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Protein structure & Functions Flashcards

1
Q

N-terminus

A

The end of a polypeptide chain that carries a amino group.

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2
Q

At low concentration of substrate the amount of enzyme-substrate complex depends on what?

A

On the concentration of the substrate

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3
Q

The shape of a protein depends on _____

A

Amino Acid sequence

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4
Q

Protein tends fold in a shape where its free energy is ________

A

Minimized

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5
Q

Renaturation

A

The process where proteins refold back into its orginal shape

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6
Q

Negative Regulation

A

Prevents an enzyme from acting

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7
Q

Peptide bond

A

Covalent chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid. (See Panel 2 - 6, pp. 76 - 77.)

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8
Q

Polar side chains tends to arrange themselves near the ________ of the folded protein where they can form hydrogen bonds

A

Outside

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9
Q

ATP hydrolysis allows ______ to produce direct movements in cells

A

Motor proteins

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10
Q

Enzyme-substrate complex

A

The rate at which products are formed

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11
Q

_______ proteins can form amyloid structures that causes disease

A

Misfolded protiens

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12
Q

Protein domain

A

Segment of a polypeptide chain that can fold into a compact, stable structure and that often carries out a specific function.

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13
Q

Conformation

A

Precise, three-dimensional shape of a protein or other macromolecule, based on the spatial location of its atoms in relation to one another.

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14
Q

_______ & ________ are the most common folding patterns

A

Alpha helix & beta sheets

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15
Q

Motor protein

A

Protein that uses energy derived from the hydrolysis of a tightly bound ATP molecule to propel itself along a protein filament or polymeric molecule. & are responsible for muscle contraction & moving organales along the cytosketcal tracks

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16
Q

Protein machine

A

The hydrolysis of bound nucleotide triphosphate (ATP or GTP) to make proteins move

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17
Q

Positive regulation

A

Enzyme’s activity is stimulated by other molecules rather than being slowed down or blocked (opposite of negative regulations)

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18
Q

Tertiary structure

A

Complete three-dimensional structure of a fully folded protein.

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19
Q

Turnover number

A

The maximum number of substrate molecules that an enzyme can convert into product per second.

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20
Q

Fibrous protein

A

A protein with an elongated, rodlike shape, such as collagen or a keratin filament.

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21
Q

Feedback regulation is a form of what?

A

Negative Regulation

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22
Q

The distrubtion of a proteins polar & nonpolar amino

acids has a factor in _________

A

Folding of a protein

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23
Q

beta sheet

A

Polypetide chains fold into a flat orderly pattern

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24
Q

Chaperone proteins assist in protein folding where some bond to partly folded chains & help them fold along the most ___________

A

Energetically favorable pathways

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25
Binding site
Region on the surface of a protein, typically a cavity or groove, that interacts with another molecule (a ligand) through the formation of multiple noncovalent bonds & attach to the ligand
26
Electrophoresis
Technique for separating a mixture of proteins or DNA fragments by placing them on a polymer gel and subjecting them to an electric field. The molecules migrate through the gel at different speeds depending on their size and net charge.
27
Nuclear magnetic resonance (NMR) spectroscopy
Technique used for determining the three-dimensional structure of a protein in solution.
28
Antiparallel beta sheet
When the segment are in the opposite dirction
29
Protein phosphorylation
Addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase; & can control protein activity by causing a conformational change
30
Lysozyme
Enzyme that severs the polysaccharide chains that form the cell walls of bacteria; found in many secretions including saliva and tears, where it serves as an antibiotic.
31
Primary structure
Structure that just the amino acid sequence of a protein.
32
Polypeptide backbone
Repeating sequence of the atoms ( - N - C - C - ) that form the core of a protein molecule and to which the amino acid side chains are attached.
33
Coiled-coil
Stable, rodlike protein structure formed when two or more α helices twist repeatedly around each other.
34
GTP-binding protein
Intracellular signaling protein whose activity is determined by its association with either GTP or GDP. Includes both trimeric G proteins and monomeric GTPases, such as Ras.
35
Prions
type of misfold protein that can cause disease
36
Aplha Helix
An elongated structure whose subunits twist in a regular fashion around a central axis, like a spiral staircase.
37
Allosteric enzymes have _______ or _____ binding sites that influence one another
Two or more
38
Quaternary structure
Complete structure formed by multiple, interacting polypeptide chains that form a larger protein molecule.
39
X-ray crystallography
Technique used to determine the three-dimensional structure of a protein molecule when a beam of x-rays is passed through an ordered array of the protein.
40
Small Km means what?
Means a substrate binds very tightly tot he enzyme
41
How are proteins controlled?
1. Gene Expression 2. Rate of protein degradation 3. Holding proteins in subcellaur compartments 4. The level of the protein itself
42
Scaffold protein
Protein with multiple binding sites for other macromolecules, holding them in a way that speeds up their functional interactions.
43
Large protien molecules usually contain more than \_\_\_\_\_\_
More than one polypetide chain
44
The reaction catalyzed by lysozyme is what?
Hyrdolysis
45
C-terminus
The end of a polypeptide chain that carries a carboxyl group ( - COOH).
46
Globular protein
Any protein in which the polypeptide chain folds into a compact, rounded shape. Includes most enzymes.
47
Protein kinase
Enzyme that catalyzes the transfer of a terminal phosphate group from ATP to a specific amino acid side chain on a target protein.
48
An antibody is _______ & has \_\_\_\_\_\_\_\_, one on each arm of the Y
Is Y shaped & has two identical antigen -binding sites
49
All proteins \_\_\_\_\_\_\_
Bind to other molecules
50
Protein
Macromolecule built from amino acids that provides cells with their shape and structure and performs most of their activities.
51
Active site
Region on the surface of an enzyme that binds to a substrate molecule and catalyzes its chemical transformation.
52
A large Km means what?
That it binds very losely/ weakly
53
Substrate
A molecule on which an enzyme acts to catalyze a chemical reaction.
54
Subunit
A monomer that forms part of a larger molecule, such as an amino acid residue in a protein or a nucleotide residue in a nucleic acid. Can also refer to a complete molecule that forms part of a larger molecule. Many proteins, for example, are composed of multiple polypeptide chains, each of which is called a protein subunit.
55
Secondary structure
Structure made of just Alpha helices & beta sheets that form within certain segments of the polypetide chain
56
Antibody
Are immunoglobin proteins produced by the immunse system in response to foreign molecules
57
Antigen
Molecule or fragment of a molecule that is recognized/ targeted by an antibody.
58
Extracellular proteins are often stablized by \_\_\_\_\_\_\_
Covalent cross - linkages
59
Protein family
A group of proteins that have similar amino acid sequence & 3-D shape
60
Enzyme
A protein that catalyzes a specific chemical reaction.
61
Proteins fold in a conformation of \_\_\_\_\_\_\_\_\_
Lowest energy
62
Side chain
Portion of an amino acid not involved in forming peptide bonds; its chemical identity gives each amino acid unique properties.
63
Disulfide bond
Type of cross-linkage & often used to reinforce a secreted protein's structure or to join two different proteins together.
64
Denatured proteins can recover its natural shape but depends on \_\_\_\_\_\_\_
Conditions
65
Feedback inhibition
A form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway. (Usually slows down the catalytic action which limits further substrates)
66
Michaelis constant (KM)
The concentration of substrate at which an enzyme works at half its maximum velocity; serves as a measure of how tightly the substrate is bound.
67
The catalytic activities of enzymes are regulated by \_\_\_\_\_\_\_\_
Other molecules
68
Chromatography
Technique used to separate the individual molecules in a complex mixture on the basis of their size, charge, or their ability to bind to a particular chemical group. In a common form of the technique, the mixture is run through a column filled with a material that binds the desired molecule, and it is then eluted from the column with a solvent gradient.
69
Parallel beta sheet
When the neighboring segments run in the same direction
70
Ligand
A small molecule that binds to a specific site on the protein
71
What are the four types of noncovalent bonds that help proteins fold?
1. Electrostatic attraction 2. Hydrogen bonds 3. Van der waals attraction 4. Hydrophobic force
72
Cryoelectron microscopy (cryo-EM)
Technique for observing the detailed structure of a macromolecule at very low temperatures after freezing native structures in ice.
73
Amyloid Structure
Are beta sheets stacked together
74
Protein phosphatase
Enzyme that catalyzes the removal of a phosphate group from a protein, often with high specificity for the phosphorylated site.
75
Amino acid sequence
The order of the amino acid in a protein chain. Sometimes called the primary structure of a protein.
76
Polypeptide chain
Linear polymer composed of multiple amino acids. Proteins are composed of one or more long polypeptide chains.
77
Coenzyme
Small molecule that binds tightly to an enzyme and helps it to catalyze a reaction.
78
Mass spectrometry
Sensitive technique that enables the determination of the exact mass of all of the molecules in a complex mixture.
79
Transition state
Transient structure that forms during the course of a chemical reaction; in this configuration, a molecule has the highest free energy; it is no longer the substrate, but is not yet the product.
80
Denatured protein
Is a unfolded protein
81
Regulatory GTP-binding proteins are switched on & off by the gain & loss of what?
A phosphate group
82
Intracellular condensate
A large aggregate of phase-separated macromolecules that creates a region with a special biochemistry without the use of an encapsulating membrane.
83
Beta sheets form \_\_\_\_\_\_
Amyloid structures
84
The nonpolar (hydrophobic) side chains tend to fold ______ in the interior of the folded protein
Inwards

Biology (64 decks)

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