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CMB - Midterms > Module 1B - Biomolecules & Enzymes > Flashcards

Module 1B - Biomolecules & Enzymes Flashcards

1
Q

Structurally complex and functionally sophisticated
molecules.

A

Proteins

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2
Q

The shape of protein is specified by its:

A

Amino acid sequence

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3
Q

Protein structure is made of:

A

Long unbranched chain of amino acids/Polypeptides

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4
Q

Repeating sequence of atoms along the core of polypeptide chains

A

Polypeptide backbone

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5
Q

Gives the amino acids their unique properties

A

Side Chains

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6
Q

Amino acids with negative side chains:

A

Aspartic Acid and Glutamic acid

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7
Q

Amino acids with positive side chains:

A

Arginine, Lysine, Histidine

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8
Q

Amino acids with uncharged polar side chains:

A

Asparagine, Glutamine, Serine, Threonine, Tyrosine

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9
Q

Amino acids with non-polar side chains:

A

Alanine, Glycine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Methionine, Tryptophan, Cysteine

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10
Q

Causes protein folding:

A

Weak non-covalent bonds

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11
Q

Non-covalent bonds of protein:

A

Hydrogen bonds, electrostatic attractions, and Van der Waals

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12
Q

The force that causes hydrophobic molecules to be forced together within an aqueous environment to reduce the disruptive effects of water molecules on the hydrogen bonded networks.

A

Hydrophobic clustering forces

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13
Q

Proteins form into a conformation of:

A

Lowest Energy

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14
Q

Class of proteins that assist in protein folding or unfolding

A

Molecular chaperones

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15
Q

Contains all the information needed for specifying the three dimensional shape of a protein.

A

Amino acid sequence

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16
Q

The 3D structure of protein has the ability to

A

Denature and Renature

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17
Q

Two regular folding patterns of protein are found within proteins:

A

α-Helix and β sheet

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18
Q

The protein folding structure takes shape due to the result of hydrogen bonding between the:

A

N-H and C=O groups in the polypeptide chain groups

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19
Q

Polypeptide chain pattern that forms from the neighboring segments of the polypeptide backbone that runs in the same orientation/direction.

A

Parallel chains

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20
Q

Polypeptide chain pattern that folds back and forth upon itself with each section of the chain running in the direct opposite direction of its immediate neighbors.

A

Anti-parallel chains

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21
Q

Folding patter that generate when a single polypeptide chain twists around itself to form a rigid cylinder.

A

α-Helix

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22
Q

Hydrogen bonds linking C=O of one peptide bond to N-H of another occurs between every:

A

4th peptide

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23
Q

Forms when two or more α-Helix chains that coil have most of their non-polar side chains on one side.

A

Coiled-coil

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24
Q

Stage of protein structure that only comprises the sequence of amino acids:

A

Primary protein structure

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25
Q

Stage of protein structure where the occurrence of hydrogen bonding in the polypeptide backbone of the protein structure that causes amino acids to fold into a repeating pattern. Appearance of α-Helix and β sheets.

A

Secondary protein structure

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26
Q

Stage of protein structure where full 3D folding of the protein structure occurs due to polypeptide chain interactions.

A

Tertiary protein structure

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27
Q

Stage of protein structure where the protein molecule forms a protein complex consisting of more than one amino acid polypeptide chain.

A

Quaternary protein structure

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28
Q

How many protein coding genes does the human genome have?

A

21,000 protein-coding genes

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29
Q

Proteins can be classified into families based on their:

A

Amino acid and 3D conformation

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30
Q

___% of our protein coding genes to known protein structure belong to ____ different families.

A

40, 500

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31
Q

The structure of proteins (such as arrangement of atoms and the interactions and dynamics of proteins at the atomic level) and their classifications are identified using:

A

X-ray crystallography and Nuclear Magnetic Resonance (NMR)

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32
Q

Basic units of protein that can fold, function, and evolve independently. They easily integrate into other proteins.

A

Protein domains

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33
Q

Process of creating new novel combinations of gene functional domains. Can be readily linked in series to form extended protein structures.

A

Domain shuffling

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34
Q

What are protein modules?

A

The subset of protein domains, mobile during evolution.

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35
Q

___% of human protein domains are vertebrate specific.

A

7%

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36
Q

A specialized function of a protein domain.

A

Major Histocompatibility Complex (MHC)

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37
Q

Vertebrates have inherited majority of their protein domains from:

A

Invertebrates

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38
Q

Given rise to many novel combinations of protein domains during the evolution of vertebrates.

A

Domain shuffling

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39
Q

Allows protein to bind to each other to create/produce structures in the cell.

A

Weak non-covalent bonds

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40
Q

Any region in the protein’s surface that can interact with other molecules.

A

Binding site

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41
Q

Formation of a symmetric complex of two protein subunits(dimer).

A

“Head to head” arrangement

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42
Q

A symmetrical arrangement of two identical α-globin subunits and two identical β-globin
subunits.

A

Hemoglobin

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43
Q

A long chain of identical protein molecules can be constructed if:

A

Each molecule has a binding site complementary to another region on the surface of the same molecule.

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44
Q

Long helical structures produced from many molecules of the protein actin.

A

Actin filament

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45
Q

An elongated three-dimensional protein structure.

A

Fibrous protein

46
Q

Main component in long lived protein structures.

A

Keratin filaments

47
Q

A dimer of two identical subunits.

A

α-keratin

48
Q

Rope-like protein structures that is the important component of the cytoskeleton.

A

Intermediate filaments

49
Q

What are the dimension of a collagen molecule?

A

300 nm x 15 nm

50
Q

This type of protein is abundant outside of the cell and is the main component for the gel like consistency of the extracellular matrix.

A

Fibrous protein

51
Q

Consists of three long polypeptide chains, each containing that non-polar amino acid glycine at every 3rd position.

A

Collagen

52
Q

Type of protein with a highly disturbed polypeptide chain and also dominant within the extracellular matrix.

A

Elastin

53
Q

Relatively loose and unstructured polypeptide chains that are covalently cross-linked to produce a rubber-like elastic meshwork that can be reversibly pulled from one conformation to another.

A

Elastin

54
Q

Why are disordered polypeptide chain proteins so frequent naturally?

A
  1. Serves as a “tether” to hold two protein domains in close proximity
  2. Form specific binding sites for other proteins that have high specificity
  3. They restrict diffusion
  4. Trigger cell signaling events
55
Q

Proteins that are secreted extracellular are often stabilized by:

A

Covalent cross-linkages

56
Q

A sample of covalent cross-linkages that does not change the conformation of a protein but instead act as atomic “staples”

A

Sulfur-sulfur bonds/disulfide bonds

57
Q

What type of reaction causes the formation of covalent cross-linkages?

A

Oxidation Reduction

58
Q

In the proteins secreted extracellular, oxidation reduction reaction forms ___________ that stabilizes those proteins.

A

Covalent cross-linkages

59
Q

The advantages of using protein molecules as subunit of large structures:

A
  1. Requires only a small amount of genetic information.
  2. Assembly and disassembly can readily be controlled.
  3. Errors in the synthesis of the structure can easily be avoided.
60
Q

Structure made from hundreds of identical protein subunits that encloses and protects the viral nucleic acid.

A

Protein coat/Capsid of viruses

61
Q

Cell subunit that is capable of spontaneous assembly into the final structure under appropriate conditions.

A

Purified subunits

62
Q

Organisms or structures that are capable of self assembly:

A

Tobacco mosaic virus (TMV) and bacterial ribosomes

63
Q

Guides the construction of complex biological structures but does not take part in the final assembled structure.

A

Assembly factors

64
Q

Self propagating stable β-sheet protein aggregates that are released from dead cells that can kill cells and damage tissues.

A

Amyloid Fibrils

65
Q

Accumulation of protein aggregates from dead cells:

A

Amyloid

66
Q

Most severe amyloid pathologies:

A

Neurodegenerative diseases (Alzheimer’s and Parkinson’s)

67
Q

A subclass of amyloid, caused by misfolded, aggregate form of a particular protein called prion protein (PrP).

A

Prions

68
Q

Acts as vesicles containing peptides and hormones.

A

Secretory granules that consists of amyloid fibrils

69
Q

Determines the BIOLOGICAL properties and function of a protein.

A

Physical interaction with other molecules.

70
Q

Characteristic of a protein that allows it to bind to just ONE or FEW MOLECULES out of a THOUSAND.

A

Specificity

71
Q

Substance that is BOUND by the PROTEIN.

A

Ligand

72
Q

The specificity and affinity of a protein to a ligand is determined by:

A

Formation of a set of weak non-covalent bonds plus- favorable hydrophobic interactions.

73
Q

Determines the CHEMISTRY of a protein molecule:

A

Surface conformation

74
Q

The region of a protein that ASSOCIATES WITH a LIGAND.

A

Binding sites

75
Q

Different types of PROTEIN-PROTEIN INTERACTION:

A
  1. Surface-string interaction
  2. helix-helix interaction
  3. surface-surface interaction
76
Q

Association of two or more alpha-helix strands that are common to the secondary structure in proteins.

A

Helix-helix interaction

77
Q

Occurs when specific regions on the surface of one protein binds to a complementary region on a surface of another protein:

A

Surface-surface interaction

78
Q

Catalysts that cause chemical transformation that make or break covalent bonds in cells.

A

Enzymes

79
Q

A complex that forms when a substrate binds with an enzyme.

A

Enzyme-substrate complex (ES)

80
Q

Protein that binds to a target molecule (antigen), causing its inactivation or making it for destruction.

A

Anti-body or immunoglobins

81
Q

Speeds up the reaction time in cells, they act as catalysts.

A

Enzymes

82
Q

Standard formula for enzyme catalyzed reactions:

A

E + S = ES —> EP —> E + P

83
Q

The formula for enzyme catalyzed reactions:

A

E + S = ES —> EP —> E + P

84
Q

What is the main function of an enzyme?

A

Lower the activation energy required for a reaction

85
Q

The maximum rate of reaction divided by the enzyme concentration:

A

Turnover number

86
Q

Unstable intermediate state of an enzyme-substrate reaction:

A

Transition state

87
Q

The free energy required to attain the transition state:

A

Activation energy

88
Q

True or False. Enzymes are capable of using an Acid and a Base Catalysis simultaneously.

A

True

89
Q

Enzymes contains precisely positioned atoms that alter the electron distribution of atoms that participate directly in:

A

Making and breaking covalent bonds

90
Q

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

A

Hydrolysis

91
Q

Addition of a water molecule between two bonded molecules, causing the bond to break:

A

Hydrolysis

92
Q

Presence of a _____________ associated on an enzymes binding site assists with the catalytic function of the enzyme.

A

Small molecule/Metal atom

93
Q

Proteins that require specific small molecules to function properly:

A

Rhodopsin and hemoglobin

94
Q

A large assembly of multiple proteins/enzymes; it allows the passage of product from enzyme a directly towards enzyme B and so on:

A

Multi-enzyme complex

95
Q

A product produce by enzyme catalysis inhibits an enzyme that acts earlier within the pathway to stop the reaction:

A

Feedback inhibition

96
Q

When a molecule binds to an enzyme that changes the conformation of its binding site that prevents another substrate binding:

A

Negative feedback/Negative regulation

97
Q

A regulation where a molecules binds to an enzyme that stimulates its activity rather that shutting the enzyme down:

A

Positive feedback/Positive regulation

98
Q

A type of enzyme that contains two binding sites on its surface; an active site that recognizes the substrate and a regulatory site that recognizes regulatory molecules:

A

Allosteric enzyme

99
Q

Allosteric came from these Greek words:

A

allos = “other”
stereo = “solid” or “3D”

100
Q

The interaction between separated sites on a protein:

A

Conformational change

101
Q

Phenomena that occurs on multimeric enzymes, where each subunit of the protein has its own ligand-binding site:

A

Cooperative allosteric transition

102
Q

Transfer of the terminal phosphate group from an ATP molecule to the hydroxyl group:

A

Protein phosphorylation

103
Q

A protein that selectively modifies other proteins by covalently adding phosphates to them (phosphorylation).

A

Protein kinase

104
Q

Enzyme that causes the removal of phosphate from proteins (dephosphorylate).

A

Protein phosphatases

105
Q

Addition and removal of phosphate regulates the state (active or inactive) of the this protein.

A

GTP-binding proteins

106
Q

GTP-binding proteins is hydrolyzed causing the loss of one phosphate group in a reaction catalyzed by the protein itself. What is the inactive state of GTP-binding proteins?

A

GDP-bound state

107
Q

Responsible for generating the forces responsible for muscle contraption and the crawling and swimming of the cells:

A

Motor proteins

108
Q

Proteins that produce large movement in the cells:

A

Motor proteins

109
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

110
Q

Membrane bound transporter that functions to export hydrophobic molecules from the cytoplasm:

A

ABC transporters

111
Q

Composes of a linked set of 10 or more proteins that catalyzes DNA replication, protein synthesis, vesicle budding, or transmembrane signaling.

A

Protein machines

112
Q

Protein binding sites for multiple proteins.

A

Scaffold proteins

CMB - Midterms (5 decks)

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