3-3D structure, tertiary

Question 1

what determines tertiary structure

Answer 1

amino acid sequence + environment where protein is

Question 2

how do soluble proteins fold best

Answer 2

when in an aqueous environment

Question 3

how do membrane proteins fold best

Answer 3

only fold properly in presence of membrane (or suitable replacements, like detergents)

Question 4

what are the critical forces in determining tertiary structures

Answer 4

hydrophobic effect!!!
van der waals interactions
H-bonds
ionic interactions

Question 5

why are van der waals important in determining 3ary structure even if they are weak

Answer 5

weak but many so they are significant

Question 6

what is delta G for folding

Answer 6

-100kJ/mol

Question 7

what energy state is the native conformation

Answer 7

low energy (folded)

Question 8

can there be more than 1 native conformation

Answer 8

yes

Question 9

why can there be more than one stable functional state (what are the other things that can make more)

Answer 9

• ligand binding (allostery)
• flexible portions of proteins (like a.a. that are not super useful/needed in that polypeptide)
• “breathing”-kinetic motions of atoms in proteins

Question 10

what are some methods to determine protein structure

Answer 10

circular dichroism
Xray crystallography
Protein NMR

Question 11

what kind of techniques can be used to yield general characteristics of secondary structure

Answer 11

circular dichrois,

Question 12

what kind of techniques can be used to yield detailed atomic information

Answer 12

X-ray crystallography

protein NMR

Question 13

how does circular dichroism work

Answer 13

depends on differential absorption of left and right circularly polarized light

Question 14

what is circular dichroism sensitive to (like what does it detect)

Answer 14

secondary structure

Question 15

when is circular dichroism most useful in (what kind of experiments)

Answer 15

denaturation/ renaturation

transition from folded to unfolded

Question 16

what kind of structures have characteristics circular dichroism spectra

Answer 16

alpha helices
beta sheets
random coil/irregular structures

Question 17

how do you make the crystals in X-ray crystallography

Answer 17

protein preparations are used to grow crystals-must be very pure samples

Question 18

what wavelength is exposed to the crystals

Answer 18

X-rays which are 1A

Question 19

what kind of info does X-ray crystals give us - directly and indirectly
(aka what info is gotten from the experiment and how is it used)

Answer 19

makes a diffraction pattern which can be used to make an electron density map

Question 20

is 6A or 1A better resolution

Answer 20

1A (smaller distance means easier to distinct between 2 points)

Question 21

what do regions of high electron density mean in X-Ray diffraction

Answer 21

location of atomic nuclei

Question 22

what are 3 pros for Xray

Answer 22

highly detailed
rapid solutions (sometimes, like drug companies wanna see quick before and after with drug)
useful for large proteins

Question 23

what are 4 cons for Xray

Answer 23

requires crystal growth (difficult)
crystals must deffract (not all do)
structures are static (cant have dynamic action)
cannot see hydrogens!!! (usually-you see things with lots of electrons, so not H)

Question 24

what are off diagonal peaks in 2D NMR

Answer 24

signals generated by close range interactions of protons

Question 25

what can you do with a combination of off diagonal peaks

Answer 25

helps provide info on the 3D structure of protein

Question 26

what does magnetic coupling provide information about

Answer 26

distances between atoms

Question 27

what kind of information is protein NMR combined with

Answer 27

ideal geometry information (dont worry just one line)

Question 28

does NMR give a single solution

Answer 28

gives a range of solution which reflects both dynamics/motions and error

Question 29

what do the multiple lines on an NMR represent

Answer 29

a family of structures consistent with the distance constraints of NMR

Question 30

what does it mean when there are areas that are less defined in protein NMR

Answer 30

they may be in motion or only have a few distances determined (not sure what is the exact conformation)

Question 31

what are 2 pros of protein NMR

Answer 31

``` dynamic info (real time) proteins are in solution (doesnt need to be a crystal which can be hard to deal with) ```

Question 32

what are 2 cons of protein NMR

Answer 32

difficult for large macromolecules synthesis of peptides containing isotopes (13C and 15N) can be expensive and time consuming

Question 33

what amino acids are often found in alpha keratin | and why

Answer 33

alanine (alpha helix) and cysteine (crosslinks)

Question 34

what reinforces the alpha keratin structure

Answer 34

disulphides

Question 35

what does more disulphides in keratin cause

Answer 35

it becomes "harder"

Question 36

what does less disulphides in keratin cause

Answer 36

it becomes "softer"

Question 37

what direction is the individual alpha helix in alpha keratin

Answer 37

right handed

Question 38

how many chains are in alpha helix

Answer 38

2 (dimer)

Question 39

what happens to the 2 alpha helices in alpha keratin +RH or LH

Answer 39

they are twisted in a left handed superhelix

Question 40

what % of protein mass in mammals is made from collagen

Answer 40

25-35%

Question 41

what are the main forms of collagen in humans

Answer 41

extracellular matrix proteins like skin bones teeth

Question 42

what kind of structure is collagen

Answer 42

regular, helical

Question 43

how many residues per turn in collagen

Answer 43

3

Question 44

what direction are the individual chains in collagen

Answer 44

left handed

Question 45

how many chains are in collagen

Answer 45

3

Question 46

what direction do the 3 chains coil into in collagen

Answer 46

right handed (superhelix)

Question 47

where are the H bonds in collagen

Answer 47

interchain

Question 48

what characterizes the primary structure of collagen (which aa)

Answer 48

glycine proline hydroxyproline

Question 49

which 4 aa is collagen rich in

Answer 49

glycine proline 4-hydroxyproline 5-hydroxylysine

Question 50

where do H bonds happen in the collagen helix

Answer 50

between strands, NOT WITHIN (like between the 3 chains, not within)

Question 51

what is 4-hydroxyproline

Answer 51

a post translational carbon with a hydroxyl group on carbon 4

Question 52

what is the point of 4-hydroxyproline

Answer 52

to ensure appropriate conformation in collagen helix

Question 53

when does hydroxylation happen of proline in collagen

Answer 53

after protein synthesis

Question 54

what does 4-hydroxyproline require to occur properly

Answer 54

vitamine c / ascorbic acid

Question 55

where does 5-hydroxylysine occur

Answer 55

at intervals in collagen polypeptides

Question 56

what is required in 5-hydroxylysine creation

Answer 56

modified lysine residues - requires vit C

Question 57

what causes cross-linking of peptides in collagen

Answer 57

lysine, hydroxylysine (and histidine) residues

Question 58

what are 4 similarities amongst soluble globular proteins

Answer 58

- mix of 2ary structures( irregular + regular required) - hydrophobic core hydrophilic exterior - closely packed interiors - maximized H bonds in interior

Question 59

what are 3 differences between soluble globular proteins

Answer 59

secondary structure composition prosthetic groups presence of disulfides

Question 60

where are disulfides present/ allowed

Answer 60

extracellular proteins

Question 61

what are 3 rules for soluble globular proteins (3ary)

Answer 61

hydrophobic interactions are critical extensive H-bonding occurs within 2ary structure (NOT between) knots do not form

Question 62

what is required to form hydrophobic interactions

Answer 62

2 layers of secondary structure must come together (interior and exterior)

Question 63

where are non polar vs polar amino acids in globular proteins

Answer 63

non polar buried inside | polar aa on surface

Question 64

where do H bonds occur in globular proteins

Answer 64

within 2ary structure

Question 65

are elements closer in 1ary usually close in 3ary

Answer 65

yes

Question 66

are elements closer in 3ary usually close in 1ary

Answer 66

no not necessarily

Question 67

what directionality are connections between sequential beta strands in parallel beta sheets

Answer 67

usually Right handed

Question 68

is structure or sequence typically conserved better

Answer 68

structure

Question 69

what are 3 different classifications for tertiary structure

Answer 69

SCOP CATH Pfam

Question 70

what do SCOP CATH and Pfam do

Answer 70

attempt to describe the structure of a protein (in search of common features and relationships) - usually describe overall strucutre like alpha, beta, alpha/beta

Question 71

what are motifs/folds

Answer 71

recognizable combinations of 2ary structure that appear in a number of different proteins (can be a large or small part of the structure)

Question 72

what are domains

Answer 72

discrete, independently-folded compact units within a polypeptide (may be composed of or include motifs)

Question 73

can domains function if another part of the protein isnt working

Answer 73

likely yes, they can fold and function without other parts (if they have different functions)

Question 74

are there more intradomain interactions or interdomain interactions

Answer 74

more intradomain (more within that between)