9/9/19

Question 1

_ make up most of the cell’s dry mass

Answer 1

protein

Question 2

proteins provide cell with

Answer 2

shape and structure, and execute many cellular functions

Question 3

the shape of a protein is specified by

Answer 3

its amino acid sequence

Question 4

proteins are assembled from a set of

Answer 4

20 different amino acids (primary sequence)

Question 5

speed up reactions

Answer 5

enzymes/catalysts

Question 6

building blocks of proteins

Answer 6

amino acids

Question 7

form polypeptide chain (primary sequence)

Answer 7

amino acids linked together by covalent peptide bonds

Question 8

polar vs non polar in terms of reaction with water

Answer 8

polar hydrophilic, non polar hydrophobic

Question 9

the polypeptide backbone is formed from

Answer 9

a repeating sequence of -N-C-C-

Question 10

two ends of the polypeptide chain

Answer 10

amino group (NH3+) and carboxyl group (COO-)

Question 11

polypeptide chain (picture)

Answer 11

N-terminus, His, Asp, Leu, Tyr, C-terminus (peptide bonds between carbon in carboxyl and nitrogen in amino group)

Question 12

__ give each amino acid its unique properties

Answer 12

side chains

Question 13

conformations definition

Answer 13

proteins folds into many different stable and functional 3D shapes

Question 14

the non covalent bonds help protein fold and maintain their shape include

Answer 14

H bonds, ionic bonds, and van Der Waals attractions

Question 15

hydrophobic force

Answer 15

the 4th weak interaction, also plays an important role in determining protein shapes

Question 16

__ can often recover their natural shapes

Answer 16

denatured proteins.
purified protein isolated from cells (expose to high conc of urea)> denatured protein, unfolded protein (remove urea)> protein refolds into its original conformation, notice or natural conformation.
Urea breaks bonds

Question 17

chaperone proteins

Answer 17

can guide the folding of a newly synthesized polypeptide chain

Question 18

isolation chambers_

Answer 18

some chaperone proteins act as _ that help a polypeptide fold without aggregating with other polypeptides in the cytoplasm

Question 19

_come in a wide variety of complicated shapes

Answer 19

proteins

Question 20

different ways to represent protein conformation

Answer 20

backbone, ribbon, wire, space filling

Question 21

common folding patterns

Answer 21

alpha helix and beta sheet

Question 22

in an alpha helix, the N-H of every peptide bond is __ to the C=O of the neighboring peptide bond located 4 amino acids away in the same chain

Answer 22

hydrogen bonded

Question 23

protein secondary structures

Answer 23

alpha and beta

Question 24

coiled coli

Answer 24

2 or 3 alpha helices wrap around one another to form a very stable structure

Question 25

alpha helix is _ handed

Answer 25

right

Question 26

in a beta sheet, several segments (Strands) of an individual polypeptide chain are held together by

Answer 26

hydrogen bonding

Question 27

coiled coli hydrophobic/phillic

Answer 27

inside is hydrophobic

Question 28

coiled coil formed

Answer 28

when the α helices have most of their hydrophobic side chains along one side so they can twist around each other with their hydrophobic side chains facing inward to minimize contact water

Question 29

Long, rodlike coiled-coils form the structural framework of many elongated proteins, including the α-keratin

Answer 29

.

Question 30

B sheets come in

Answer 30

2 varieties

Question 31

B sheets give silk fibers

Answer 31

extraordinary tensile strength, also stack to form an amyloid structure

Question 32

misfolded proteins can form

Answer 32

amyloid structures that cause disease

Question 33

disease examples from amyloid structures

Answer 33

Alzheimer’s disease and Huntington’s disease.

Question 34

misfolded proteins called

Answer 34

prions, can cause infectious neurodegenerative diseases-

Question 35

prions cause

Answer 35

amyloid structures

Question 36

proteins have _ _ of organization

Answer 36

several levels, primary, secondary, tertiary, quaternary

Question 37

protein domain

Answer 37

any segment of a polypeptide chain that can fold independently into a compact, stable structure

Question 38

info

Answer 38

Different protein domains are often associated with different functions. The bacterial catabolite activator protein (CAP) shown below has 2 domains: DNA-binding and cAMP-binding domains. When cAMP binds to the cAMP-binding domain, it causes a conformational change in the protein that enables the small domain to bind to a specific DNA sequence and thereby promote the expression of an adjacent gene.

Question 39

proteins can be classified into

Answer 39

families

Question 40

proteases are a

Answer 40

class of enzyme that cleaves protein

Question 41

extracellular proteins are often stabilized by

Answer 41

covalent cross-linkages

Question 42

disulfide bonds are formed by _. Purpose is _

Answer 42

Disulfide bonds (S-S bonds) formed by linking together two –SH groups from cysteine side chains that are adjacent in the folded protein. Disulfide bonds often help stabilize the structure of proteins that are secreted

Question 43

all proteins bind to

Answer 43

other molecules

Question 44

The biological properties of a protein molecule depend on

Answer 44

its physical interaction with other molecules with great specificity.

Question 45

ligand

Answer 45

"to bind", substance that is bounded by a protein

Question 46

The ability of a protein to bind selectively and with high affinity to a ligand is due to the formation of

Answer 46

a set of weak, noncovalent interactions

Question 47

When molecules have poorly matching surfaces,

Answer 47

w noncovalent interactions occur, and the 2 molecules dissociate as rapidly as they come together.

Question 48

ligand and protein connected with

Answer 48

non covalent bonds

Question 49

binding site

Answer 49

The region of a protein that associates with a ligand

Question 50

binding site consists of

Answer 50

a cavity in the protein surface formed by a particular arrangement of amino acid side chains

Question 51

Although the atoms buried in the interior of a protein have no direct contact with the ligand, they provide an

Answer 51

essential framework that gives the surface its contours and chemical properties

Question 52

Humans produce billions of _, each with a different binding site

Answer 52

different antibodies

Question 53

Antibodies are

Answer 53

immunoglobulin proteins produced by the immune system in response to foreign molecules