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Cell and Molecular Biology > Module 1B Biomolecules and Enzymes (Proteins) > Flashcards

Module 1B Biomolecules and Enzymes (Proteins) Flashcards

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1
Q

structurally complex and functionally sophisticated molecules.

A

Proteins

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2
Q

What specifies the shape of a protein?

A

amino acid sequence

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3
Q

How many amino acids make up proteins?

A

20

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4
Q

What type of chain are proteins made of?

A

long, unbranched chains of amino acids.

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5
Q

What is the term for a chain of amino acids in a protein?

A

Polypeptides

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6
Q

It is the repeating sequence of atoms along the core of the polypeptide chains.

A

polypeptide backbone

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7
Q

What gives each amino acid its unique properties?

A

side chains

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8
Q

influenced by weak noncovalent bonds: hydrogen bonds, electrostatic attractions, and van der Waals forces.

A

protein folding

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9
Q

What is protein folding influenced by? (3)

A

weak noncovalent bonds:
- hydrogen bonds
- electrostatic attractions
- van der Waals forces

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10
Q

They force hydrophobic molecules, including nonpolar side chains, together in an aqueous environment to minimize disruption of the hydrogen-bonded network of water molecules.

A

hydrophobic clustering forces

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11
Q

What are the two types of groups based on solubility found in proteins? (2)

A

Hydrophobic (nonpolar) and polar groups.

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12
Q

Into what structure do proteins fold?

A

into a three-dimensional structure of lowest energy.

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13
Q

__ is when a protein loses its structure; __ is when it regains it.

A
  • Denaturation
  • renaturation
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14
Q

What contains all the information needed for the three-dimensional shape of a protein?

A

amino acid sequence

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15
Q

What assists in the folding of proteins?

A

Molecular chaperones

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16
Q

What are the two common folding patterns found within proteins? (2)

A
  • α helix
  • β sheet
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17
Q

They result from hydrogen-bonding between the N-H and C=O groups in the polypeptide chain.

A
  • α helix
  • β sheet
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18
Q

α helix and β sheet result from hydrogen-bonding between the __ and __ groups in the polypeptide chain.

A
  • N-H
  • C=O
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19
Q

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

A

parallel chains

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20
Q

form when the polypeptide backbone folds back and forth, with sections running in opposite directions.

A

antiparallel chains

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21
Q

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

A

α helix

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22
Q

How often do hydrogen bonds form in an α helix?

A

form between every fourth peptide, linking the C=O of one peptide bond to the N-H of another.

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23
Q

formed from two or more α helices with most of their nonpolar side chains on one side.

A

coiled-coil structure

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24
Q

What is the primary structure of a protein?

A

amino acid sequence

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25
Q

Structure of protein: Hydrogen bonding of the peptide backbone, forming helices and β sheets.

A

secondary structure

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26
Q

Structure of protein: The full three-dimensional organization of a polypeptide chain.

A

tertiary structure

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27
Q

Structure of protein: A protein molecule formed as a complex of more than one polypeptide chain.

A

quaternary structure

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28
Q

How can proteins be classified? (2)

A
  • based on their amino acid sequence; and
  • three-dimensional conformation.
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29
Q

What is an example of a protein family?

A

Serine proteases, which are protein-cleaving (proteolytic) enzymes.

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30
Q

Which has been more conserved in protein families, structure or amino acid sequence?

A

structure

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31
Q

Give an example of two regulatory proteins in the homeodomain family. (2)

A
  • yeast α2 protein
  • Drosophila engrailed protein.
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32
Q

How many amino acid residues are identical in the yeast α2 protein and the Drosophila engrailed protein?

A

only 17 of 60 amino acid residues.

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33
Q

How are protein families identified in a sequenced genome?

A

when the genome of an organism is sequenced.

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34
Q

Approximately how many protein-coding genes are in the human genome?

A

about 21,000 protein-coding genes.

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35
Q

What percentage of human protein-coding genes relate to known protein structures?

A

About 40%, spanning 500 different families.

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36
Q

What techniques are used to study protein structure? (2)

A
  • X-ray crystallography
  • nuclear magnetic resonance (NMR).
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37
Q
  • the basic units of proteins that can fold, function, and evolve independently.
  • can be easily integrated into other proteins and linked in series to form extended structures.
A

protein domains

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38
Q

the process of creating new combinations of gene functional domains.

A

domain shuffling

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39
Q

a subset of protein domains that are mobile during evolution.

A

Protein modules

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40
Q

What is an example of a domain with a specialized function?

A

Major Histocompatibility Complex (MHC) antigen-recognition domain, found only in humans.

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41
Q

Where have most vertebrate protein domains been inherited from?

A

invertebrates

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42
Q

What percentage of identified human protein domains are vertebrate-specific?

A

7%

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43
Q

What has domain shuffling during vertebrate evolution resulted in?

A

many novel combinations of protein domains.

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44
Q

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

A

Weak noncovalent bonds

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45
Q

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

A

binding site

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46
Q

The “head-to-head” arrangement forms a symmetric complex of two protein subunits, known as a __.

A

dimer

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47
Q

The __ arrangement forms a symmetric complex of two protein subunits, known as a dimer.

A

“head-to-head”

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48
Q

What subunits make up hemoglobin?

A
  • two identical α-globin subunits; and
  • two identical β-globin subunits

symmetrically arranged.

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49
Q

How can a long chain of identical protein molecules be constructed?

A

By having each molecule with a binding site complementary to another region of the surface of the same molecule.

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50
Q

Give an example of a long helical structure formed by protein molecules.

A

The actin filament, formed from many molecules of the protein actin.

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51
Q

In a chain of identical subunits, the only way they fit together is rarely in a straight line, resulting in a __, which resembles a staircase. This is a common structure in biology.

A

helix

52
Q
  • A protein that have an elongated three-dimensional structure.
  • abundant outside the cell, where they form the main component of the gel-like extracellular matrix.
A

fibrous proteins

53
Q

What is the main component in long-lived structures composed of fibrous proteins?

A

keratin filaments

54
Q
  • a type of keratin with a dimer of two identical subunits.
  • a fibrous structural protein, meaning it is made up of amino acids that form a repeating secondary structure.
A

α-keratin

55
Q

ropelike structures that are important components of the cytoskeleton.

A

intermediate filaments

56
Q

A protein molecule that consists of three long polypeptide chains, each containing glycine at every third position.

A

collagen

57
Q

an abundant protein in the extracellular matrix (ECM) with highly disordered polypeptide chains. These chains are covalently cross-linked to create a rubberlike, elastic meshwork that can stretch and return to its original shape.

A

elastin

58
Q

Intrinsically disordered regions are common because they serve multiple functions such as forming specific binding sites for other proteins with __.

A

high specificity

59
Q

What is one function of intrinsically disordered regions in proteins?

A

can trigger cell signaling events

59
Q

intrinsically disordered regions assist in protein structure because they can act as “__” to hold two protein domains in close proximity.

A

tethers

59
Q

What role do intrinsically disordered regions play in molecular movement?

A

help restrict diffusion within cellular structures.

59
Q

provide stability for proteins secreted extracellularly, preventing degradation.

A

Covalent cross-linkages

60
Q

What type of bond commonly stabilizes extracellular proteins?

A

Disulfide bonds, or sulfur-sulfur (S-S) bonds.

61
Q

Do disulfide bonds change the conformation of a protein?

A

No, disulfide bonds do not change the protein’s conformation but act as atomic “staples” for stability.

62
Q

disulfide bonds act as atomic “__” for stability.

A

staples

63
Q

What are the advantages of using protein molecules as subunits for large structures? (3)

A
  1. Requires only a small amount of genetic information
  2. Allows controlled assembly and disassembly through multiple low-energy bonds
  3. Errors in the synthesis of the structure can be more easily avoided
64
Q

What shapes can protein subunits form when assembled? (often enclose specific RNA or DNA molecules) (3)

A
  • tubes
  • spheres
  • capsids
65
Q

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

A

protein coats or capsid in viruses

66
Q

What are examples of a structure in cells that can self-assemble? (2)

A
  • tobacco mosaic virus (TMV)
  • bacterial ribosomes
67
Q

It is the process by which purified subunits spontaneously form into the final structure without additional cellular machinery.

A

self-assembly

68
Q

It guides the construction of complex biological structures but are not part of the final assembled product.

A

assembly factors

69
Q

Do all cellular structures self-assemble through noncovalent bonds?

A

No, some require assembly factors for proper formation.

70
Q

What is an example of a process involving assembly factors in protein formation?

A

Proteolytic cleavage is involved in the assembly of insulin, where specific segments are removed to form the active structure.

71
Q

involved in the assembly of insulin, where specific segments are removed to form the active structure.

A

Proteolytic cleavage

72
Q

are self-propagating, stable β-sheet aggregates that can form from many proteins.

A

Amyloid fibrils

73
Q

__ may be released from dead cells and accumulate as amyloid, which can kill cells and damage tissues.

A

Protein aggregates

74
Q

Protein aggregates may be released from dead cells and accumulate as __, which can kill cells and damage tissues.

A

amyloid

75
Q

What are some severe amyloid pathologies? (2)

A

neurodegenerative diseases, such as Alzheimer’s and Parkinson’s disease.

76
Q
  • Disease caused by a misfolded, aggregate form of a particular protein called PrP (prion protein), which forms infectious amyloid fibrils.
  • transmissible, untreatable, and fatal brain diseases of mammals
A

Prion diseases

77
Q

Give examples of prion diseases:
- in sheeps; (1)
- humans; and (2-3)
- cattles. (4)

A

1) scrapie
2) Creutzfeldt-Jakob disease (CJD) - leads to dementia
3) Kuru
4) bovine spongiform encephalopathy (BSE) - “mad cow disease”

78
Q
  • consist of amyloid fibrils and act like vesicles containing peptides and hormones.
  • membrane-bound vesicles that store biologically active substances, including peptide hormones and proteins.
  • Some of these can contain amyloid fibrils, which allow for dense packing of hormones like insulin and glucagon.
  • Upon signaling (e.g., changes in blood glucose), this undergo exocytosis, releasing their contents into the bloodstream. The amyloid fibrils dissociate upon release, ensuring that the hormones become active and functional.
A

specialized “secretory granules”

79
Q

In this organisms, amyloid structures secrete proteins that form long amyloid fibrils projecting from the cell exterior, which help bind their neighbors to biofilms. What organism is this?

A

bacteria

80
Q

In bacteria, amyloid structures secrete proteins that form __ projecting from the cell __, which help bind bacterial neighbors to __.

A
  • long amyloid fibrils
  • exterior
  • biofilms (a community of microorganisms attached to an inert or living surface)
81
Q

help bind bacterial neighbors together, contributing to the formation and stability of biofilms.

A

amyloid fibrils

82
Q

A protein molecule’s biological properties are determined by its __ with other molecules.

A

physical interaction

83
Q

refers to a protein molecule’s ability to bind just one or a few molecules out of many thousands.

A

specificity

84
Q

the substance that is bound by a protein.

A

ligand

85
Q

What types of noncovalent bonds facilitate a protein’s binding to a ligand? (4)

A
  • hydrogen bonds
  • electrostatic attractions
  • van der Waals attractions
  • along with favorable hydrophobic interactions.
86
Q

How does the surface conformation of a protein influence its chemistry? (2)

A

1) the interaction of neighboring parts of the polypeptide chain may
restrict the access of water molecules to that protein’s ligand-binding site
2) the clustering of neighboring polar amino acid chains can alter their reactivity

87
Q

What are the three types of interfaces through which proteins bind to other proteins? (3)

A
  • surface-string interactions
  • helix-helix interactions
  • surface-surface interactions.
88
Q
  • bind tightly to a specific target molecule (antigen), inactivating it directly or marking it for destruction.
  • Y-shaped molecules with two identical binding sites that are complementary to a small portion of the surface of the antigen molecule.
A

Antibodies (immunoglobulins)

89
Q

Antibodies are __-shaped molecules with __ identical binding sites that are complementary to a small portion of the surface of the antigen molecule.

A
  • Y-shaped
  • two
90
Q

powerful and highly specific catalysts that cause the chemical transformations that make and break covalent bonds in cells.

A

enzymes

91
Q

What is the equation representing the enzyme-catalyzed reaction sequence?

A

E + S → ES → EP → E + P

92
Q

indicates the maximum rate of reaction that a single enzyme molecule can process in a given time, calculated as the maximum rate of reaction divided by the enzyme concentration.

A

turnover number

93
Q

Enzymes achieve extremely high rates of chemical reactions by ______ and greatly increasing the local concentration of substrate molecules at the catalytic site.

A

selectively stabilizing transition states

94
Q

an unstable intermediate state that occurs during the conversion of substrates to products.

A

transition state

95
Q

the free energy required to attain the transition state in a chemical reaction.

A

activation energy

96
Q

Enzymes __ the activation energy required to reach the transition state, facilitating faster reaction rates.

A

lower

97
Q

Enzymes can bind tightly to a __ and contain precisely positioned atoms that alter electron distributions in the atoms that participate directly in the making and breaking of __

A
  • transition state
  • covalent bonds
98
Q

It is a mechanism where enzymes use both acid and base catalytic actions simultaneously to stabilize transition states and enhance reaction rates.

A

acid-base catalysis

99
Q

an enzyme that catalyzes hydrolysis, adding a water molecule to break the bond between two adjacent sugar groups in a polysaccharide chain.

A

Lysozyme

100
Q

These small molecules or metal atoms assist enzymes in their catalytic function by enhancing the enzyme’s reactivity and specificity.

A

coenzyme

101
Q

Give examples of proteins that require small molecules to function properly. (2)

A
  • Rhodopsin requires retinal
  • hemoglobin requires a heme group
102
Q
  • a large protein assembly that allows the product of one enzyme to be passed directly to the next enzyme, increasing metabolic efficiency.
  • It speeds up metabolism by facilitating the direct transfer of intermediate products between enzymes in a pathway.
A

multienzyme complex

103
Q

Cell regulate the number of enzyme molecules produced by regulating the __ of the __ that encodes the enzyme.

A
  • expression
  • gene
104
Q

One way cells control enzymatic activity spatially is by confining sets of enzymes to specific __ within the cell.

A
  • compartments
105
Q

A process where a product produced late in a reaction pathway inhibits an enzyme that acts earlier in the pathway.

A

feedback inhibition

106
Q

It is a type of regulation that prevents an enzyme from acting/creating more products.

A

negative regulation

107
Q

Involves a regulatory molecule stimulating an enzyme’s activity instead of inhibiting it.

A

positive regulation

108
Q
  • Enzymes with at least two binding sites: an active site for substrates and a regulatory site for regulatory molecules.
  • Greek words __ meaning “other”, and __ meaning “solid” or “3D”
A
  • allosteric enzymes
  • allos
  • stereo
109
Q

The conformational change in an allosteric enzyme is because of the Interaction between the enzyme’s __ site and the __ site, often due to binding of a __.

A
  • active
  • regulatory
  • regulatory molecule
110
Q

When two ligands with coupled binding sites interact on a protein, they reciprocally affect each other’s binding, where a ___ caused by one ligand can alter the __ for the other.

A
  • conformational change
  • affinity
111
Q

Describe an example of negative regulation due to conformational coupling between two binding sites.

A

If glucose binding causes a shape change that decreases a protein’s affinity for molecule X, the binding of X will also decrease the protein’s affinity for glucose.

112
Q

It is a phenomenon in multimeric proteins where each subunit has its own ligand-binding site, allowing the protein to undergo a coordinated allosteric change when a ligand binds.

A

cooperative allosteric transition

113
Q

In what type of protein structure does cooperative allosteric transition commonly occur?

A

multimeric proteins with multiple subunits

114
Q

The transfer of the terminal phosphate group of an ATP molecule to a protein’s hydroxyl group.

A

protein phosphorylation

115
Q

It phosphorylates proteins by adding a phosphate group.

A

protein kinase

116
Q

They remove phosphate groups from proteins, a process called dephosphorylation.

A

protein phosphotases

117
Q
  • Proteins that use the guanine nucleotide GTP
  • they regulate cellular processes by switching between active (GTP-bound) and inactive (GDP-bound) states.
A

GTP-binding proteins

118
Q

GTP-binding proteins become __ by hydrolyzing GTP to GDP, with the loss of a phosphate group, a reaction catalyzed by the protein itself.

A

inactive

119
Q

They produce forces for processes like muscle contraction and cell movement (crawling and swimming).

A

motor proteins

120
Q

Proteins produce __, by coupling conformational changes to the hydrolysis of a tightly bound ATP molecule.

A

unidirectional conformational changes

121
Q

export hydrophobic molecules from the cytoplasm and are associated with chemotherapy resistance in tumor cells when overproduced.

A

ATP-binding cassette (ABC) transporters

122
Q

consist of 10 or more proteins that coordinate essential cellular processes like DNA replication, protein synthesis, vesicle budding, and transmembrane signaling.

A

Large protein complexes, or “protein machines”

123
Q

have binding sites for multiple other proteins, linking specific sets of interacting proteins and positioning them at specific cellular locations.

A

Scaffold proteins

Cell and Molecular Biology (8 decks)

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