lecture 7

Question 1

the twist angle

Answer 1

between beta strands, forms the beta sheet

Question 2

Why are beta sheets so stable?

Answer 2

hydrogen bonds (and the cumulative strength of them)

Question 3

protein domains definition

Answer 3

distinct structural units, separate functions, fold independently and as compact units

Question 4

protein domains can

Answer 4

move as a single entity w respect to entire protein

Question 5

How many protein domains does a protein have?

Answer 5

they may have one or more.

each domain is usually made of a single stretch of primary sequence

Question 6

Src Protein kinase

Answer 6

has 4 functional domains, diff functions

this is one protein

Question 7

intrinsically disordered sequences functional importance

Answer 7

binding
tethering
scaffolding
flexibility

Question 8

tertiary structure of protein stabilized by

Answer 8

non covalent interactions
(usually between R groups or R groups and backbones)

Question 9

noncovalent interactions (4)

Answer 9

help proteins fold and maintain shape
1. h bonds
2. electrostatic interactions
3. van der waals
4. hydrophobic interactions

Question 10

Cysteine can

Answer 10

stabilize proteins through covalent interactions. (disulfide bonds)

cysteine-cysteine
or
cycteine-polypeptide

Question 11

Backbone model

Answer 11

shows the backbone

Question 12

ribbon model

Answer 12

shows the backbone and emphasizes the secondary structure

Question 13

wire model

Answer 13

shows the backbone and side chains

Question 14

space-filling model

Answer 14

contour map of the surface

Question 15

proteins have different shapes

Answer 15

structure and function are closely related

Question 16

two major groups of proteins

Answer 16

fibrous proteins
globular proteins

Question 17

fibrous proteins

Answer 17

-dominated by a single repeating element of secondary structure
-has properties that give strength/flexibility

ex. alpha keratin and silk, elastin, collagen

Question 18

globular proteins

Answer 18

-spherical, often contain several types of secondary structure

ex. myoglobin, lysozyme, cytochrome c

Question 19

alpha keratin (fibrous)

Answer 19

right handed alpha helix

coil composed of two alpha keritin chains that is left handed

Question 20

silk (fibrous proteins)

Answer 20

anitparallel beta strands held together by H bonds to form beta sheets

small R groups

Question 21

Fibroin in silk is rich in Ala and Gly– why?

Answer 21

allows the close packing of beta sheets and interlocking arrangement of R groups

Question 22

Globular proteins structural diversity

Answer 22

for diverse functions:
enzymes, motor proteins regulatory proteins etc.

Question 23

native state of the protein

Answer 23

usually the most stable (lowest energy) state of the folded protein

Question 24

chaperone proteins

Answer 24

help the folding process of proteins

Question 25

misfolded proteins can form

Answer 25

large aggregates, affecting cellular functions

Question 26

Anfinsen dogma

Answer 26

3D structure of a protein is determined only by its protein’s amino acid sequence

Not true for all proteins!!!

Question 27

Chris Anfinsen Refolding Experiment

Answer 27

Some denatured proteins will spontaneously refold in vitro

Question 28

Anfinsen’s Refolding experiment is not true for all proteins

Answer 28

-generally only true for small proteins

-some must fold during protein synthesis

-some need the help of chaperones

Question 29

Some proteins contain more than one

Answer 29

polypeptide chain

Question 30

each polypeptide chain is called a

Answer 30

subunit

Question 31

CAP protein structure

Answer 31

quaternary structure

composed of two identical subunits

Question 32

Hemoglobin structure

Answer 32

quaternary structure

composed if two identical alpha subunits and two identical beta subunits

Question 33

proteins can be classified into

Answer 33

protein families where each member has an amino acid sequence and 3D conformation that closely resembles eachother

ex. Elastase and chymotrypsin
-they are similar but w different substrate specificity

Question 34

Substrate specificity: Elastase

Answer 34

Ala, Val, Gly

Question 35

Substrate specificity: Chymotrypsin

Answer 35

Tyr, Phe, Trp

Question 36

protein assembly

Answer 36

proteins can spontaneously self assemble!
all info needed for self assembly is in the macromolecule itself

Question 37

proteins can form large assemblies such as

Answer 37

filaments, sheets, or spheres made up of many subunits bound to eachother