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BIO107 - CELL AND MOLECULAR BIOLOGY > Module 1B - Biomolecules and Enzymes > Flashcards

Module 1B - Biomolecules and Enzymes Flashcards

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1
Q

What is the shape and structure of proteins

A

structurally complex and
functionally sophisticated
molecules

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2
Q

The Shape of a Protein Is Specified by Its ____ ___Sequence

A

Amino Acid

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3
Q

How many types of amino acids in proteins

A

20 amino acids

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4
Q

Proteins are made of long ____ ___of amino acids

A

unbranched chain

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5
Q

Proteins are also known as?

A

polypeptides

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6
Q

-repeating sequence of atoms along the core of the polypeptide chains

A

polypeptide backbone

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7
Q

give amino acids its unique properties

A

Side chains

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8
Q

Polar amino acids

A

Aspartic acid (Asp)
Glutamic acid (Glu)
Arginine (Arg)
Lysine (Lys)
Histidine (His)
Asparagine (Asn)
Glutamine (Gln)
Serine (Ser)
Threonine (Thr)
Tyrosine (Tyr)

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9
Q

Non-polar amino acids

A

alanine (Ala)
Glycine (Gly)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Proline (Pro)
Phenylalanine (Phe)
Methionine (Met)
Tryptophan (Trp)
Cysteine (Cys)

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10
Q

2 polar amino acids that have negative side chain

A

Aspartic acid and Glutamic acid

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11
Q

3 polar amino acids that have positive side chain

A

Arginine
Lysine
Histidine

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12
Q

5 polar amino acid that has uncharged polar

A

Asparagine
Glutamine
Serine
Threonine
Tyrosine

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13
Q

Has weak noncovalent bonds

A

Protein folding

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14
Q

3 weak noncovalent bonds

A
  • hydrogen bonds
    -electrostatic attractions
    -van der Waals
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15
Q

hydrophobic molecules, including the nonpolar side chains of amino acids, tend to be forced together in an aqueous environment to minimize their disruptive effect on the hydrogen bonded network of water

A

hydrophobic clustering forces

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16
Q

_____ ____, including the _____ ___ ___tend to be forced together in an aqueous environment to minimize their disruptive
effect on the hydrogen-bonded network of water molecules

A

hydrophobic molecules, including the nonpolar side chains of amino acids

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17
Q

In the folded confirmation in aqueous environment of protein, it can form hydrogen bonds to water

A

Polar side chain on the outside of the molecule

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18
Q

the folded confirmation in aqueous environment of protein has hydrophobic core region which contains _____ __ __

A

nonpolar side chains

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19
Q

an important factor governing the folding of any protein is the distribution of its ___ and ___ ___

A

hydrophobic (nonpolar) and polar groups

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20
Q

determined by the order of the amino acids in its chain

A

three-dimensional structure of protein

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21
Q

reversible changes in a protein’s structure

A

denatures ↔ renatures

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22
Q

contain all the information needed for specifying the three-dimensional shape of a protein

A

Amino acids

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23
Q

A protein can be unfolded, or ____, by treatment with certain solvents, which disrupt the noncovalent interactions holding the folded chain together. This treatment converts the protein into a flexible polypeptide chain that has lost its natural shape

A

denatured

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24
Q

When the denaturing solvent is removed, the protein often refolds spontaneously, or _____, into its original conformation, indicating that all the information needed for specifying the three-dimensional shape of a protein is contained in its amino acid sequence.

A

renatures

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25
Q

Assist in the protein folding

A

Molecular chaperones

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26
Q

2 regular folding patterns

A

The α Helix and the β sheet

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27
Q

α helix and β sheet are particularly common because they result from hydrogen-bonding between ___-__ and __=__ in the polypeptide group

A

N-H and C=O groups

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28
Q
  • The first folding pattern to be discovered
  • was found in the protein α-keratin, which is abundant in skin and its derivatives—such as hair, nails, and horns.
A

α helix

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29
Q

found in the protein fibroin, the major constituent of silk.

A

β sheet

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30
Q

β sheets can form either from ____ ___ or ______ __

A

parallel chains or antiparallel chains

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31
Q

form from neighboring segments of the polypeptide backbone that run in the same orientation

A

Parallel chains

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32
Q

from a polypeptide backbone that folds
back and forth upon itself, with each section of the chain running in the direction opposite of that of its immediate neighbors

A

antiparallel chains

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33
Q

generated when a single
polypeptide chain twists around on itself to form a rigid cylinder

A

a helix

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34
Q

A hydrogen bond is made between every ___ peptide – linking C=O of one peptide bond to N-H of another

A

4th

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35
Q

wrap around each other to form a particularly stable structure, known as a coiled-coil.

A

α helices

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36
Q

formed from two or more have most of their nonpolar (hydrophobic)
side chains on one side

A

coiled-coil

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37
Q

Modular units from
which larger proteins are built

A

Protein domains

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38
Q
  • a substructure produced by any part of a polypeptide chain that can fold independently into a compact, stable structure
    -contains between 40 and 350 amino acids
A

Protein domains

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39
Q

four levels of organization in the structure of a protein

A
  1. Primary structure
  2. Secondary structure
  3. Tertiary structure
  4. Quaternary structure
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40
Q

Primary structure of protein

A

Amino acid sequence

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41
Q

Secondary structure of protein

A

hydrogen bonding of the peptide backbone; helices and β sheets

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42
Q

tertiary structure of protein

A

full 3D organization of a polypeptide chain

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43
Q

Quaternary structure of protein

A

protein molecule formed as a complex of more than one polypeptide chain

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44
Q

many present-day
proteins can be grouped
into protein ____

A

families

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45
Q

each protein family member has an ___ ___ ___ and a __-____conformation that resemble those of the other family members.

A

amino acid sequence and a three-dimensional conformation

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46
Q

a large family of protein-cleaving (proteolytic) enzymes that includes the digestive enzymes chymotrypsin, trypsin, and elastase, and several proteases involved in blood clotting

A

serine proteases

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47
Q

has been more highly conserved than the amino acid sequence

A

the structure of the
different members of a
protein family

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48
Q
  • both gene regulatory proteins in the homeodomain family4
  • identical in only 17 of 60 aa residues
A

yeast α2 protein and the
Drosophila engrailed
protein

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49
Q

protein families are readily recognized when the ___ of any organism is
sequenced

A

genome

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50
Q

human genome = ____ protein-coding genes

A

21,000

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51
Q

40% of our protein-coding genes to known protein structures, ___ diff
families

A

500

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52
Q

are the most powerful and predominant techniques used to experimentally determine the three-dimensional structures of biological macromolecules at near atomic resolution

A

x-ray crystallography and nuclear
magnetic resonance (NMR)

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53
Q

the basic units of proteins that can fold, function, and evolve independently

A

Protein domains

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54
Q

process of creating new combination of gene functional domains

A

Domain shuffling

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55
Q

– subset of protein domains, mobile
during evolution

A

protein modules

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56
Q

The three-dimensional structures of some protein modules

A
  1. Immunoglobulin module
  2. Fibronectin type 3 module
  3. Kringle module
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57
Q

easily integrated into other proteins

A

Protein domains

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58
Q

can be readily linked in
series to form extended
structures

A

Domains

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59
Q

Major Histocompatibility Complex (MHC) has ____-___ ___ that bind to and present fragments of pathogens (antigens) to immune cells.

A

antigen-recognition domain (only in humans)

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60
Q

Human genome encodes
how many protein-coding genes

A

21,000 protein-coding genes

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61
Q

genome sequences also reveal that _____
have inherited
nearly all of their protein
domains from invertebrates with only 7% identified human domains being vertebrate-specifics

A

Vertebrate

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62
Q

has given rise to many novel combinations of protein domains

A

domain shuffling during
vertebrate evolution

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63
Q

allow proteins to bind to each other to produce
structures in the cell

A

weak noncovalent bonds

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64
Q

any region of a protein’s
surface that can interact with another
molecule

A

binding site

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65
Q

forming a symmetric complex of two protein
subunits (dimer)

A

“head-to-head” arrangement

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66
Q

Contains two identical α-globin subunits and two identical β-globin subunits, symmetrically arranged

A

hemoglobin

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67
Q

a long chain of identical
protein molecules can be
constructed if each molecular
has a ___ __
complementary to another
region of the surface of the
same molecule

A

binding site

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68
Q

long helical structure produced from many
molecules of the protein actin

A

actin filament

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69
Q

why is a helix a common
structure in biology?

A

all subunits are identical, they can only fit together in one way – rarely straight line –resulting in a helix (resembles
a staircase

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70
Q

Elongated, fibrous shapes protein molecules

A

-fibrous protein
- keratin filaments
- a-keratin
- intermediate filaments

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71
Q

elongated three-dimensional
structure

A

Fibrous protein

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72
Q

main component in long
lived structures

A

Keratin filaments

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73
Q

a dimer of two identical subunits

A

a-keratin

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74
Q

rope-like structures; important component of the cytoskeleto

A

intermediate filaments

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75
Q
  • abundant outside the cell
  • main component of the
    gel-like extracellular
    matrix
A

Fibrous protein

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76
Q

consists of three long polypeptide chains,
each containing
that nonpolar
amino acid glycine
at every 3rd position

A

collagen

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77
Q

collagen consists
of three long
polypeptide chains,
each containing
that nonpolar
amino acid ____
at every ___ position

A

glycine
3rd

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78
Q

another abundant
protein in ecm; highly
disordered polypeptide

A

elastin

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79
Q

Ep1 PHD PHD Ep2

A

Yeast

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80
Q

Ep1 PHD PHD Ep2 Br

A

Worm

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81
Q

Znf Ep1 PHD PHD Ep2 Br BMB

A

Human

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82
Q

Elastin molecules are formed from relatively ___ and ___ polypeptide chains that are covalently cross-linked into a rubberlike elastic meshwork

A

loose and unstructured

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83
Q

The loose and unstructured chains that forms elastin molecules are covalently cross-linked into a rubberlike ____ ____

A

elastic meshwork

84
Q

intrinsically disordered regions of
proteins are frequent in nature,
WHY?

A

to form specific binding sites for other protein molecules that are of high specificity

85
Q

What does intrinsically disordered regions of
proteins trigger?

A

cell signaling events

86
Q

intrinsically disordered regions of
proteins serve as a ____, to hold two
protein domains in close
proximity

A

tether

87
Q

intrinsically disordered regions of proteins create regions with ___ _____

A

restrict diffusion

88
Q

proteins secreted
extracellular are often
stabilized by ____ ___ ____

A

covalent
cross-linkages

89
Q

The most common cross-linkages in proteins

A

sulfur–sulfur bonds- disulfide bonds (also called S–S bonds)

90
Q

do not change the conformation of a protein but instead act as atomic staples to reinforce its most favored conformation

A

disulfide bonds

91
Q

disulfide bonds act as ____ ____

A

atomic
staples

92
Q

3 advantages of using smaller subunits to build larger structures

A
  1. requires only a small amount of genetic information
  2. Both assembly and disassembly can be readily controlled, because the subunits associate through multiple bonds of relatively low energy.
  3. Errors in the synthesis of the structure can be more easily avoided
93
Q

some form into ____ and
____ that bind specific
RNA and DNA molecules in
their interior.
- the formation of closed structures provides additional stability because it increases the number of bonds between the protein subunits

A

tubes and spheres

94
Q

made of hundreds of identical
protein subunits that enclose
and protect the viral nucleic
acid

A

protein coat or capsid of
viruses

95
Q

_____ _____ can spontaneously assemble into the final structure under the appropriate conditions.

A

purified subunits

96
Q

first large macromolecular aggregate shown to be capable of self-assembly from its component parts

A

tobacco mosaic virus (TMV)

97
Q

Not all cellular structures held together by noncovalent bonds are capable of ____-_____

A

self-assembly

98
Q

guide
construction but take no part in
the final assembled structure

A

assembly factors

99
Q

self-propagating, stable β-sheet
aggregates

A

amyloid fibrils

100
Q

may be
released from dead cells and
accumulate as amyloid

A

protein aggregates

101
Q

protein aggregates may be released from dead cells and accumulate as

A

amyloid

102
Q

can kill cells and damage
tissues

A

Amyloid

103
Q

most severe amyloid pathologies

A

neurodegenerative diseases
(Alzheimer’s & Parkinson’s)

104
Q

group of disorders caused by a specific type of misfolded protein called the prion protein (PrP)

A

Prion diseases

105
Q

Example of prion disease in sheep

A
  • scrapie
106
Q

Example of prion disease in humans

A
  • Creutzfeldt-Jakob disease (CJD)
  • Kuru in humans
107
Q

Example of prion disease in cattles

A

bovine
spongiform encephalopathy (BSE)

108
Q

Prion disease is caused by a misfolded, aggregate
form of a particular protein called ____

A

PrP
(prion protein)

109
Q

PrP
(prion protein) can form ____ ___ that are “infectious”

A

amyloid fibrils

110
Q
  • acts like a vesicle containing peptide
    and hormones
  • in bacteria, secretes proteins
    that form long amyloid fibrils
    projecting from the cell
    exterior that help to bind
    bacterial neighbors to biofilms
A

specialized “secretory
granules” that consist of
amyloid fibrils

111
Q

a protein molecule’s
physical interaction with
other molecules determines
its ___ ___

A

biological properties

112
Q

each protein
molecule can usually bind
just one or a few molecules
out of many thousands

A

specificity

113
Q

the substance that
is bound by the protein

A

ligand

114
Q

The ability of a
protein to bind
selectively and with
high affinity to a
ligand depends on
the formation of a set
of ___ ___ bonds

A

weak noncovalent
bonds

115
Q

the region
of protein that associates
with a ligand

A

binding site

116
Q

their interaction may
restrict the access of water molecules to that protein’s ligand-binding sites

A

neighboring parts of the polypeptide chain

117
Q

can alter
their reactivity

A

the clustering of neighboring polar amino acid chains

118
Q

Proteins bind to other proteins through three types of interfaces, namely:

A
  • surface-string interaction
  • helix-helix
  • surface-surface
119
Q

binds tightly to a particular
target molecule (antigen),
inactivating directly or
making it for destruction

A

antibody or
immunoglobulins

120
Q

Where does antibody or
immunoglobulins binds to

A

target molecule (antigen)

121
Q

2 purposes of the binding of an antibody to its antigen

A

Direct inactivation or
making it for destruction

122
Q

Antibodies are typically ____shaped molecules

A

Y-shaped

123
Q

The arms of the Y-shaped molecules form two identical ___ ___ that are complementary to
a small portion of the
surface of the ____
molecule

A

binding sites
antigen

124
Q
  • cause the chemical
    transformations that
    make and break
    covalent bonds in cells
  • speed up reactions,
    act as catalysts
A

enzymes

125
Q

_____ + ___→ products

A

enzymes + substrates

126
Q

Michaelis-Menten mechanism or the enzyme-substrate complex reaction pathway

A

E + S → ES → EP → E + P

127
Q

there is a limit to the amount of
_____ that a single enzyme
molecule can process in a
given time

A

substrate

128
Q

the
maximum rate of reaction
divided by the enzyme
concentration

A

turnover number

129
Q

What do enzymes achieve?

A

enzymes achieve extremely high
rates of chemical reactions

130
Q

Where do enzymes greatly increases the
local concentration of both these
substrate molecule

A

catalytic
site

131
Q

unstable
intermediate state

A

transition state

132
Q

the free
energy required to attain the
transition state

A

activation energy

133
Q

enzymes not only bind tightly
to a transition state, they also
contain precisely ____ ___

A

positioned
atoms

134
Q

What do precisely positioned atoms do?

A

alter the electron
distributions in the atoms that
participate directly in the
making and breaking of
covalent bonds

135
Q

adds a molecule of water to a single bond
between two adjacent sugar groups in the polysaccharide chain, thereby causing the bond to
break

A

hydrolysis

136
Q

enzymes have a ____ ___ or ___ ___ tightly associated
with their active site that assists with their catalytic funciton

A

small molecule or metal atom

137
Q

General term for enzymes that catalyze a hydrolytic cleavage reaction

A

Hydrolases

138
Q

What are the more specific names for subclasses of hydrolases

A

Nucleases and proteases

139
Q
  • Break down nucleic acids by hydrolyzing bonds between nucleotides.
  • Endo- and exonucleases cleave nucleic acids within and from the ends of the polynucleotide chains, respectively
A

Nucleases

140
Q

Break down proteins by hydrolyzing bonds between amino acids

A

Proteases

141
Q

Synthesize molecules in anabolic reactions by condensing two smaller molecules together

A

Synthases

142
Q

-Join together (ligate) two molecules in an energy - dependent process.

A

Ligases

143
Q

Joins two DNA molecules together end-to-end through phosphodiester bonds

A

DNA ligase

144
Q

Catalyze the rearrangement of bonds within a single molecule

A

Isomerase

145
Q

Catalyze polymerization reactions such as the synthesis of DNA and RNA

A

polymerases

146
Q

Catalyze the addition of phosphate groups to molecules.

A

Kinases

147
Q

Important group of kinases that attach the phosphate groups to protein

A

Protein kinases

148
Q

Catalyze the hydrolytic removal of a phosphate group from a molecule

A

Phosphatases

149
Q

General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced

A

Oxido-Reductases

150
Q

Oxido-Reductases are often more specifically names as?

A

Oxidases , reductases, or dehydrogenase

151
Q

-hydrolyze ATP
- Many proteins with a wide range of roles have an energy-harnessing ___ activity as part of their function; for example, myosin and sodium-potassium pump

A

ATPases

152
Q

-Hydrolyze GTP
- A large family of GTP-binding proteins, with central roles in the regulation of cell processes

A

GTPases

153
Q

Enzymes that were discovered and named before the convention became generally accepted at the end of 19th cent.

A

pepsin, trypsin, thrombin, lysozyme

154
Q

Coenzyme of thiamine (vitamin B1)

A

Thiamine pyrophosphate

155
Q

Enzyme-catalyzed reactions requiring the coenzyme thiamine pyrophosphate

A

Activation and transfer of aldehydes

156
Q

Coenzyme of Riboflavin (vitamin B2)

A

FADH

157
Q

Enzyme-catalyzed reactions requiring the coenzyme FADH

A

Oxidation-reduction

158
Q

Coenzyme of Niacin

A

NADH, NADPH

159
Q

Enzyme-catalyzed reactions requiring the coenzyme NADH, NADPH

A

Oxidation-reduction

160
Q

Coenzyme of pantothenic acid

A

Coenzyme A

161
Q

Enzyme-catalyzed reactions requiring the coenzyme A

A

Acyl group activation and transfer

162
Q

Coenzyme of pyridoxine

A

Pyridoxal phosphate

163
Q

Enzyme-catalyzed reactions requiring the coenzyme pyridoxal phosphate

A

Amino acid activation; also glycogen phosphorylase

164
Q

Coenzyme of biotin

A

Biotin

165
Q

Enzyme-catalyzed reactions requiring the coenzyme biotin

A

CO2 activation and transfer

166
Q

Coenzyme of lipoic acid

A

Lipoamide

167
Q

Enzyme-catalyzed reactions requiring the coenzyme lipoamide

A

Acyl group activation; oxidation-reduction

168
Q

Coenzyme of folic acid

A

Tetrahydrofolate

169
Q

Enzyme-catalyzed reactions requiring the coenzyme tetrahydrofolate

A

Activation and transfer of single carbon groups

170
Q

Coenzyme of Vitamin B12

A

Cobalamin coenzyme

171
Q

Enzyme-catalyzed reactions requiring the coenzyme cobalamin coenzyme

A

Isomerization and methyl group transfers

172
Q

other proteins also frequently
require specific ___ ___ adjuncts to
function properly

A

small molecule

173
Q
  • receptor protein in the eye involved in vision
  • produced when light enters retina
A

rhodopsin

174
Q

a small molecule derived from vitamin A, binds tightly to rhodopsin and enables it to detect light, which is essential for vision

A

Retinal

175
Q

a protein in red blood cells that carries oxygen

A

hemoglobin

176
Q

a small iron-containing molecule, binds tightly to hemoglobin and allows it to capture and release oxygen molecules effectively.

A

heme
group

177
Q

a
large protein assembly;
allows the product of enzyme
A to be passed directly to
enzyme B, and so on

A

multienzyme complex

178
Q

controls how many
molecules of each enzyme
it makes by regulating the
expression of the gene that
encodes that enzyme

A

Cells

179
Q

How do cells control the number of enzyme molecules they produce

A

by regulating the
expression of the gene that
encodes that enzyme

180
Q

How does the cell controls enzymatic
activities

A

by confining sets
of enzymes to particular
compartments

181
Q

a
product produced late in a
reaction pathways inhibits
an enzyme that acts earlier
in the pathway

A

feedback inhibition

182
Q

prevent an enzyme from
acting

A

negative regulation

183
Q

regulatory molecule
stimulates the enzyme’s
activity rather than shutting
the enzyme down

A

positive regulation

184
Q

Greek words meaning
“other”

A

allos

185
Q

Greek words meaning
“solid” or “3D”

A

stereo

186
Q

have at least
two binding sites on their surface –
an active site and a regulatory site

A

allosteric enzymes

187
Q

recognizes the
substrates

A

active site

188
Q

recognizes a regulatory
molecule

A

regulatory site

189
Q

interaction between separated
sites on a protein

A

conformational change

190
Q

can occur in
multimeric proteins, where
each subunit of the protein
has its own ligand-binding
site

A

cooperative allosteric
transition

191
Q

Where does cooperative allosteric transition occur

A

multimeric proteins

192
Q

transfer
of the terminal phosphate group
of an ATP molecule to the
hydroxyl group

A

protein phosphorylation

193
Q

phosphorylates

A

protein kinase

194
Q

phosphate removal,
dephosphorylate

A

protein phosphatases

195
Q

phosphate is part of guanine
nucleotide GTP; addition and
removal of phosphate

A

GTP-binding proteins

196
Q

the loss of a phosphate
group occurs when?

A

the
bound GTP is hydrolyzed to
GDP in a reaction catalyzed
by the protein itself, and in its
GDP-bound state the protein
is inactive

197
Q

generate forces responsible for
muscle contraction and the crawling and
swimming of cells

A

motor proteins

198
Q

Undergo a series of conformational changes; these
changes are reversible

A

motor proteins

199
Q

coupling one of the
conformational changes to the
hydrolysis of an ATP molecule that is
tightly bound to the protein

A

unidirectional conformation
changes

200
Q

function to export
hydrophobic molecules from the cytoplasm

A

ABC transporters (ATP-binding
cassette)

201
Q

overproduction of these proteins
contributes to the resistance of
tumor cells to chemo

A

ABC transporters (ATP-binding
cassette)

202
Q

each of the central processes in a
cell—such as DNA replication,
protein synthesis, vesicle budding,
or transmembrane signaling—is
catalyzed by a highly coordinated,
linked set of how many proteins

A

10 or more proteins (protein machines)

203
Q

proteins binding sites
for multiple other
proteins

A

scaffold proteins

204
Q

scaffold proteins serve both to:

A
  1. link together
    specific sets of interacting
    proteins, and
  2. to position them at
    specific locations inside a cell
205
Q
A

BIO107 - CELL AND MOLECULAR BIOLOGY (16 decks)

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