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Biology > Protein structure & Functions > Flashcards

Protein structure & Functions Flashcards

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AP® Biology flashcards Biology 101 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
Q

Binding site

A

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

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26
Q

Electrophoresis

A

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.

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27
Q

Nuclear magnetic resonance (NMR) spectroscopy

A

Technique used for determining the three-dimensional structure of a protein in solution.

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28
Q

Antiparallel beta sheet

A

When the segment are in the opposite dirction

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29
Q

Protein phosphorylation

A

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

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30
Q

Lysozyme

A

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.

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31
Q

Primary structure

A

Structure that just the amino acid sequence of a protein.

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32
Q

Polypeptide backbone

A

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.

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33
Q

Coiled-coil

A

Stable, rodlike protein structure formed when two or more α helices twist repeatedly around each other.

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34
Q

GTP-binding protein

A

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
Q

Prions

A

type of misfold protein that can cause disease

36
Q

Aplha Helix

A

An elongated structure whose subunits twist in a regular fashion around a central axis, like a spiral staircase.

37
Q

Allosteric enzymes have _______ or _____ binding sites that influence one another

A

Two or more

38
Q

Quaternary structure

A

Complete structure formed by multiple, interacting polypeptide chains that form a larger protein molecule.

39
Q

X-ray crystallography

A

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
Q

Small Km means what?

A

Means a substrate binds very tightly tot he enzyme

41
Q

How are proteins controlled?

A
  1. Gene Expression
  2. Rate of protein degradation
  3. Holding proteins in subcellaur compartments
  4. The level of the protein itself
42
Q

Scaffold protein

A

Protein with multiple binding sites for other macromolecules, holding them in a way that speeds up their functional interactions.

43
Q

Large protien molecules usually contain more than ______

A

More than one polypetide chain

44
Q

The reaction catalyzed by lysozyme is what?

A

Hyrdolysis

45
Q

C-terminus

A

The end of a polypeptide chain that carries a carboxyl group ( - COOH).

46
Q

Globular protein

A

Any protein in which the polypeptide chain folds into a compact, rounded shape. Includes most enzymes.

47
Q

Protein kinase

A

Enzyme that catalyzes the transfer of a terminal phosphate group from ATP to a specific amino acid side chain on a target protein.

48
Q

An antibody is _______ & has ________, one on each arm of the Y

A

Is Y shaped & has two identical antigen -binding sites

49
Q

All proteins _______

A

Bind to other molecules

50
Q

Protein

A

Macromolecule built from amino acids that provides cells with their shape and structure and performs most of their activities.

51
Q

Active site

A

Region on the surface of an enzyme that binds to a substrate molecule and catalyzes its chemical transformation.

52
Q

A large Km means what?

A

That it binds very losely/ weakly

53
Q

Substrate

A

A molecule on which an enzyme acts to catalyze a chemical reaction.

54
Q

Subunit

A

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
Q

Secondary structure

A

Structure made of just Alpha helices & beta sheets that form within certain segments of the polypetide chain

56
Q

Antibody

A

Are immunoglobin proteins produced by the immunse system in response to foreign molecules

57
Q

Antigen

A

Molecule or fragment of a molecule that is recognized/ targeted by an antibody.

58
Q

Extracellular proteins are often stablized by _______

A

Covalent cross - linkages

59
Q

Protein family

A

A group of proteins that have similar amino acid sequence & 3-D shape

60
Q

Enzyme

A

A protein that catalyzes a specific chemical reaction.

61
Q

Proteins fold in a conformation of _________

A

Lowest energy

62
Q

Side chain

A

Portion of an amino acid not involved in forming peptide bonds; its chemical identity gives each amino acid unique properties.

63
Q

Disulfide bond

A

Type of cross-linkage & often used to reinforce a secreted protein’s structure or to join two different proteins together.

64
Q

Denatured proteins can recover its natural shape but depends on _______

A

Conditions

65
Q

Feedback inhibition

A

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
Q

Michaelis constant (KM)

A

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
Q

The catalytic activities of enzymes are regulated by ________

A

Other molecules

68
Q

Chromatography

A

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
Q

Parallel beta sheet

A

When the neighboring segments run in the same direction

70
Q

Ligand

A

A small molecule that binds to a specific site on the protein

71
Q

What are the four types of noncovalent bonds that help proteins fold?

A
  1. Electrostatic attraction
  2. Hydrogen bonds
  3. Van der waals attraction
  4. Hydrophobic force
72
Q

Cryoelectron microscopy (cryo-EM)

A

Technique for observing the detailed structure of a macromolecule at very low temperatures after freezing native structures in ice.

73
Q

Amyloid Structure

A

Are beta sheets stacked together

74
Q

Protein phosphatase

A

Enzyme that catalyzes the removal of a phosphate group from a protein, often with high specificity for the phosphorylated site.

75
Q

Amino acid sequence

A

The order of the amino acid in a protein chain. Sometimes called the primary structure of a protein.

76
Q

Polypeptide chain

A

Linear polymer composed of multiple amino acids. Proteins are composed of one or more long polypeptide chains.

77
Q

Coenzyme

A

Small molecule that binds tightly to an enzyme and helps it to catalyze a reaction.

78
Q

Mass spectrometry

A

Sensitive technique that enables the determination of the exact mass of all of the molecules in a complex mixture.

79
Q

Transition state

A

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
Q

Denatured protein

A

Is a unfolded protein

81
Q

Regulatory GTP-binding proteins are switched on & off by the gain & loss of what?

A

A phosphate group

82
Q

Intracellular condensate

A

A large aggregate of phase-separated macromolecules that creates a region with a special biochemistry without the use of an encapsulating membrane.

83
Q

Beta sheets form ______

A

Amyloid structures

84
Q

The nonpolar (hydrophobic) side chains tend to fold ______ in the interior of the folded protein

A

Inwards

Biology (64 decks)

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