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Cell and Molecular Biology > Chapter 4: Protein Structure and Function > Flashcards

Chapter 4: Protein Structure and Function Flashcards

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1
Q

When we look at a cell in a microscope or analyze its electrical or _______, we are, in essence, observing the handiwork of proteins.

A

Biochemical activity

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2
Q

The main building blocks from which cells are assembled, and they constitute most of the cell’s dry mass.

A

Proteins

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3
Q

Proteins are the main building blocks from which cells are assembled, and they constitute most of the cell’s ______.

A

Dry mass

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4
Q

Enzymes promote _____ chemical reactions by providing intricate molecular surfaces contoured with particular bumps and crevices that can cradle or exclude specific molecules.

A

Intracellular

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5
Q

It catalyze covalent bond breakage or formation

A

Enzymes

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6
Q

It makes the alcohol in wine

A

Alcohol dehydrogenase

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7
Q

Degrades dietary proteins in the stomach

A

Pepsin

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8
Q

Helps convert carbon dioxide into sugars in plants

A

Ribulose bisphophate carboxylase

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9
Q

An enzyme that copies DNA

A

DNA polymerase

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10
Q

It adds a phosphate group to a protein molecule

A

Protein kinase

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11
Q

The common constituents of extracellular matrix and form fibers in tendons and ligaments

A

Collagen and elastin

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12
Q

It forms long, stiff microtubules inside cells

A

Tubulin

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13
Q

It forms filaments that underlie and support the plasma membrane

A

Actin

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14
Q

It forms fibers that reinforce epithelial cells and is the major protein in hair and horn

A

Keratin

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15
Q

It carries lipids in the bloodstream

A

Serum albumin

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16
Q

Proteins that provide mechanical support to cells and tissues

A

Structural proteins

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17
Q

Type of proteins that carry small molecules or ions

A

Transport proteins

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18
Q

Type of proteins that generate movement in cells and tissues

A

Motor proteins

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19
Q

Type of proteins that stores amino acids or ions

A

Storage proteins

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20
Q

Type of proteins that carry extracellular signals from cell to cell

A

Signal proteins

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21
Q

Type of proteins that detect signals and transmit them to the cell’s response machinery

A

Receptor proteins

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22
Q

Type of proteins that bind to DNA to swith genes on or off

A

Transcription regulators

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23
Q

It carries oxygen

A

Hemoglobin

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24
Q

Carries iron in thr bloodstream

A

Transferrin

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25
Q

A bacterial protein that is a light-activated proton pump that transports H+ ions out of the cell

A

Bacteriorhodopsin

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26
Q

Shuttle glucose into and out of cells

A

Glucose transporters

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27
Q

It clears Ca2+ from a muscle cell’s cytosol sfter the ions have triggered a contraction

A

Ca2+ pump

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28
Q

It provides the motive force for humans to move

A

Myosin

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29
Q

It interacts with microtubules to move organelles around the cell

A

Kinesin

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30
Q

It enables eukaryotic cilia and flagella to beat

A

Dynein

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31
Q

Iron is stored in the liver by binding to the small protein called

A

Ferritin

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32
Q

Iron is stored in the ____ by binding to the small protein ferritin

A

Liver

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33
Q

Found in egg white which is used as a source of amino acids for the developing bird embryo

A

Ovalbumin

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34
Q

Source of amino acids for baby mammals found in milk

A

Casein

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35
Q

A small protein that controls glucose levels in the blood

A

Insulin

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36
Q

It attracts growing nerve cell axons to specific locations in the developing spinal cord

A

Netrin

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37
Q

It stimulates some types of nerve cells to grow axons

A

Nerve growth factor (NGF)

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38
Q

It stimulates the growth and division of epithelial cells

A

Epidermal growth factor (EGF)

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39
Q

Found in the retina that detects light

A

Rhodopsin

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40
Q

Allows a cell to respond to the hormone insulin by taking up glucose

A

Insulin receptor

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41
Q

It increases the rate of heartbeat when it binds to epinephrine secreted by the adrenal gland

A

Adrenergic receptor

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42
Q

The adrenergic receptor on heart muscle increases the rate of heartbeat when it binds to _____ secreted by the adrenal gland

A

Epinephrine

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43
Q

The adrenergic receptor on heart muscle increases the rate of heartbeat when it binds to epinephrine secreted by the _____

A

Adrenal gland

44
Q

Found in bacteria. Silences the genes for the enzymes that degrade the sugar lactose

A

Lac repressor

45
Q

It acts as genetic switches to control development in multicellular organisms, including humans

A

DNA-binding proteins

46
Q

From a ____ point of view, proteins are by far the most structurally complex and functionally sophisticated molecules known

A

Chemical

47
Q

A protein molecule is made from a long chain of these amino acids, held together by ____

A

Covalent peptide bonds

48
Q

Proteins are therefore referred to as

A

Polypeptides, or polypeptide chains

49
Q

In each type of protein, the amino acids are present in a unique order, called the

A

Amino acid sequence

50
Q

Each polypeptide chain consists of a backbone called ____ that is adorned with a variety of chemical side chains. It is formed from a repeating sequence of the core atoms (-N-C-C-) found in every amino acid

A

Polypeptide backbone

51
Q

Proteins are typically made up of chains of several hundred amino acids, whose sequence is always presented starting with the _____, and read from ____ to ____.

A

N-terminus ; left to right

52
Q

Amino group in a polypeptide chain is written as

A

NH3+, also written as NH2

53
Q

Carboxyl group is written as

A

COO, or COOH

54
Q

The end carrying the amino group (NH3+/NH2) is called _________

A

Amino terminus or N-terminus

55
Q

The end carrying the free carboxyl group is the __________

A

Carboxyl terminus or C-terminus

56
Q

Projecting from the polypeptide backbone are the ___________ - the part of the amino acid that is not involved in forming peptide bonds

A

Amino acid side chains

57
Q

It gives each amino acid its unique properties

A

Side chains

58
Q

Long polypeptide chains are very flexible, as many of the covalent bonds that link the carbon atoms in the polypeptide backbone allow free rotation of the atoms they join. Thus, proteins can fold in an enormous number of ways. The shape of these folded chains however, is constrained by many sets of ______ bonds that form within proteins that help protein fold up and maintain their shape.

A

Weak noncovalent bonds

59
Q

The non covalent bonds that help proteins fold up and maintain their shape include

A

Hydrogen bonds
Electrostatic attractions
Van der Waals attractions

60
Q

The stability of each folded shape is largely determined by the combined strength of large numbers of

A

Noncovalent bonds

61
Q

Protein folding has been studied in the laboratoru using ___

A

Highly purified proteins

62
Q

A process where proteins gets unfolded by treatment with solvents that disrupt the noncovalent interactions holding the folded chain together

A

Denaturation (denatured protein)

63
Q

Under the right conditions, when the denaturing solvent is removed, the protein often refold sponaneously into its original conformation , a process called

A

Renaturation

64
Q

The final folded structure of a protein is called

A

Conformation

65
Q

Although a protein chain can fold into its correct conformation without outside help, protein folding in a living cell is generally assisted by a large set of special proteins called ____ that bind to partly folded chains and help them to fold along the most energetically favorable pathway. The function of thede chaperones requires ATP binding and hydrolysis

A

Chaperone proteins

66
Q

Others form ____ in which single polypeptide chains can fold without the risk of forming aggregates in the crowded conditions of the cytoplasm

A

Isolation chambers

67
Q

The conformation of a protein is determined solely by its

A

Amino acid sequence

68
Q

A model that shows the overall organization of the polypeptide chain and provides a straightforward way to compare the structures of related proteins

A

Backbone model

69
Q

A model that shows the polypeptide backbone in a way that emphasizes its most conspicuous folding patterns

A

Ribbon model

70
Q

A model that includes the positions of all the amino acid side chains; this view is essentially useful for predicting which amino acids might be involved in the protein’s activitiy

A

Wire model

71
Q

A model that provides a contour map of the protein surface, which reveals which amino acids are exposed on the surface and shows how the protein might look to a small molecule such as water or to another macromolecule in the cell

A

Space-filling model

72
Q

The first folding pattern discovered that was found in the protein a-keratin which is abundant in skin and hair, nails, and horns

A

a helix

73
Q

A second folded structure that was found in the protein fibroin, the major constituent of silk

A

B sheet

74
Q

The two folding patters (a helix and B sheets) are particularly common because they result from ____ bonds that form between N-H and C=O groups in the polypeptide backbone

A

Hydrogen

75
Q

True or false. The helix is not a channel: no ions or small molecules can pass through it

A

true

76
Q

It is generated simply by placing many similar subunits next to one another, each in the same strictly repeated relationship to the one before

A

helix

77
Q

A hydrogen bond is made between every ____ amino acid, linking the C=O of one peptide bond to the N-H of another. This pattern gives rise to a regular right-handed helix with a complete turn every 3.6 amino acids

A

Fourth

78
Q

Sometimes two (or three) α helices will wrap around one another to form a particularly stable structure called

A

coiled-coil

79
Q

A folding structure that form the basis of amyloid structures, in
which they are stacked together in long rows with their amino acid
side chains interdigitated like the teeth of a zipper

A

B sheets

80
Q

It can convert the properly
folded version of the protein in an infected brain into the abnormal conformation. This allows the to form aggregates which can spread rapidly from cell to cell, eventually causing the death of
the affected animal or human

A

misfolded prion form of a protein

81
Q

a protein’s structure begins with its amino acid sequence, this is considered its

A

primary structure

82
Q

The next level of organization includes the α helices and β sheets that form within certain segments of the polypeptide chain; these folds are elements of the protein’s

A

secondary structure

83
Q

The full, three-dimensional conformation formed by an entire polypeptide chain—including the α helices, β sheets, and all other loops and folds that form between the N- and C-termini—is sometimes referred to as the

A

tertiary structure

84
Q

It is defined as any segment of a polypeptide chain that can fold
independently into a compact, stable structure. It usually contains between 40 and 350 amino acids—folded into α helices and β sheets and other elements of structure—and it is the modular unit from
which many larger proteins are constructed

A

protein domain

85
Q
A
86
Q

Any region on a protein’s surface that interacts with other molecule through sets of noncovalent bonds is termed as

A

Binding site

87
Q

Two protein subunits

A

Dimer

88
Q

These proteins generally have a relatively simple, elongated three-dimensional structure and are commonly referred to as

A

Fibrous proteins

89
Q

Fibrous proteins are especially abundant outside the cell, where they form the gel-like ______ that helps bind cells together to form tissues

A

Extracellular matrix

90
Q

It enables skin and other tissues, such as arteries and lungs, to stretch and recoil without tearing

A

Elastic fibers (produced by elastin molecules)

91
Q

A component of the cytoskeleton that gives cells mechanical strength

A

Intermediate filaments

92
Q

Any substance that is bound by a protein- whether it is an ion, a small organic molecule or a macromolecule is referred to as

A

Iigand

93
Q

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

A

Weak noncovalent interactions

94
Q

These are immunoglobulin proteins produced by the immune system in response to foreign molecules, especially those in the surface of an invading microorganism.

A

Antibodies

95
Q

The target molecule that the antibody recognizes

A

Antigen

96
Q

This generates an enormous diversity of antigen-binding sites by changing only the length and amino acid sequence of this thing which is how the wide variety of different antibodies is formed

A

Hypervariable loops

97
Q

It gives hemoglobin and blood its red color

A

Heme

98
Q

It is a form of negative regulation that prevents an enzyme from acting

A

Feedback inhibition

99
Q

Large molecules that contain binding sites recognized by multiple proteins. It allows proteins to be assembled and activated only when and where they are needed

A

Scaffold proteins

100
Q

The resulting slurry of breaking open the cells to release their contents

A

Cell homogenate or extract

101
Q

The standard approach involves purifying the protein through a series of _____ steps to separate the individual components of a complex mixture into portions or fractions

A

chromatography

102
Q

The most efficient forms of protein chromatography separate a polypeptides on the basis of their ability to bind to a particular molecule - a process called

A

Affinity chromatography

103
Q

A technique where an electric field is applied to a solution or a polymer gel containing protein molecules and migrate them in a direction and at a speed that reflects their size and net charge

A

Electrophoresis

104
Q

A technique that determines the exact mass of peptide fragment in a purified protein, which then allows the protein thought to be encoded by the genome of the relevant organism.

A

Mass spectrometry

105
Q

After the peptides pass through the first mass spectrometer, they are broken into even smaller fragments and analyzed by a second mass spectrometer

A

Tandem mass spectrometry

106
Q

Not a question. The predominant way to discover the precise folding pattern of any protein is by experiment, using
X-ray crystallography,
Nuclear magnetic resonance spectroscopy
Cryoelectron microscopy

A

Cell and Molecular Biology (6 decks)

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