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BIOL 600 > Unit 1 > Flashcards

Unit 1 Flashcards

1
Q

DNA nucleotides

A

adenine, guanine, cytosine, thymine

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2
Q

unbranched polymer that, when folded into its three dimensional shape, performs much of the work of the cell

A

Proteins

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3
Q

of hydrogen bonds formed between A and T

A

2

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4
Q

of hydrogen bonds formed between C and G

A

3

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5
Q

transfer of info from DNA to RNA

A

transcription

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6
Q

__________ are cells which are composed of multiple specialized compartments.

A

Eukaryotes

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7
Q

Broad class of biological macromolecules which serve as a barrier, signaling component and performs several other duties

A

Lipids

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8
Q

Highly organized region of the cell where protein glycosylation occurs

A

Golgi

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9
Q

Responsible for protein processing and xenobiotic metabolism

A

Endoplasmic Reticulum

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10
Q

Filled with proteases and other digestive enzymes

A

Lysosomes

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11
Q

Four key classes of biomolecules

A

proteins, nucleic acids, lipids, carbs

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12
Q

Eukaryotic vs Prokaryotic

A

Eukaryotic have membrane-bound compartments, prokaryotes do not.

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13
Q

Intracellular, membrane-bounded compartments

A

organelles

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14
Q

What is the role of the Endoplasmic Reticulum?

A

Rough ER: synthesizes proteins

Smooth ER: chemical processing

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15
Q

Which macromolecule class is chiefly responsible for catalysis of cellular processes?

A

Proteins

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16
Q

DNA and RNA are composed of what basic biochemical compounds

A

nucleotides

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17
Q

What are the important functions of carbs

A

fuel and information; cell to cell communication

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18
Q

Type of bond between oxygen and hydrogen in water

A

Hydrogen bond

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19
Q

Electric _________ is the result of an electronegative atom in a covalent bond with a non-electronegative bond.

A

dipole

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20
Q

Electrostatic interaction between atoms with opposite electrical charges are also called _______.

A

ionic

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21
Q

Water shields the electrostatic interaction of ions due to its high ____________.

A

dielectric constant

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22
Q

The distance when two atoms no longer repulse each other yet have a strongest attractions is known as the _________ radii or contact distance.

A

Van der Waals

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23
Q

Thermodynamic force that drives hydrophobic interactions

A

Entropy

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24
Q

A molecule with two distinctive chemical properties or characteristics

A

amphiphatic

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25
Q

Using Coulomb’s Law, describe how water is an ideal solvent for the ions found in cells

A

Water has a high dielectic constant

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26
Q

What is the significance of hydrogen bonding in biochemical structures such as DNA?

A

Hydrogen bonding allows bonds to be broken and rebuilt.

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27
Q

What is an electrostatic interaction?

A

Interaction between ions, Na+ Cl-

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28
Q

What is the net effect of many van der Waals interactions?

A

stability in numbers

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29
Q

If most proteins are found surrounded by water in the cell, what type of functional groups would you expect to find on the surface of a water soluble protein?

A

Hydrophillic/Polar

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30
Q

What is the second law of thermo?

A

Entropy must always increase.

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31
Q

How do hydrophobic interactions aid in protein folding?

A

They force the nonpolar sidechains to come together.

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32
Q

Henderson-Hasselbach Equation

A

pH = pKa +log_10 (A-/HA-)

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33
Q

Chiral type of amino acids found in proteins

A

L-amino acid

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34
Q

Another name for dipolar molecules

A

Zwitter ions

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35
Q

Disulfide bonds are formed by pairs of which amino acid?

A

Cysteine

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36
Q

The amino acid with a pKa near neutral

A

Histidine

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37
Q

The amino acid with whose side group leads to a less flexible peptide bond

A

Proline

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38
Q

The amino acid with an imidazole side chain

A

Histidine

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39
Q

An amino acid which must be supplied by the diet

A

Essential

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40
Q

The amino acid with a negative charged sidechain at neutral pH.

A

Aspartate or Glutamate

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41
Q

Amino acid with sulfide side chains

A

Cysteine

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42
Q

The amino acid with the abbreviation Ser.

A

SErine

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43
Q

Amino acid that contains a weakly acidic “phenolic” group

A

Tyrosine

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44
Q

Amino acid with the smallest sized chain allowing great flexibility in a protein

A

Glycine

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45
Q

Charge of alanine when the pH is 2.0

A

+1

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46
Q

Amino acid with an iodine ring

A

Tryptophan

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47
Q

General structure of amino acid

A

NH3, COOH, H, R

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48
Q

What is the importance of the central carbon on an amino acid?

A

alpha-carbon

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49
Q

When a peptide bond is formed, what molecule is also made?

A

H2O

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50
Q

According to convention, _____________ is the terminus drawn on the left side of a peptide.

A

alpha amino group

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51
Q

Where are proteins with extensive disulfide links likely to be found?

A

extra-cellular

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52
Q

This amino acid disrupts the alpha helix

A

Proline

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53
Q

Name of the plot that shows the possible phi and psi angles in proteins.

A

Ramachandran

54
Q

Why are all the theoretical combinations of phi and psi not possible?

A

steric clashes between atoms

55
Q

Type of structure to which alpha helices, beta sheets, and turns are referred to

A

Secondary Structure

56
Q

Overall 3D structure of a protein is referred to as its __________________.

A

Tertiary Structure

57
Q

These reagents disrupt protein dislufide bonds

A

BME DTT

58
Q

Almost all peptide bonds are this due to side group steric clash

A

Trans

59
Q

__________ is a fibrous protein and is the primary component of wool and hair.

A

Alpha Keratin

60
Q

Every third residue in the protein collagen is ________. Collagen contains _____________, a modified amino acid.

A

glycine; hydroxyproline

61
Q

The _________ beta-sheet structure occurs when the two strands are oriented in opposite directions.

A

anti-paralllel

62
Q

A protein is considered to be _________ when it is converted into a random coil structure without its normal activity.

A

denatured

63
Q

__________ refers to the spatial arrangement of polypeptide subunits and the nature of their interactions.

A

Quaternary

64
Q

How does a protein’s amino acid sequence influence the tertiary structure?

A

The side chains of the amino acids affect the way in which the protein folds.

65
Q

Name two methods that can be used to disrupt/break cells and tissues for protein purification

A

enzymatic; mechanical

66
Q

A type of protein chromatography that is based on the attraction of the protein for a particular chemical group.

A

?

67
Q

________ is added prior to protein gel electrophoresis to coat proteins with negative charges and to denature the proteins

A

SDS (Sodium ______ Sulfate)

68
Q

Proteins with different sedimentation coefficients can be separated by _________.

A

centrification

69
Q

Protein primary sequence can be determined by ________ and __________.

A

Edman Degredation; Mass spec

70
Q

2D protein gel electrophoresis is separation of proteins based on _______ and ________.

A

isoelectric point (pi); size

71
Q

Proteins can be separated from small molecules, ions, or buffers through a semi-permeable membrane by a method known as ________.

A

Dialysis

72
Q

Chromatic method that separates proteins based on their charges

A

Gel filtration

73
Q

__________ is a chemical reagent that is often used to detect the presence of amino acids

A

Ninhydrin

74
Q

Chromatographic method that separates proteins based on their sizes

A

ion exchange

75
Q

A nickel column used in purifying proteins will bind proteins that contain a ________ tag.

A

Hystine

76
Q

In the Edman method for protein sequencing, phenyl isothiocyanate is used to selectively remove the _________ residue.

A

N-terminus

77
Q

Disulfide bonds in proteins are readily oxidized by _______ or ________

A

BME; DTT

78
Q

Polypeptides can be fragmented into smaller peptides by cleavage with trypsin, which hydrolyzes the peptide bond at the C-terminal side of ___________ residues

A

Lysine; Arginine; Histidine

79
Q

_________ gels are often used media for electrophoretic techniques such as SDS-PAGE and isoelectric focusing.

A

Poly Acrylamine

80
Q

The mobility of proteins in SDS-PAGE is inversely proportional to their _______.

A

mass

81
Q

Websites where you can find published literature about proteins

A

PubMed

82
Q

Websites where you can find published literature about protein primary sequence

A

Swiss Prot

83
Q

Website where you can find published literature about protein 3D structures

A

Protein Data Bank

84
Q

Determines protein tertiary structures at atomic resolution through diffraction of protein crystals

A

X-ray crystallography

85
Q

Determines protein tertiary structures at atomic resolution through the use of atoms in the protein’s magnetic properties

A

NMR

86
Q

The site on the enzyme where the reaction occurs.

A

Active Site

87
Q

The substance that the enzyme binds and converts to product

A

Substrate

88
Q

Enzymes that do not have the required cofactor bound

A

Apoenzyme

89
Q

A tightly bound cofactor (heme) might be called a ____________.

A

prosthetic group

90
Q

Enzymes will decrease the energy of activation but does not change the ________ of a chemical reaction.

A

delta G

91
Q

The enzyme active site amino acids facilitate a lower ___________.

A

activation energy

92
Q

The two methods in which enzymes bind to a substrate

A

Lock and key; induced fit

93
Q

Enzymes accelerate the rate of a chemical reaction by ________ the free energy of activation of the reaction.

A

lowering

94
Q

An enzyme which loosely binds substrate will have a ________ level of specificity.

A

lower

95
Q

Organic cofactors are referred to as _______.

A

coenzymes

96
Q

A reaction can occur spontaneously only if delta G is __________.

A

negative

97
Q

When delta G for a system is zero, the system is at __________.

A

equilibrium

98
Q

The total change of free energy in a reaction depends on __________ and _________.

A

free energy product; substrate

99
Q

Competitive inhibitors which mimic the substrate while in the transition state are called _________ inhibitors.

A

transition state

100
Q

How do enzymes facilitate the formation of the transition state?

A

Enzymes lower the activation energy by bringing A closer to B.

101
Q

Cooperativity

A

sigmoidal; allsoteric enzyme

102
Q

Michaelis-Menten enzyme

A

hyperbolic curve with Vmax

103
Q

_______ is the study of chemical reactions.

A

Kinetics

104
Q

A reaction that is directly proportional to the concentration of reactant is a ________.

A

first order reaction

105
Q

An enzyme reaction with two substrates is considered to be a _________ reaction.

A

second order reaction

106
Q

At __________ there will be no net change of substrate or product.

A

steady state

107
Q

The value _______ is called the initial velocity.

A

V_0

108
Q

The k_cat/K_M is often referred to as the _________.

A

catalytic efficiency

109
Q

An enzyme’s affinity for its substrate is measured by what constant

A

K_M

110
Q

________ Enzymes do not obey Michaelis-Menten kinetics

A

Allosteric

111
Q

The type of inhibition by a product of one enzyme on another enzyme in an earlier protein in a metabolic pathway is a ________ inhibitor.

A

feedback

112
Q

The straight-line kinetic plot of 1/V_0 versus 1/S is called a ___________.

A

double reciprocal

113
Q

Aspartic Acid

A

Asp, D, Polar Acidic

114
Q

Glutamic Acid

A

Glu,E, Polar Acidic

115
Q

Histidine

A

His, H, Polar Basic pKa ~7

116
Q

Arginine

A

Arg, R, Polar Basic

117
Q

Lysine

A

Lys, K, Polar Basic

118
Q

Serine

A

Ser, S, Polar Uncharged

119
Q

Threonine

A

Thr, T, Polar Uncharged

120
Q

Tyrosine

A

Tyr, Y, Polar Uncharged

121
Q

Asparagine

A

Asn, N, Polar Uncharged

122
Q

Cysteine

A

Cys, C, Polar Uncharged

123
Q

Glutamine

A

Gln, Q, Polar Uncharged

124
Q

Tryptophan

A

Trp, W, Hydrophobic

125
Q

Phenylalanine

A

Phe, F, Hydrophobic

126
Q

Proline

A

Pro, P, Hydrophobic

127
Q

Methionine

A

Met, M, Hydrophobic

128
Q

Leucine

A

Leu, L, Hydrophobic

129
Q

Isoleucine

A

Ile, I, Hydrophobic

130
Q

Glycine

A

Gly, G, Hydrophobic

131
Q

Alanine

A

Ala, A, Hydrophobic

132
Q

Valine

A

Val, V, Hydrophobic

BIOL 600 (5 decks)

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