Proteins Dash 3 (Part 2)

Question 1

Experiments have
shown that the final
3D tertiary structure
of a protein ultimately
is determined by the

Answer 1

Primary structure (amino acid sequences)

Question 2

The 3D fold (shape) of
the protein determines
its .

Answer 2

function

Question 3

The primary structure of a
protein refers to its

Answer 3

Amino acid sequence

Question 4

Amino acids in peptides ( — aas) and proteins (typically —- to —– aas) are joined together by peptide bonds (amide bonds) between the carboxyl and amino groups of adjacent amino
acids.

Answer 4

<30 aas
200 to 1,000

Question 5

Only the R-group side-chains vary. By
convention, protein sequences are
written from left-to-right, from
the proteins ——–

Answer 5

N- to C-terminus.

Question 6

The average yeast protein
contains how many amino acids?

Answer 6

466

Question 7

molecular weight of an amino acid is — daltons (Da), the average
molecular weight of a yeast
protein is 52,728 Da. Note that
1 Da = 1 a.m.u. (1 proton mass).

Answer 7

113

Question 8

refers to short-range, periodic folding
elements that are common in proteins.

Answer 8

Secondary Structure

Question 9

Secondary structure includes the

Answer 9

a-helix and b sheet and in turns

Question 10

In the α helix (Fig. 3.4), the backbone
adopts a ——- —– structure
in which there are 3.6 aas per
turn.

Answer 10

Cylindrical spiral

Question 11

The α helix is stabilized by ??? between backbone carbonyl oxygen and amide nitrogen atoms that are oriented ??? to the helix axis.

Answer 11

H-bonds
parallel

Question 12

H-bonds occur between residues located in the n and —- positions relative to one another.

Answer 12

n + 4

Question 13

In β sheets (a.k.a. “???? ???? ”), each β strand adopts an ?????

Answer 13

pleated sheets

Extended conformation

Question 14

ß strands tend to occur in
pairs or multiple copies in β
sheets that interact with one
another via —— directed
——
to the axis of each
strand.

Answer 14

H-bonds
Perpendicular

Question 15

Strands can orient ———— or —— to one another in β sheets

Answer 15

Antiparallel or parallel

Question 16

ß Turns consist of 3-4 amino acids
that form

Answer 16

tight bends

Question 17

Longer connecting
segments between ß strands are called

Answer 17

Loops

Question 18

refers to the
folded 3D structure of a protein

Answer 18

Tertiary Structure

Question 19

Tertiary structure is also known as the —— structure or —— ——-

Answer 19

Native structure or active conformation

Question 20

Tertiary structure mostly is
stabilized by ——— ——- between secondary structure elements and other internal sequence regions that
cannot be classified as a particular
type of secondary structure.

Answer 20

noncovalent
interactions

Question 21

The structures of
hundreds of proteins have been
determined by techniques such as

Answer 21

x-ray crystallography and NMR.

Question 22

are evolutionarily conserved collections of secondary structure elements which have a ——
conformation. They also have a ——- sequence because the aa sequence ultimately determines structure.

Answer 22

Secondary structure motifs
Defined
Consensus

Question 23

Multisubunit (multimeric)
proteins have another level
of structural organization
known as —— ——-.

Answer 23

Quaternary Structure

Question 24

refers to the
number of subunits, their
relative positions, and
contacts between the
individual monomers in a
multimeric protein

Answer 24

Quaternary
structure

Question 25

independently folding and functionally specialized tertiary structure units within a protein.

Answer 25

Domains

Question 26

The modular domain structure of many proteins has resulted from the -------- and ------- together of their coding sequences within longer genes.

Answer 26

shuffling and splicing

Question 27

multimeric proteins achieve extremely large sizes, e.g., of subunits

Answer 27

10s-100s

Question 28

Such complexes exhibit the highest level of structural organization known as

Answer 28

Supramolecular structure

Question 29

Typically, supramolecular complexes function as "-------- --------" in reference to the fact that the activities of individual subunits are coordinated in the performance of some overall task

Answer 29

macromolecular machines

Question 30

Through ------- ------- and -------- ----- ---- approaches, the sequences of an enormous number of proteins have been compiled.

Answer 30

Genome sequencing and classical gene cloning

Question 31

Proteins that have a common ancestor are called

Answer 31

Homologs

Question 32

These ----- proteins are composed of mostly α helical secondary structure

Answer 32

Globular

Question 33

Comparison of the sequences of the members of protein families has brought to light the fact that amino acids within a given class exhibit a large degree of ---------- -------

Answer 33

functional redundancy

Question 34

Many experiments have shown that proteins can spontaneously fold from an unfolded state to their

Answer 34

folded native state

Question 35

tends to occur via successive conformational changes leading to secondary and then tertiary structure elements

Answer 35

Folding

Question 36

The --------- conformation of a protein can be generated by heating or treatment with certain organic solvents.

Answer 36

unfolded (denatured)

Question 37

The folding of many proteins, particularly large ones, is kinetically slow and is assisted in -------- by folding agents known as -------

Answer 37

Vivo chaperone

Question 38

Chaperones assist in 1) folding of ------- polypeptides made by ------ , and 2) re- folding of proteins denatured by --------- ------- such as heat shock.

Answer 38

nascent polypeptides Translation environmental damage,

Question 39

Molecular chaperones bind to unfolded nascent polypeptide chains as they emerge from the ------ , and prevent aggregation, misfolding, and degradation.

Answer 39

ribosome

Question 40

The hydrolysis of ATP by the chaperone drives conformational changes that prevent ------ and help drive -------- -------.

Answer 40

aggregation protein folding.

Question 41

Eukaryotic chaperonins such as the ---- ------ are large multimeric complexes related to the bacterial GroEL and GroES proteins.

Answer 41

TriC complex

Question 42

In neurodegenerative diseases such as ---------- disease and ----- ---- disease, insoluble misfolded proteins accumulate in the brain in pathological lesions known as --------- , resulting in neurodegeneration

Answer 42

plaques

Question 43

In Alzheimer's disease, the protein known as ------ ------- protein is cleaved into a peptide product (β-amyloid) that aggregates and precipitates in amyloid filaments.

Answer 43

amyloid precursor protein

Question 44

The misfolding of β-amyloid, which involves a transition from α helical to β sheet conformation leads to -------- -------

Answer 44

filament formation.

Question 45

In mad cow disease, ------- proteins precipitate causing lesions.

Answer 45

Prion

Question 46

The term ----- refers to any molecule that can be bound by a protein

Answer 46

Ligand

Question 47

Ligand binding requires ------- complementarity. The greater the degree of complementarity, the higher the ------ and ------ of the interaction

Answer 47

molecular specificity and affinity

Question 48

The complementarity-determining regions (CDRs) of the antibody make highly specific contacts with ------ in the antigen

Answer 48

epitopes

Question 49

Enzymes are proteins (a few are RNAs called -------) that catalyze chemical reactions within living organisms.

Answer 49

Ribozymes

Question 50

In an enzyme-catalyzed reaction, the reactant or what we called a ----- ) is converted into the product

Answer 50

Substrate

Question 51

is achieved due to the fact that enzymes are most complementary to the transition state structure formed in the reaction

Answer 51

Rate enhancement

Question 52

The transformation of a substrate to the product occurs in the ------- of an enzyme

Answer 52

Active site

Question 53

The active site can be subdivided into a ------------ wherein amino acids that catalyze the reaction reside, and a -------- ---- that recognizes a specific feature of the substrate, conferring specificity to the enzyme-substrate interaction

Answer 53

catalytic site binding pocket

Question 54

The French mathematicians ----- and ------ developed a kinetic equation to explain the behavior of most enzymes

Answer 54

Michaelis and Menten

Question 55

They showed that the maximal rate of an enzyme-catalyzed reaction (Vmax) depends on the -------- (Fig. 3.22a) and the ------ ----- for the rate-limiting step of the reaction

Answer 55

concentration of enzyme rate constant

Question 56

Michaelis and Menten also derived a kinetic constant, the ------- ------ (KM),

Answer 56

Michaelis constant

Question 57

The lower the KM the higher the ----- of the enzyme for the substrate

Answer 57

Affinity

Question 58

is the indicative of the affinity of most enzymes for their substrates.

Answer 58

Michaelis Constant (KM)

Question 59

The KM happens to be the concentration of substrate at which the reaction rate is ----- ------.

Answer 59

half-maximal

Question 60

are enzymes that cleave peptide bonds in other protein

Answer 60

Proteases

Question 61

The ____ proteases, which are important for digestion and blood coagulation

Answer 61

Serine

Question 62

Also present are aspartate and histidine residues that together with serine make up what is called the

Answer 62

catalytic triad.

Question 63

The active sites of serine proteases also contain ------- ---- that confer specificity by positioning the peptide bond that is to be cleaved next to the reactive serine

Answer 63

binding pockets

Question 64

Trypsin- Chymotrypsin- Elastase-

Answer 64

basic aas aromatic aas small side-chain aa

Question 65

In the serine protease reaction mechanism, ----------- is formed transiently after peptide bond cleavage by serine.

Answer 65

An acyl enzyme intermediate

Question 66

the rates of pathway reactions can be increased if the substrates and products of each step are ------ to the next enzyme in the pathway

Answer 66

Channeled

Question 67

is enhanced in multisubunit enzyme complexes and by attachment of enzymes to scaffolds or even by fusion of encoded enzymes into a single polypeptide chain

Answer 67

Channeling

Question 68

The proteolytic ------- (------) of proteins is important for regulatory processes, cell renewal, and disposal of denatured and damaged proteins.

Answer 68

Degradation (turnover)

Question 69

carry out degradation of endocytosed proteins and retired organelles.

Answer 69

Lysosomes

Question 70

Cytoplasmic protein degradation is performed largely by the molecular machine called the

Answer 70

Proteasome

Question 71

is a 76-amino- acid protein that after conjugation to the protein, targets it to the proteasome

Answer 71

Ubiquitin

Question 72

recognize and degrade ubiquinated proteins

Answer 72

Proteasome

Question 73

is a very important messenger in cell signaling

Answer 73

Calcium ion (Ca2+)

Question 74

contains 4 helix-loop-helix motifs (EF hands) each of which can bind calcium

Answer 74

Calmodulin

Question 75

Protein function also can be regulated by allosteric transitions caused by covalent modification via

Answer 75

phosphorylation

Question 76

typically occurs on serine, threonine, and tyrosine

Answer 76

Phosphorylation

Question 77

Cells maintain cytoplasmic calcium concentration at about . When calcium concentration rises above this level due to hormone- receptor signaling processes, etc., it binds to a protein known as

Answer 77

10-7 M calmodulin

Question 78

Enzymes known as ------ carry out phosphorylation

Answer 78

Kinases

Question 79

The bindinf of a ligand to a protein typically triggers an ---------- (------ -----) conformational change resulting in the modification of its activity.

Answer 79

Allosteric (other shape)

Question 80

Enzyme catalyzed reactions typically are highly specific, and rate enhancements of

Answer 80

10⁶-10¹²