 3D structures within proteins could maintain shape if cut away from rest of protein rest of protein contributes little to the stability structurally independent entities, covalently joined to the rest of the protein

Question 26

what are the four major structural classes of proteins?

Answer 26

fibrous proteins globular proteins integral membrane proteins intrinsically disordered proteins

Question 27

what are intrinsically disordered proteins?

Answer 27

proteins or protein segments that exist as random coils under physiological conditions may adopt a specific secondary/tertiary structure upon binging to a well structured partner protein

Question 28

what are supramolecular complexes and an example?

Answer 28

large molecular machines made up of multiple distinct proteins, each of which may contain multiple subunits example: transcription initiation complex

Question 29

what are structural proteins?

Answer 29

determine the shape of cells and their extracellular environments serve as guides to direct the movement of organelles and molecules usually formed by assembly of multiple proteins subunits into very large and very long structures

Question 30

what are scaffold proteins?

Answer 30

bring other proteins together into ordered arrays to perform specific functions more efficiently than if they were separate

Question 31

what are enzymes?

Answer 31

proteins that catalyse chemical reactions

Question 32

what are membrane transport proteins?

Answer 32

embedded in cellular membranes and permit the flow of ions and molecules across the membranes

Question 33

what are regulatory proteins?

Answer 33

signals, switches and sensors to control activities of cells by altering the functions of other proteins and genes

Question 34

what are signalling proteins?

Answer 34

hormones and cell surface receptors and transmit extracellular signals to cell interior

Question 35

what are motor proteins?

Answer 35

responsible for the movement of other proteins

Question 36

what are amino acids sometimes reffered to as?

Answer 36

residues

Question 37

how many residues per turn in an alpha helix? and why is it that number and not a whole number?

Answer 37

3.6 (a 36 amino acid long helix will have 10 turns) not 4 because Hydrogen bonds are tilted

Question 38

how can the different strands be arranged in a beta sheet?

Answer 38

parallel (all strands point to the same side) or antiparallel (the strands point to different sides

Question 39

what is a functional domain?

Answer 39

a region of a protein that exhibits a particular activity characteristic of that protein

Question 40

what is the domain architecture?

Answer 40

the organisation (order) of domains within a multidomain protein

Question 41

what are topological domains?

Answer 41

regions of proteins that are defined by their distinct spatial relationships to the rest of the protein can comprise one or more structural and functional domains

Question 42

what are proteins that have a common ancestor called?

Answer 42

homologs

Question 43

what are globular proteins?

Answer 43

generally water soluble compactly folded structures often spheroidal mixture of secondary structures (both alpha and beta)

Question 44

what are fibrous proteins?

Answer 44

large, elongated often stiff long chain comprised of many tandem copies of a short AA sequence motif that forms a repeating pattern usually play a structural role or participate in cellular movements

Question 45

what is an intrinsically disordered region (IDR)?

Answer 45

a segment of a protein that is very flexible, with no fixed well ordered conformation if the entire protein has no well ordered conformation, is it called an intrinsically disordered protein (IDP)

Question 46

what is the native state of a protein?

Answer 46

one or a few closely related conformations that proteins are in when they are in their normal functional states

Question 47

what is metabolic coupling?

Answer 47

when proteins assemble together to be more efficient

Question 48

what are biomolecular condensates?

Answer 48

membraneless compartments in cells, often compared to liquid droplets chemically and physically distinct from their surroundings can break apart into smaller droplets or fuse together

Question 49

what affects the capacity of proteins to form condensates?

Answer 49

depends on their structures and the surrounding environment (pH, temperature etc)

Question 50

between what elements are hydrogen bonds created in protein secondary structure?

Answer 50

between carbonyl O (C double bond O) atoms on one amino acid and the amino group H (N--H) on another amino acid

Question 51

which amino acid binds to which amino acid in an alpha helix?

Answer 51

amino acid n bonds with amino acid n+4 (1 to 5, 2 to 6, 3 to 7 etc)

Question 52

explain how the coiled-coil motif is oriented/works?

Answer 52

heptad repeat of amino acids, and amino acids 1 and 4 are hydrophobic hydrophobic amino acids cannot be exposed to water therefore two molecules join together (2 coils)

Question 53

how are side chains arranged in a beta sheet and how does that affect the protein?

Answer 53

side chains protrude above and below the plane of the beta sheet determines the interactions of the beta sheet with other parts of the protein and also its propensity to form

Question 54

what type of stereoisomers are amino acids?

Answer 54

L stereoisomers it's the way it was chosen by nature