Protein structures (primary, secondary, tertiary, etc.)

Question 1

Why would a protein want to have a quaternary structure (subunits)?

Answer 1

1) Error frequency in translation
2) Ease of folding of small vs. large polypeptide chains
3) Signalling/communication (“division of labor”, regulatory functions…)
4) Use of same subunit in different multi‐subunit proteins/complexes

Question 2

Do all proteins have quaternary structures?

Answer 2

no, only proteins that have more than one polypeptide chain (subunits) have quaternary structure

also most proteins with a MW greater than 100kD is most likely comprised of subunits

Question 3

subunits in quarternary structures are held together by what types of bonds/

Answer 3

non covalent interactions, salt bridges, van der waal’s, hydrogen bonds, and hydrophobic interactions

Question 4

What are oligomers?

Answer 4

proteins with more than one subunits, if identical they are called protomers

Question 5

if you have two identical subunits you call them?

Answer 5

dimers (2 protomers)

Question 6

What happens if there are two non identical subunits?

Answer 6

the efficiency of the enzyme is detrimentally affected b/c the reaction would depend on the diffusion of the intermediate to the second subunit and there might be other enzymes in the cell that would compete for the intermediate

Question 7

How is cn rotational symmetry classiified?

Answer 7

by a single rotational axis

Question 8

What is the meaning of quasi equivalent?

Answer 8

subunits that are not strictly equivalent in environment

Question 9

What is tertiary structure of proteins?

Answer 9

3D arrangement of secondary structures and side chains

Question 10

What two methods can be used to determine tertiary structure?

Answer 10

x-ray crystallography or NMR spectroscopy

Question 11

Which amino acids are hydrophobic and what does it mean when it comes to interactoins?

Answer 11

F, I, L, M, V, W

hydrophobic interactions usually drive these into the interior

Question 12

Which amino acids are uncharged polar? where are they located in a peptide

Answer 12

H, N, Q, S, T Y

located either in or exterior but when interior they are usually bonded with a Hydrogen

Question 13

Which amino acids are charged polar? where are they located?

Answer 13

D, E, K R

located mostly on the exterior but if interior will either be in a salt bridge or involve in a specific function such as catalysis, metal ligation etc.

These are very unstable internally if they don’t interact w/another species

Question 14

If uncharged residues are found interior what type of bond will they have?

Answer 14

predominantly be H bonded

Question 15

Are hydrogen bonds stronger in a non-polar environment or an aqueous solution?

Answer 15

stronger in non-polar

Question 16

what is. domain?

Answer 16

a region of polypeptide or protein that fold independently of each other and are functioning units that are connected by polypeptide segments

Question 17

How can we classify domains?

Answer 17

using the CATH classification

C-class overall secondary-structure of the domain

A- architecture - high structural similarity but no evidence of homology

T-topology/fold - large-scale grouping of topologies which share particular structural features

Homologous superfamily: demonstrable evolutionary relationship

Question 18

What is the dominant secondary structure seen in fibrous proteins?

Answer 18

coiled coil structure and it is the basic building block of fibrous proteins

Question 19

What gives keratin its fibrous nature?

Answer 19

the alpha helix.

the fundamental building block of keratin is the two chain coiled coil, where two alpha helices twist around each other.

Question 20

What are protofilaments?

Answer 20

part of the keratin structure - two chain coiled coil comes together w/another two chain coiled coil in a staggered arrangement and form protofilaments

Question 21

a bunch of protofilaments for what?

Answer 21

protofibril

Question 22

Keratin is a component of what?

Answer 22

hair, nails, horn, feathers, porcupine quills etc.

Question 23

What is the differences between type I and type II alpha helices in keratin? What do they do together?

Answer 23

Type I: acidic, right handed structure

Type II: basic, right handed structure

Type I and Type II twist around each other to form the coiled coil structure. and become a combined left handed structure

Question 24

What motif do you look for in any protein primary structure to see if it has a twisted coil-coil structure associate w/it?

Answer 24

-look for a 7 amino acid sequence (a, b, c, d, e, f, g) that repeats one after another. this heptad repeat can extend over hundred residues

in position a (1) and position d (4) are usually hydrophobic amino acids ( Leu, Ile, Val, etc) the residues in the e and g positions are generally charged

Question 25

What is a pseudorepeat?

Answer 25

when some keratin repeats do not have hydrophobic residues at site a or site d

Question 26

Why are residues in a and d in the keratin pseudo-repeat usually hydrophobic?

Answer 26

residues a and d ffrom the two strands in the coil-coil interact with each other due to helix alignment and are buried at the helix helix interface due to hydrophobic effect e and g are charged and can form ion ion interactions or salt bridges

Question 27

Alpha keratin is rich in what type of residues?

Answer 27

cys residues = disulfide bridges

Question 28

why is one form of keratin as in hair flexible and springy while the other form as in the horn, hard and inflexible?

Answer 28

due to its chemical composition of different forms Springy characteristic: low concentration of Cys and more hydrogen bonds Stiffness: cysteine forms disulfide bonds and more cystine and more disulfide bonds decrease springiness and increase hardness

Question 29

How do amyloid fibrils form?

Answer 29

from globular soluble proteins

Question 30

What are amyloid fibrils?

Answer 30

important fibrous protein involved in bovine spongiform encephalopathy (BSE = mad cow disease) and other prion diseases -alzheimer's disease and transthyretin amyloidosis

Question 31

How do amyloid fibrils contribute to diseases like mad cow and other prion disease?

Answer 31

normally globular soluble proteins become deposited as stable insoluble plaques in the extracellular space of the brain or eye in prions, the alpha helix globular protein becomes beta sheet fibril in transthyretin beta sheet globular protein becomes beta sheet fibril

Question 32

What is the role of transthyretin (amyloid fibrils)?

Answer 32

thransthyretin is a transpor protein | in the serum and cerebrospinal fluid that carries hormone thyroxine and retinol-binding protein in bloodstream

Question 33

What mutation causes transthyretin to cause amyloidosis?

Answer 33

single point mutation from Valine to Methionine and unfolding of c and d strands leads to fibril development

Question 34

What is the structure of amyloid fibrils of transthyretin? How does it differ from keratin?

Answer 34

twisted beta sheets, each around 10 amino acids long. Has a repeat unit of 24 beta strand and each repeat unit is 4 transthyretin molecules. Unlike keratin, there are no consensus sequences

Question 35

collagen is comprised of how many polypetide chains?

Answer 35

3 polypeptide chains termed alpha chains that form LEFT HANDED HELICES -the 3 LEFT HANDED helices in turn form a coiled-coil RIGHT HANDED structure (tropocollagen)

Question 36

How are the triple helical tropocollagen elements in collagen cross linked?

Answer 36

via lysine side chains

Question 37

collagen is found where?

Answer 37

``` bone cartilage teeth skin blood vessels ``` provides strong stress bearing material

Question 38

What is the amino acid composition of collagen?

Answer 38

33% glycine and 15-30% 4-hydroxyproline it typically has a sequence repeat that is glycine-proline-4-hydroxyproline sometimes 5 hydroxylysine - but only needed to add sugars groups

Question 39

What is 4-hydroxyproline?

Answer 39

found in collagen, it is a post-translational modification of proline

Question 40

How is vitamin C related to collagen?

Answer 40

primates can not synthesize collagen - leads to vitamin c deficiency aka scurvy - gum disease vitamin c is a reducing agent (antiscorbutic factor) and donates 2 electrons in propyl 4-hydroxylase reaction vitamin c is also required to keep the iron atoms in the ferrous or +2 state

Question 41

How are the cross link between tropocollagen molecules formed?

Answer 41

oxidation and aldol condensation of lysine side groups as catalyzed by the enzyme lysyl oxidase

Question 42

What are the three criteria that must be met for ordered tertiary structures?

Answer 42

1) nearly all residues must be in low energy conformation to be thermodynamically stable 2) fulfill hydrogen bonding requirements of buried polar groups 3) form compact packed structures so van der waals can have a strong effect

Question 43

If there are polar groups buried in the interior of a peptide, what must happen?

Answer 43

polar groups must be hydrogen bonded or form ionic interactions to a suitable partner since water is not an available partner

Question 44

Rotation occurs about which atom?

Answer 44

alpha carbon ins the common point of rotation between consecutive planes ( phi and psi bonds)

Question 45

What is trans and cis configuration and which is the most common? What is an exception?

Answer 45

Trans - the two alpha carbons are on opposie sides of the peptide bond - most common cis - the two alpha carbons are on the same side of hte peptide bond - rare Proline can adopt the cis configuration and trans since both have steric hindrance

Question 46

Rotation is allowed between which carbon bonds on a peptide? what is the name of these rotational angles?

Answer 46

rotational angles: phi and psi Phi: alpha carbon and N bond Psi: alpha carbon and carboxyl bond carboxyl and amide do not rotate

Question 47

When do ramachandran plots of amino acids look similar? what is the exception

Answer 47

Plots look similar w/amino acids that have a larger R group having a smaller allowed area. Glycine is exception - has the smallest R group and can adopt widest range of conformations

Question 48

Which amino acid is the most constrained?

Answer 48

Proline due to the cyclic side chain and it limits its phi (alpha carbon - N) range from -60 to +/- 25

Question 49

What are the four basic types of ramachandran plots? q

Answer 49

1) generic (18 amino acids no G or P) 2) Glycine 3) proline 4) pre-proline (refers to residues that precede

Question 50

What are the most common and stable regular secondary structures? What role do they play?

Answer 50

alpha helix and beta sheet conformations play a role in protein stability beta turns and w loops also play a role but not as common

Question 51

What is the main driving folding force when there is a water soluble globular protein?

Answer 51

the need to pack the hydrophobic side chains into the interior or core of the protein.

Question 52

Is the polypeptide backbone chain polar or non polar?

Answer 52

it is polar and hydrophilic with one hydrogen bond donor N-H and one H bond acceptor C00- in each peptide unit

Question 53

In an alpha helix how are the hydrogen bonds between amino acids?

Answer 53

the H bond are between one amino acid and another acid that is 4 residues awy H bonds occur between the amino N and the O atom of the carbonyl. AKA every main chain c=o and N-H group is hydrogen bonded.

Question 54

For L amino acids, which alpha helix is preferred the right-handed or left handed? Why?

Answer 54

Right handed is preferred and energetically favored due to less steric clash between side chains and back bones. AKA essentially all alpha helices are RIGHT HANDED

Question 55

Can all amino acids form an alpha helix? What determines if they do? Which amino acid has the greatest probability of being found in an alpha helix? which has the least?

Answer 55

Each of the 20 amino acids has an inherent propensity to form an alpha helix. this propensity is determined by the properties of its R group in how it affects the ability of the main chain atoms to take on the characteristics of phi and psi? Alanine has the greatest as its free energy change is closer to negative and proline has the least probability as its value is high

Question 56

What are the helix breakers?

Answer 56

amino acids least likely to for an alpha helix; proline and glycine

Question 57

which residues prefer beta sheets?

Answer 57

``` Valine Isoleucine Tyrosine Cysteine Tryptophan Phenylalanine Threonine ```

Question 58

What is antiparallel beta sheets? what makes it antiparallel?

Answer 58

the beta strands are opposite to one another and R groups alternate above and below the plane.

Question 59

how many strands are needed to form an antiparallel beta sheet?

Answer 59

a minimum of 2 strands for a sheet; 15 strands is the max and overall average is 6 strands

Question 60

How does H bonding occur in antiparallel beta sheets?

Answer 60

antiparallel beta sheets are almost fully extended and when strands align with each other the C=O can hydrogen bond with the N-H of the neighboring strand and vice versa. The H-binding patter is narrowly spaced H bond pairs that alternate with wider spaces between them. The H bonds connect each amino acid of one strand to a single amino acid of the adjacent strands all possible H bonds are formed except for the two flanking strands of the beta sheet AKA the hydrogen bonds are linear and stronger than the bent H bonds in parallel sheets

Question 61

What is the minimum required beta strands for parallel beta sheets?

Answer 61

minimum of 5 strands

Question 62

How do hydrogen bonds form in parallel beta sheets?

Answer 62

Hydrogen bonding is not linear and this makes the H bonds of the parallel sheet weaker. the H bond density per residue is also lower than antiparallel b/c the H bonds connect each amino acid of one strand w/two different amino acids of the adjacent. H bond are also evenly spaced

Question 63

Why is the parallel beta sheet not as stable as antiparallel?

Answer 63

H-bonds of parallel are weaker since they are not linear and the hydrogen bond density is lower in parallel

Question 64

Can a protein have both parallel and antiparallel beta sheets?

Answer 64

yes, you can have a mix

Question 65

are beta sheets left or right handed? why?

Answer 65

they are right handed twist ; thought to be a consequence of non-bonded interactions between the L-amino acid residues in the extended polypeptide chain

Question 66

In beta and alpha sheets are R groups extended in or out?

Answer 66

extend out!

Question 67

What is the 3-10-helix

Answer 67

A type of helix that rarely occurs but when it does it is mostly as a single turn transition between one end of the helix and the adjoining portion of the peptide chain. It is thinner and longer than the alpha helix due to its pitch and residues per turn . its R groups can encounter steric hindrance

Question 68

What are loops and turns?

Answer 68

part of secondary protein structures that connect alpha helices and/or beta sheets . they can be of various lengths and irregular shapes

Question 69

What occurs to residues in loops and why?

Answer 69

Residues in loops make good sites for hypervariable substitution, insertions and deletions. and when homologous amino acid sequences from different species are aligned, insertions and deletions occur almost exclusively in the loop regions

Question 70

Where do loops and turns lie on proteins?

Answer 70

the surface of proteins and for this reason are involved in interactions with other proteins and other molecules

Question 71

Due to their flexibility turns and loops are good for what?

Answer 71

to cap off protein active sites and provide catalytic residues as substrates bind and products are released.

Question 72

A helix-turn-helix motif is known for?

Answer 72

DNA binding

Question 73

A helix-loop-helix is known for?

Answer 73

Calcium binding proteins, parvalbumin and calmodulin

Question 74

What are disordered regions?

Answer 74

usually involved in recognition and/or binding

Question 75

How are peptide bonds formed?

Answer 75

formed via dehydration between alpha carboxyl acid and alpha amino groups of the two acids aka you're losing water

Question 76

Are amino acid condensation reactions are favored when in the forward or reverse reaction?

Answer 76

favored in the reverse reaction. The forward reaction takes place even though it is not thermodynamically favorable b/c during protein synthesis at the ribosome, the carboxyl group of one of the amino acids is modified or activated making it thermodynamically more favorable -even during chemical synthesis of polypeptides in the lab the carboxyl group has to be modified so that the forward reaction is favored

Question 77

Why do primary structures or sequence of amino acids/residues dictate the way the protein fold in 3D space when exposed to an aqueous environment?

Answer 77

B/c peptide folds is dependent on the R groups of the residues that form that chain. R groups are hydrophobic and hydrophilic

Question 78

How do we determine primary sequences of proteins?

Answer 78

1) Edman degradation - chemical sequencing of proteins 2) Proteomics - mass spec or crystallography 3) Bioinformatics and genomics (DNA sequencing) - can lead to errors b/c it cannot account for protein processing or post-translational modifiction

Question 79

How do you determine if a residue is important in a mechanism of actin like binding, catalysis etc?

Answer 79

use site directed mutagenesis to probe structure function

Question 80

Walker motif in proteins means what about your protein? What is the motif?

Answer 80

Motif: G-X-X-X-XG-K-T/S -means protein likely binds to ATP

Question 81

What is the p-loop sequence?

Answer 81

protein has an Ala or Gly in the first position then any four amino acids followed by glycine in the 5th position, lysine in 6th and either Thr or serine in 7th. P look also bind to ATP or similar compound

Question 82

What do motifs tell us about a protein?

Answer 82

motifs are certain patterns that we can recognize in the primary sequence and associated it to a function

Question 83

can we know the function of a protein just by knowing its primary sequence and not its 3D?

Answer 83

yes, by looking at motifs or mutagenesis

Question 84

When changes in residues occur what is it due to?

Answer 84

-chemical mutations of DNA changes in codon sequence it is not due to DNA rep or RNA translation errors

Question 85

What are the three types of sequence change that may occur in proteins?

Answer 85

1) Neutral drift 2) deleterious mutations 3) Deletion and insertions

Question 86

What is a neutral drift?

Answer 86

if sequence undergoes neutral drift then the primary structure has changed from the original form but the protein still has the same function and 3D structure as before

Question 87

What happens in deleterious mutation?

Answer 87

the protein encoded will not fold and/or function properly and the organism will be at a competitive disadvantage. Natural selection works against these mutations being fixed in a population aka lethal effect

Question 88

What do insertion and deletions do to a protein?

Answer 88

affect protein structure by either deleting an amino acid or inserting amino acids into sequence

Question 89

What are invariant residues?

Answer 89

residues that don't change over long evolutionary periods. Changes in these residues lead to deleterious mutations and are important for chemical structural properties that are critical for proteins structure/function

Question 90

What is conservative residues/substitution? give an example of this type of substitution

Answer 90

occur frequently in proteins as they evolve as long as they are not deleterious. this type of change leads to substitutions of similar amino acids but the side chain chemistry has not changed much Example: aspartic acid could be mutated to glutamic acid or lysine to arginine or one hydrophobic amino acid for another

Question 91

What are hypervariable residues?

Answer 91

residues where a position may tolerate several different amino acids indicating that that particular position is non-specific

Question 92

What can sequence alignment tell us?

Answer 92

how closely related organisms or species are

Question 93

what are homologous proteins?

Answer 93

proteins derived from a common ancestor that share similarities in both sequence and overall 3D structure

Question 94

What is homology scoring?

Answer 94

align sequences (accounting for gaps) and calculate the % identity. Works best for proteins over 100a.a % identity tells us how many residues have not changed between the two proteins