Biochemistry - Protein Structure

Front 1

Why can proteins form so many different conformations?

Back 1

Free rotation around the bonds

Front 2

The conformations that exist under a given set of conditions are usually the ones that are the most ___ ___

Back 2

thermodynamically stable (having the lowest gibbs free energy)

Front 3

native proteins

Back 3

proteins in their functional unfolded conformations

Front 4

stability in protein structure can be defined as?

Back 4

the tendency to maintain a native conformation

Front 5

the delta G separating the folded and unfolded states of proteins is in what range?

Back 5

20 - 65 kJ/mol

Front 6

the unfolded state of a protein is characterized by a high degree of conformational __ that in addition to hydrogen bonding with the solvent (water) does what?

Back 6

entropy, maintains the unfolded state

Front 7

What are the chemical interactions that counteract entropy and the hydrogen bonding that try to keep proteins in their unfolded state?

Back 7

disulfide covalent bonds, and weak noncovalent interactions like hydrogen bonds and hydrophobic and ionic interactions

Front 8

Disulfide bonds are uncommon in __ and __

Back 8

bacteria and eukaryotes

Front 9

___ and ___ have many proteins with disulfide bonds. Why do we think this is?

Back 9

archaea and thermophilic bacteria, a side effect of life at high temperatures

Front 10

__ interactions are important in folding polypeptide chains into their secondary and tertiary structures

Back 10

weak

Front 11

solvation layer

Back 11

shel that water forms around hydrophobic molecules

Front 12

hydrophobic amino side chains tend to cluster where?

Back 12

inside the protein away from water, clustered when the protein is folded forming a hydrophobic protein core

Front 13

the number of __ ___ and ___ __ are maximized in the structural patterns of proteins, reducing the number of them that are not paired

Back 13

hydrogen bonds and ionic interactions

Front 14

True or false, the solvation layer can also form around polar molecules.

Back 14

true

Front 15

Most of the net change of free energy as weak interactions form within a protein is derived from?

Back 15

the increase in entropy in the surrounding water, resulting from buried hydrophobic forces

Front 16

The interior of a structured protein is generally a densely packed core of what?

Back 16

hydrophobic amino acid side chains

Front 17

__ ___ occur buried in the proteins of thermophilic organisms

Back 17

salt bridges

Front 18

__ ___ ___ interactions are dipole-dipole interactions that when increase in number can have an effect on protein structure

Back 18

van der waals

Front 19

Two rules of structural patterns of proteins

Back 19

1. hydrophobic cores buried away from water

2. the number of hydrogen bonds and ionic interactions within a protein is maximized

Front 20

six atoms of the peptide group?

Back 20

C-C-N-C

and the carboxyl O

and the amino H

Front 21

The six atoms of the peptide bond form what shape?

Back 21

a plane

Front 22

phi describes what angle

Back 22

C-N-Ca-C bonds

Front 23

psi describes what angle

Back 23

N-Ca-C-N bonds

Front 24

omega describes what angle, what is the typical value of omega?

Back 24

Ca-C-N-Ca, +-180 (trans), rarely 0 (cis)

Front 25

ramachandran plot

Back 25

shows phi and psi on a chart, used to test the quality of a 3d protein structure in an international database

Front 26

peptides are?

Back 26

linear unbranched chains connecting amino acid residue via a condensation reaction, loss of water (2 H from amino group, O from carbonyl group)

Front 27

peptide bond forms between

Back 27

the C of the carbonyl group and the N of the amino group

Front 28

formation of a peptide bond ___ energy, where does this energy come from?

Back 28

absorbs, ATP, GTP via a translation process

Front 29

the peptide bond is generally in a ___ conformation, what is the exception?

Back 29

trans, proline (cis)

Front 30

peptide bonds assume a partial double bond character restricting ___

Back 30

rotation

Front 31

do the bonds on either side of the peptide bond rotate?

Back 31

yes

Front 32

some proteins have multiple ___ comprised of more than one polypeptide chain

Back 32

subunits

Front 33

amphipathic

Back 33

having hydrophobic and hydrophilic regions

Front 34

secondary structure describes? without regards to?

Back 34

local spacial arrangement of a polypeptide chain's main-chain atoms, positioning of the side chains

Front 35

What is a regular secondary structure

Back 35

when each dihedral angle psi and Phi remain nearly the same throughout the segment

Front 36

3 typical types of secondary structures

Back 36

alpha helix, B conformations, B turns

Front 37

what is it called where a regular pattern is not defined?

Back 37

random coil or undefined

Front 38

Who discovered the alpha helix?

Back 38

Pauling and Corey

Front 39

Describe the alpha helix

Back 39

polypeptide chain is tightly wound around imaginary axis, the r groups and amino acid residues protrude from the backbone

Front 40

a single turn of the helix is ___ A long

Back 40

5.4

Front 41

How many amino acid residues are in each turn of the alpha helix?

Back 41

3.6

Front 42

Is right hand or left hand helix more common? Why?

Back 42

right, left are theoretically less stable, and have not been observed in proteins

Front 43

What fraction of amino acids have an alpha helix secondary structure?

Back 43

1/4

Front 44

Why does an alpha helix form more readily than other conformations?

Back 44

It uses hydrogen bonding optimally, it is stabilized bey the hydrogen bonds between the hydrogen atom attached to the electronegative nitrogen atom and the electronegative oxygen atom of the carbonyl group

Every peptide bond participates in hydrogen bonding.

At the ends the groups cannot bond with other parts of the protein so they bond with water, that acts as a cap to the helix.

Front 45

___ shows the greatest tendency to form an alpha helix, why?

Back 45

Alanine,

Front 46

If a segment of the chain has a long block of __ residues, this segment will not form an alpha helix, why?

Back 46

Glu, the negatively charged adjacent carboxyl groups repel eachother

Front 47

Which two amino acid residues have the least proclivity to form alpha helices?

Back 47

Pro and Gly, proline because of the rigid aromatic ring and lack of hydrogen atom for bonding, Gly because it has more flexibility and tends to coil

Front 48

Five constraints to alpha helix formation.

Back 48

1._propensity of residues to form alpha helix

2. interactions between r groups 3 and 4 apart

3. bulkiness of adjacent r groups

4. occurrence of pro and gly

5. interactions between residues at the ends

Front 49

B conformation - B sheet

Back 49

backbond extended in a zigzag, with several segments side by side forming a sheet

Front 50

In B-sheet, what is parallel and atiparallell

Back 50

parallel is with amino groups at the same ends, anti is with them at opposite ends

Front 51

What is a B turn? Which amino acid is most likely to form a B turn?

Back 51

A turn in the polypeptide change, change of direction, usually connecting two alpha helix or two ends of an antiparallel B sheet. Gly and Pro.

Front 52

This type of spectroscopy is used to determine if proteins are properly folded by using left-handed and right-handed polarized light.

Back 52

CD circular dichroism spectroscopy

Front 53

What is tertiary structure?

Back 53

the overall 3D arrangement of the atoms in a protein, atoms that are far apart and in different types of secondary structures may interact into a completely folded structure

Front 54

What are the bend producing residues?

Back 54

Pro, Thr, Ser, Gly

Front 55

How are proteins held in their tertiary structure?

Back 55

By several types of weak interactions and sometimes by covalent bonds like disulfide links

Front 56

What is a quaternary structure?

Back 56

When two or more separate polypeptide chains, or subunits are held together (two or more different tertiary structures)

Front 57

What are the two major classifications of protein structure?

Back 57

fibrous (like muscles or tissue) or globular (enzymes)

Front 58

Fibrous proteins provide __, and are __ in water.

Back 58

strength, insoluble

Front 59

alpha keratins have evolved for their ___ and make up what?

Back 59

strength, hair, nails, claws, and outer layer of skin

Front 60

collagen also provide ___ and are found in __

Back 60

strength, tendons, cartilage, bone, etc.

Front 61

silk is in what conformation?

Back 61

B conformation

Front 62

Globular proteins include what?

Back 62

enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobulins, etc.

Front 63

myoglobin is found in __, why?

Back 63

the muscles of diving animals, because it can store a lot of oxygen permitting mammals to dive for a long time

Front 64

hemoglobin is found in ___

Back 64

human blood

Front 65

Where do hydrobphobic R groups generally go in a protein?

Back 65

To the center to avoid water.

Front 66

Why does each protein have a different structure?

Back 66

Because they have adapted to their particular function.

Front 67

Where do hydrophilic side chains go in a protein?

Back 67

on the surface

Front 68

motif or fold

Back 68

a folding pattern involving two or more elements of secondary structure and the connections between them

Front 69

Examples of motifs or folds

Back 69

B-alpha-B loop, B barrel

Front 70

domain

Back 70

a section of the chain that is independently stable and usually in polypeptides with more than a few hundred amino acid residues

Front 71

Rules of folding

Back 71

1. hydrophobic interactions get buried in the middle and hold the structure together

2. alpha helices and B-sheets are found in different structural layers

3. segments adjacent to each other in the amino acid sequence are usually stacked in the folded structure

4. B-conformation is most stable when twisted slightly right-handedly

Front 72

Subunits of a quaternary structure often take on different functions in a process, like __ and __.

Back 72

catalysis and regulation

Front 73

a mutlisubunit protein is also called a ___

Back 73

multimer

Front 74

a multisubunit with just a few units is called a ___

Back 74

oligomer

Front 75

a multisubunit with repeating subunits is calle a __

Back 75

protomer

Front 76

Proteins that have significant unstructured segments.

Back 76

intrinsically disordered proteins

Front 77

intrinsically disordered proteins often have a lot of ___ residues

Back 77

Pro

Front 78

What is the lack of order in a protein good for?

Back 78

wrapping around other proteins and holding them in place in order for a reaction with another protein to occur or inhibiting other reactions from occuring

Front 79

proteostasis

Back 79

the coordination of pathways for protein synthesis and folding, refolding when denatured, and degradation when irreversibly unfolded

Front 80

Life cycle of a protein

Back 80

1. synthesized on ribosomes

2. folded either spontaneously or with chaperones

3. could partially unfold and create sticky aggregates - causing disease

4. degradation

Front 81

denaturation

Back 81

loss of 3D structure of protein, causing loss of function

Front 82

most proteins can be denature by?

Back 82

heat, becuase it breaks weak interactions, extremes of pH, solvents, solutes, detergents

Front 83

denaturing agents do not break __

Back 83

covalent bonds in the polypeptide chain

Front 84

renaturation

Back 84

when proteins regain their structure after denaturationi

Front 85

In what order do proteins fold?

Back 85

first secondary structure, then tertiary then quaternary, moving towards lower free energy

Front 86

chaperones

Back 86

proteins that assist in protein folding

Front 87

Two major types of chaperones

Back 87

Hsp70, chaperonins

Front 88

PDI (protein disulfide isomerase_

Back 88

an enzyme that catalyzes the interchange of disulfide bonds until the native conformation is reached

Front 89

PPI (peptide polyl cistrans isomerase

Back 89

catalyzes the interconversion of the cis trains isomers of Pro residue peptide bonds

Front 90

Protein misfolding leads to __

Back 90

disease

Front 91

amyloid, amyloidoses

Back 91

when a protein is secreted in a misfolded stated it creates these and causes these diseases

Front 92

proteosome

Back 92

responsible for degradation, chews up proteins and spits out peptide fragments

Front 93

Most proteins are __ and __.

Back 93

globular, soluble

Front 94

What can cause a protein to unfold? Name 5 things.

Back 94

temperature (heat), pH, proteases, presence of oxygen, bacterial contamination

Front 95

amyloid fibril

Back 95

a generic term for a highly organized, "thread-like" aggregate protein structure which is typically rich in β-sheets.

Front 96

protein homeostasis

Back 96

The ensemble of cellularprocesses that regulates thebehaviour of proteins in termsof their conformations,interactions, concentrationsand localizations.

Front 97

Parkinson's - what protein clusters to form amyloid fibril?

Back 97

alpha-sinuclein

Front 98

Alzheimer's disease is characterized by the accumulation of amyloid structures comprised of__.

Back 98

amyloid B peptide

Front 99

how is tertiary structure determined? what technologies?

Back 99

x-Ray crystallograpy, NMR

Front 100

What does PDI (protein disulfide isomerase do?)

Back 100

ensures that disulfide bonds are created in the correct position