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Biochemistry Flashcards

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1
Q

Amphoteric

A

a molecule can act as an acid or base because it can either accept or donate a proton

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2
Q

Zwitter ion

A

a overall neutral molecule, but has positive and negative groups . They are called dipolar ions

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3
Q

Isoelectric point (pI)

A

The pH at which the molecule is electrically neutral
pI = (pKa(amino) + pKa(carboxy)) / 2
pI (acidic AA) = (pKa(carboxyl)+pKa(side chain)) / 2
pI (basic AA) = (pKa(amino)+pKa(side chain)) / 2

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4
Q

Peptide

A

Composed of amino acid subunits (residues). There can be dipeptides, tripeptides, oligopeptides (up to 20), or polypeptides.

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5
Q

Peptide bonds

A

Links residues between the -COO of 1 AA and the N of another AA. It is hard to denature them with heat, unlike secondary, tertiary, and quaternary structure. Their formation is a condensation or dehydration reaction because its results in the removal of a water molecule

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6
Q

Chymotrypsin

A

Hydrolytic enzyme that cleaves peptide bonds next to large hydrophobic amino acids

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7
Q

Antiparallel

A

When strands are running in opposite directions. It is more stable

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8
Q

Common beta turns

A

Proline and Glycine, in position 2 and 3

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9
Q

Tertiary structure

A

Overall spatial arrangement of atoms in a polypeptide chain or in a protein, the arrangement of secondary structure. Makes up the active site! Ex/ disulfide bridges

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10
Q

Solvation layer

A

Formed when solvent molecules form around a solute when a solute dissolves in the solvent. If hydrophobic side chains are placed in aqueous solution, water molecules can not interact with the side chain and are forced to arrange themselves in organized fashion to maximize H bonds. This decreases entropy (non-spontaneous process)

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11
Q

Quarternary structure

A

Aggregate of subunits (smaller globular proteins). Ex/ hemoglobin and immunoglobulin

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12
Q

Conjugated proteins

A

Proteins with covalently attached prosthetic groups

Ex/ carbohydrate, nucleic acid, lipid, vitamins, metal ions

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13
Q

Lipoproteins

A

lipid prosthetic groups

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14
Q

Glycoproteins

A

carbohydrate prosthetic groups

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15
Q

Nucleoproteins

A

nucleic acid prosthetic groups

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16
Q

Association rule

A

Groups of similar polarity tend to group together. This interaction between side chains is what influences the tertiary structure of a protein

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17
Q

Competitive inhibition

A

Inhibitors that bind the active site and prevent substrate access. Increase Km (cause the [S] to be higher in order to reach Km) and do no effect Vmax. Can only be overcome with the addition of more [S]

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18
Q

Noncompetitive inhibition

A

Allosteric inhibitors that induce a conformation change in the enzyme when binding. Do not alter Km (any copies of the enzyme that are active maintain the same affinity) and decrease Vmax (less [E] available to react). Adding more [S] has no effect. Only adding more [E] overcomes the inhibitor

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19
Q

Mixed inhibition

A

Allosteric inhibitors that can either increase Km if bound to free enzyme or decrease Km if bound to the ES complex, depending on the affinity for each. They decrease Vmax. They cause less [E] to be available to react

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20
Q

Uncompetitive inhibition

A

Allosteric inhibitors that decrease the Km and decrease Vmax. They lock the ES complex and dont allow the formation of P

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21
Q

Irreversible inhibition

A

When the active site is made unavailable for a prolonged period of time, or the enzyme is permanently altered

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22
Q

Zymogens

A

Enzymes that are secreted in inactive forms

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23
Q

Binding proteins

A

They have the ability to transport substances that are otherwise insoluble. They can regulate gene transciption but do not have enzymatic activity @ active site

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24
Q

Enzyme

A

Lower activation energy, increase reaction rate, do not alter Keq, are not consumed in the reaction, are pH and temperature sensitive, and do not effect ΔG

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25
Q

Lyase

A

Enzymes that cleave a molecule into 2 products

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26
Q

Synthase

A

A lyase that can catalyze the synthesis of 2 molecules into a single molecule

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27
Q

Isomerase

A

Enzymes that catalyze the rearrangement of bonds within a molecule

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28
Q

Ligase

A

Enzymes that catalyze addition or synthesis reactions

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29
Q

Hydrolase

A

Enzymes that catalyze the breaking of a compound into 2 molecules using the addition of water.
Ex/ phosphatase, peptidase (protease), nuclease, lipase

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30
Q

Phosphatase

A

A type of hydrolase that cleaves a phosphate group

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31
Q

Oxidoreductase

A

Enzymes that catalyze redox reactions (transfer of e- between molecules)

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32
Q

Transferase

A

Enzymes that catalyze the movement of a functional group between molecules
Ex/ aminotransferase in protein metabolism

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33
Q

Kinase

A

a type of transferase that catalyze the transfer of phosphate groups

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34
Q

Mutase

A

a type of transferase that moves a functional group

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35
Q

Substrate

A

the molecule that the enzyme acts upon

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36
Q

Apoenzyme

A

enzymes without their cofactors

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37
Q

Holoenzyme

A

enzymes with their cofactors

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38
Q

Prosthetic groups

A

Cofactors or coenzymes that determine (permit) the function of proteins. They are tightly bound and can direct a protein to be delivered to a specific location. Ex/ heme, glycoproteins, lipoproteins, nucleoproteins

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39
Q

Cofactors

A

Inorganic molecules or ions that help an enzyme carry out its function (like carrying charge through ionization, protonation, or deprotonation) Ex/ ingested dietary minerals

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40
Q

Coenzymes

A

Organic molecules that help an enzyme carry out its function (like carrying charge through ionization, protonation, or deprotonation) Ex/ vitamin derivatives like NAD, FAD and CoA

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41
Q

Vmax

A

The maximum velocity of an enzyme when it reaches saturation. All active sites are filed. The only way to increase Vmax is to increase [E]

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42
Q

Michaelis-Menten equation

A

Describes how the rate of reaction (v) depends on [E] and [S] which forms the products [P]. It is a measure of enzyme-substrate affinity.
v = vmax[S] / Km + [S]

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43
Q

Michaelis constant, Km

A

the [S] when the enzymes active sites are 1/2 full. It is a measure of enzyme affinity for the substrate. High Km = low affinity

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44
Q

Turnover number, Kcat

A

the number of substrate molecules converted into product per enzyme molecule per second

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45
Q

Catalytic efficiency

A

This is how enzyme efficiency is measured

= kcat/Km

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46
Q

Lineweaver-Burk plots

A

Double reciprocal plot of the Michaelis-Menten equation that is used to better visualize the values of the MM equation because it plots them as a strait line
1/V = Km/Vmax( 1/[S] ) + 1/Vmax
X-intercept = Km
Y-intercept = 1/Vmax

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47
Q

Cooperativity (enzymes)

A

Binding of a substrate to an enzyme encourages the transition from the low affinity tense state (T state) to the high affinity relaxed state (R state).

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48
Q

Hill’s coefficient

A

The numerical value of cooperativity
HC > 1 = (+) cooperative binding
HC < 1 = (-) cooperative binding

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49
Q

Collagen

A

Structural protein that contains cross linked triple helices. Makes up most of the ECM

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50
Q

Elastin

A

Structural protein that stretches and recoils within the ECM

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51
Q

Keratin

A

Intermediate filament in epithelial cells. Ex/ hair

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52
Q

Actin

A

Structural protein that makes up microfilaments and thin filaments in myofibrils. They have a (+) and (-) pole which allows them to travel unidirectionally

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53
Q

Tubulin

A

Structural protein that makes up microtubules. Important when separating chromosomes and intracellular transport with kinesin and dynein

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54
Q

Myosin

A

Primary motor protein (power stroke in sarcomere contraction). Thick filament in myofibril

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55
Q

Kinesin

A

Motor protein that aligns chromosomes in metaphase. Transports vessels along microtubule via anterograde transport (away from cell body)

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56
Q

Dynein

A

Motor protein that is involved in sliding movement of cilia and flagella. Transports vessels along microtubules to via retrograde transport (toward the cell body)

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57
Q

Cadherins

A

Cell adhesion proteins that mediate Ca dependent cell adhesion. They hold similar cell types together

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58
Q

Integrins

A

Cell adhesion proteins with membrane spanning chains. Important for binding/communicating w/ the ECM and white blood cell migration

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59
Q

Selectins

A

Cell adhesion proteins that bind to carbohydrate molecules. They are expressed on WBC and endothelial cells of blood vessels. Important for inflammation (immune function) and WBC migration

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60
Q

Opsonization

A

marking an antigen for destruction

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61
Q

Agglutination

A

clumping of antigens into insoluble protein complexes to get eaten my macrophages

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62
Q

Facilitated diffusion

A

passive transport of molecules (charged particles) down a concentration gradient through a pore created by a transmembrane protein

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63
Q

Ungated channels

A

unregulated channels (always open). Free movement of particles until equilibrium is achieved. Ex/ K channels

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64
Q

Voltage gate channels

A

regulated by the membrane potential. Opened during depolarization or whenever the voltage changes. Ex/ Na/K channels in the SA node

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65
Q

Ligand gated channels

A

the binding of a ligand to a channel causes it to open or close. Ex/ GABA, glycine, serotonin

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66
Q

Homogenization

A

crushing, grinding, or blending a tissue of interest into an evenly mixed solution

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67
Q

Electrophoresis

A

Subjecting compounds to an electric field which will move them according to their charge (towards the anode or cathode) and size (larger molecules move slower)

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68
Q

SDS-PAGE

A

Method used to separate proteins based on charge to mass ratio while also linearizing the proteins. Used in gel electrophoresis of proteins (not nucleic acids) to denature proteins and coat them with a uniform charge, so the electrophoresis depends on size alone. Measured in daltons (1 Da = 1 g/mol)

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69
Q

Isoelectric focusing

A

Seperating proteins by their isoelectric point (pI) by placing them in a gel with a pH gradient. Proteins that are (+) charged will move towards the (-) cathode and (-) charged proteins move towards the (+) anode

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70
Q

Southern blot

A

used for identifying specific sequences of DNA

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71
Q

Northern blot

A

used to detect specific sequences of RNA using hybridization of complementary DNA

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72
Q

Western blot

A

Used to identify specific sequences of amino acids in proteins. A larger band indicates increased protein expression

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73
Q

Glycosidic bond

A

bond between the anomeric and hydroxyl carbon

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74
Q

D and L classifications

A

Stereochemistry of a carbohydrate is dictated by the chiral center farthest from the carbonyl carbon. All D-sugars have the hydroxide of their highest numbered chiral center on the right. All L sugars have it on the left. Only L amino acids exist in cells

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75
Q

Enantiomers

A

Stereoisomers that have the same chemical formula but are stereoisomers with non-superimposable mirror images. They have chiral centers with opposite S and R designations

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76
Q

Diastereomers

A

Stereoisomers that are not identical mirror images.

These are 2 molecules that differ at 1 or more chiral centers

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77
Q

Epimers

A

Differ in configuration at only one chiral center. Ex/ glucose and galactose

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78
Q

Anomer

A

An epimer at the hemiacetal/ketal carbon or the anomeric carbon

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79
Q

Anomeric carbon

A

formed from the carbonyl that is attacked by the nucleophilic alcohol intramolecularly

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80
Q

Hemiacetal

A

1 OR group, 1 OH group, 1 R group, and a H bound to it

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81
Q

Hemiketal

A

1 OR group, a OH group, and 2 R groups attached to it

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82
Q

Acetal

A

2 OR groups, a R group, and a H bound to it

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83
Q

Ketal

A

2 OR group and 2 R groups

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84
Q

Carbohydrate β configuration

A

when the OH- group on the anomeric carbon and the CH2OH group are both above or below the plane of the sugar (cis)

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85
Q

Carbohydrate α configuration

A

when the OH- and CH2OH group are on opposite sides of the plane (trans)

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86
Q

Mutorotation

A

Spontaneous change in configuration around C1. The OH- group on the anomeric carbon of the hemiacetal within a glycosidic bond can rotate from the α or B config

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87
Q

Aldonic acids

A

An oxidized aldose. Strait chain carboxylic acids formed from the aldehyde when there is a shift between α and β configurations

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88
Q

Tollen’s reagent

A

used to detect sugars

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89
Q

Benedict’s reagent

A

oxidizes the aldehyde of an aldose and produces a precipitate Cu₂O

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90
Q

Tautomerization

A

rearrangement of bonds in a compound, usually moving a H and forming a double bond

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91
Q

Alditol

A

when an aldose aldehyde is reduced to an alcohol

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92
Q

Deoxy sugar

A

when a H replaces a hydroxyl group on the sugar

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93
Q

Esterification

A

Formation of esters that occurs when hydroxyl groups of carbohydrates participate in reactions with carboxylic acids and their derivatives

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94
Q

Glycoside

A

formed from a glycosidic bond between two acetals

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95
Q

Furanosides

A

glycosides formed from furanose rings (5 membered ring)

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96
Q

Pyranosides

A

glycosides formed from pyranose rings (6 membered ring)

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97
Q

Homopolysaccaride

A

polysaccharide composed entirely of 1 monosaccharide

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98
Q

Heteropolysaccaride

A

polysaccharide composed of more than 1 monosaccharide

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99
Q

Glycerophospholipids

A

Contain a glycerol backbone bounded by ester linkages to one saturated fatty acid on the C1 and an unsaturated fatty acid on the C2, and a phosphodiester linkage on C3 to a polar head group. The head group is at the surface of membranes and is important for signaling, cell recognition, and binding. These are named by their head group

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100
Q

Amphipathic

A

A molecule that contains hydrophobic and hydrophilic regions

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101
Q

Sphingolipids

A

Contain a sphingosine backbone, long chain nonpolar fatty acid tails connected by amide linkages, and polar head groups. Ex/ cell surface antigens on RBC

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102
Q

Spingosine

A

Backbone of sphingolipids. It is an amino alcohol (secondary alcohol/*amide bond/ether attached to head group)

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103
Q

Glycospingolipids

A

Also called glycolipids, they are sphingolipids with sugar head groups bound by glycosidic linkages. Found mainly on the outer surface of the plasma membrane.

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104
Q

Gangliosides

A

Glycosphingolipids with polar head groups composed of oligosaccharides, *sialic acid (N-acetylneuraminic acid), and a negative charge. Play a role in cell interaction, recognition, and signal transduction

*Sialic acid distinguishes gangliosides from globosides

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105
Q

Wax

A

Esters of long chain saturated/unsaturated fatty acids with long chain alcohols

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106
Q

Cholesterol

A

Steroid that is an amphipathic molecule that maintains the constant fluidity of the membrane. At low temp, it prevents the membrane from solidifying. At high temp, it prevents the membrane from becoming to permeable

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107
Q

Prostaglandins

A

Regulate the synthesis of cAMP. Downstream effects include effects on smooth muscle function, influence on the sleep-wake cycle, and elevation of body temp. They act as vasodilators and inhibit platelet formation

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108
Q

Vitamins

A

Nutrients that can not be synthesized by the body. They are either water soluble (excreted in urine) or fat soluble (accumulate in fat)

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109
Q

Vitamin A

A

Carotene. Important for vision, growth, and immune function

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110
Q

Vitamin D

A

Consumed or formed in a UV light reaction in the skin. It is used for calcium regulation

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111
Q

Vitamin E

A

Antioxidants (lipids called tocopherols and tocotrienols, the aromatic ring interacts with free radicals and destroys them)

112
Q

Vitamin K

A

Important for post-translational modification of prothrombin (blood clotting factor for coagulation)

*K is for Koagulation

113
Q

Triacylglycerols

A

Composed of 3 fatty acids bonded by ester linkages to glycerol. Used to store energy as adipocytes

114
Q

Free fatty acids

A

circulate in the blood bonded non-covalently to serum albumin

115
Q

Saponification

A

Ester hydrolysis of triglycerides using a strong base (NaOH, lye). It results in the cleavage of the fatty acid -> glycerol and the salt of the fatty acid

116
Q

Nucleotide

A

Base with a pentose and phosphate group

117
Q

Nucleoside

A

Base with a pentose group

118
Q

Histones

A

proteins that come together to form nucleosomes

119
Q

Nucleosomes

A

bead-like, primary structure of chromatin

120
Q

Heterochromatin

A

chromatin that remains compacted during interphase. It appears dark and is transcriptionally silent (genetically inactive DNA)

121
Q

Euchromatin

A

appears light and contains genetically active DNA

122
Q

Telomere

A

repeating unit at the end of DNA (TTAGGG). Their high GC content has strong attractions that prevent unraveling. They shorten after every round of replication

123
Q

Centromere

A

located within the chromosome. Sometime centrally, sometimes not. Breaking point of chromosomes

124
Q

Helicase

A

unwinds DNA

125
Q

ssDNA binding proteins

A

bind to unraveled strand and prevents reassociation and degredation by nucleases

126
Q

Topoisomerase

A

works ahead of helicase and introduces negative supercoils by relaxing the torsional pressure. Reseals the cut strands afterwards

127
Q

Semiconservative

A

1 parental strand is retained in each of the resulting strands

128
Q

DNA glycosylase

A

Used in base excision repair. Removes bases by cleaving the N-glycosl bond and forms an apurinic/apyrimidinic site (AP, abasic site)

129
Q

Restriction enzymes

A

used prior to electrophoresis to cut DNA into pieces by cleaving specific sequences (recognize palindromic sequences)

130
Q

Palindromic sequences

A

The 5’ to 3’ sequence of one strand is the same as the 5’ to 3’ sequence of the antiparallel strand (2 complementary strands that have the same sequence)

131
Q

Genomic libraries

A

contain large fragments of DNA and include both coding (exon) and noncoding (intron) regions of the genome

132
Q

Hybridization (DNA)

A

Joining of complementary base pair sequences. Can be DNA-DNA or DNA-RNA recognition

133
Q

Polymerase chain reaction (PCR)

A

When you have a DNA region of interest, you use specific primers that are complementary to the DNA and flank the region on both sides in order to produce multiple copies of DNA. Used to amplify DNA sequences present in a sample

134
Q

Restriction fragment length polymorphisms

A

Variations in the length of restriction fragments. They are the most reliable and accessible way to compare DNA using electrophoresis

135
Q

Dideoxyribonucleotide

A

modified base that contains a H at C3 rather than a hydroxyl. When incorporated in strands, the fragments will terminate at those modified bases making it easier to read the bases in order after a gel electrophoresis

136
Q

Gene therapy

A

if a gene is mutated or inactive (giving rise to pathology), it can be replaced with a normal copy of the gene

137
Q

Prokaryote ribosome

A

30s and 50s (70s)

138
Q

Eukaryote ribosome

A

40s and 60s (80s)

139
Q

Ribozyme

A

Enzymes made of RNA molecules instead of peptides

140
Q

Stop codons

A

UAA, UAG, UGA

141
Q

Point mutation

A

Affecting 1 nucleotide in a codon. They are called expressed mutations because they effect the primary sequence of the AA

142
Q

Missense mutation

A

Point mutation where 1 AA substitutes for another

143
Q

Nonsense mutation

A

Point mutation where the codon encodes for a premature stop codon

144
Q

Frameshift mutation

A

when a number of nucleotides are added or deleted from the mRNA sequence

145
Q

Template strand

A

The antisense strand. One of the 2 unwound DNA strands used for transciption

146
Q

Coding strand

A

The sense strand. Complementary to the template strand and identical to the mRNA transcript (except all T’s are U’s)

147
Q

Introns

A

Non-coding sequence

148
Q

Exons

A

Coding sequences

149
Q

Alternative splicing

A

When the primary transcript of the hnRNA is spliced together in different ways to produce variants of proteins encoded by the same gene

150
Q

Chaperones

A

Assist in the protein folding process which is necessary for the final product. They also inhibit the formation of nonprotein aggregates

151
Q

Phosphorylation

A

addition of a phosphate group by kinases to activate or deactivate proteins

152
Q

Glycosylation

A

addition of oligosaccharides as proteins pass through the ER and Golgi to determine their destination

153
Q

Operon

A

A cluster of genes transcribed as a single mRNA. They contain structural genes, an operator site, a promotor site, and a regulatory gene

154
Q

Structural gene

A

Site on the operon that codes for a protein of interest

155
Q

Operator site

A

Site on the operon upstream of the structural gene. Capable of binding a repressor protein. It is non-transcribable

156
Q

Promotor site

A

Site on the operon upstream of a operator site where RNA polymerase binds

157
Q

Regulator gene

A

Site on the operon upstream of a promotor site. Codes for a repressor protein which can inhibit transciption

158
Q

Inducible system

A

Type of operon where a repressor is bound to the operator site and RNA pol is not able to start transciption (negative control mechanism). This is overcome when an inducer binds the repressor. Genes are produced when needed

159
Q

Lac operon

A

Inducible system that is used when lactose is high and glucose is low (because it is more energetically expensive to digest lactose). The structural gene codes for lactase

160
Q

Repressible system

A

allow the constant production of a protein product. It is active until bond by a repressor at the operator site (negative feedback)

161
Q

Enhancer

A

response elements outside the normal promotor region that allow for control of gene expression by binding to receptors on the DNA strand

162
Q

Histone acetylation

A

acetylation of histone proteins decreases the (+) charge on Lys residues and weakens the interaction with DNA which allows the chromatin to open up and allow easy access for transciption

163
Q

Flippase

A

enzyme that catalyze transverse diffusion of lipids from the outside to the inside of a membrane

164
Q

Cell adhesion molecules

A

proteins that allow cells to recognize each other and contribute to proper cell differentiation

165
Q

Gap junctions

A

Allow for direct communication. Also called connexons. Permit the movement of water and some solutes

166
Q

Tight junctions

A

prevent solutes from leaking into the space between cells by a paracellular route. They form a continuous band around the cell

167
Q

Desmosomes

A

bind adjacent cells by anchoring to their cytoskeleton. Interaction between transmembrane proteins and intermediate filaments

168
Q

Hemidesmosomes

A

attach epithelial cells to underlying structures like the basement membrane

169
Q

Hypotonic

A

when the concentration of solutes inside the cell is greater than outside

170
Q

Hypertonic

A

when the concentration of solutes outside the cell is greater than inside

171
Q

Resting potential of cell

A

between -40 and -80 mV

172
Q

Hexokinase

A

converts glucose into glucose 6-phosphate. Phosphorylation prevents glucose from crossing the membrane

173
Q

PFK-1

A

phosphorylates fructose 6 phosphate —> fructose 1,6 bisphosphate using ATP

174
Q

PFK-2

A

converts fructose 6 phosphate —> fructose 2,6 bisphosphate. F2,6-BP activates PFK-1

175
Q

G3P DHase

A

converts G3P —> 1,3 bisphosphoglycerate using NAD (oxidation rxn)

176
Q

Phosphoglycerate kinase

A

converts 1,3 bisphosphoglycerate —> 3 phosphoglycerate using ADP

177
Q

Pyruvate kinase

A

converts phosphoenolpyruvate —> pyruvate using ADP

178
Q

Lactate dyhygrogenase

A

reduces pyruvate into lactate using NADH (oxidized to NAD)

179
Q

Pyruvate DHase complex

A

Converts pyruvate into acetyl CoA if ATP is needed or for fatty acid synthesis if ATP is sufficient. Uses CoA-SH and NAD+. CO2 is lost

180
Q

Glycogen

A

Branched polymer of glucose that is stored in the cytoplasm as granules in the liver and skeletal muscle

181
Q

Isoforms

A

different versions of the same protein

182
Q

NADPH

A

used for lipid and cholesterol (steroid hormone precursor) biosynthesis

183
Q

The Cori cycle

A

Conversion of lactate into glucose for use in muscles

184
Q

β-Oxidation

A

Breakdown of fatty acids and occurs in the mitochondria. Fatty acyl CoA can be converted to Acetyl CoA or ketone bodies (primary method). Each round generates 1 FADH2 and NADH

185
Q

Hormone sensitive lipase

A

hydrolyzes triacylglycerols in adipose tissue and yields fatty acids and glycerol. It is released when insulin levels are low (like at night)

186
Q

Lipoprotein lipase

A

Necessary for the metabolism of chylomicrons and VLDL. It can release triacylglycerols in lipoproteins

187
Q

Very low density lipoproteins (VLDL)

A

Produced in liver cells. High triacylglycerol to protein ratio. Transports triacylglycerols and fatty acids to tissues.

188
Q

Low density lipoproteins (LDL)

A

Delivers cholesterol into cells

189
Q

High density lipoproteins (HDL)

A

“good cholesterol”. It picks up cholesterol accumulating in blood vessels. Synthesized in the liver and released into the blood

190
Q

Apoproteins

A

The protein component of lipoproteins. They are receptor molecules and are involved in signaling

191
Q

Fatty acid synthase

A

converts malonyl CoA into palmitate (16C)

192
Q

Ketone bodies

A

Converted from acetyl CoA into acetoacetate or β-hydroxybutyrate+ acetone after fasting

193
Q

Ketogenesis

A

Occurs in the mitochondria. HMG synthetase takes acetyl CoA and forms HMG CoA. This is used to form ketone bodies by HMG CoA lyase

194
Q

Glucogenic amino acids

A

All but Leu and Lys. They can be converted to glucose by gluconeogenesis

195
Q

Ketogenic amino acids

A

Leu, Lys, Ile, Phe, Thr, Trp, and Try. They can be converted to acetyl CoA and ketone bodies

196
Q

Flavoproteins

A

Modified vitamin B₂ or riboflavin. They function as coenzymes for enzymes in the oxidation of fatty acids and the decarboxylation of pyruvate. Ex/ FAD, FMN

197
Q

Counter regulatory hormones

A

Glucagon, cortisol, epinephrine, norepinephrine, and GH all oppose insulin

198
Q

Glucocorticoids

A

Steroid hormones that regulate glucose levels

199
Q

Catecholamines

A

They increase glucose output by the liver by increasing activity of glycogen phosphorylase in liver and muscle (glycogenolysis). Ex/ Epinephrine and norepinephrine

200
Q

Respiratory quotient

A

A way to measure metabolic function

RQ = CO₂ produced / O₂ consumed

201
Q

Transient enzyme modifications

A

Reversible modifications to enzymes. Ex/ allosteric activation and inhibition

202
Q

Allosteric activators

A

binds and results in a conformational shift that makes the active site more available for binding of the substrate

203
Q

Allosteric inhibitors

A

binds and results in a conformational shift that makes the active site less available for binding of the substrate

204
Q

Covalent enzyme modifications

A

activation or deactivation of enzymes by glycosylation or phosphorylation

205
Q

Silent mutation

A

Mutations in the wobble position that have no effect on expression of the amino acid and therefore no adverse effects on the polypeptide sequence

206
Q

Monocistronic

A

1 molecule is translated into one protein product. Ex/ eukaryotic mRNA

207
Q

Polycistronic

A

1 molecule is translated into multiple different proteins. Ex/ prokaryotic mRNA

208
Q

Messenger RNA

A

Carries information specifying the amino acid sequence of the protein to the ribosome. Read in codons

209
Q

Transfer RNA

A

Converts nucleic acids into amino acids and peptides. It contains an anticodon that recognizes and pairs with the appropriate codon on the mRNA molecule while in the ribosome.

210
Q

Aminoacyl-tRNA synthase

A

Activates each type of amino acid and transfers it to the 3’ end of the correct tRNA. Requires 2 high energy bonds from ATP

211
Q

Ribosomal RNA

A

Synthesized in the nucleolus. Many rRNA function as ribozymes and help catalyze the formation of peptide bonds.

212
Q

Trp operon

A

The cluster of genes that code for tryptophan in E.Coli

213
Q

Negative control mechanisms

A

Operon systems in which binding of a protein reduces transcriptional activity

214
Q

Positive control mechanisms

A

Operon systems in which binding of a molecule increases transcription of a gene

215
Q

Catabolite activator protein (CAP)

A

Transcriptional activator used by the lac operon. Decreasing levels of glucose cause an increase in cAMP which binds CAP -> CAP binds promotor -> increase lactase gene. Positive control mechanism

216
Q

A site

A

Holds the incoming aminoacyl-tRNA complex (the next amino acid to be added to the growing chain determined by the mRNA codon within the A site)

217
Q

P site

A

Holds the tRNA that carries the growing polypeptide chain

218
Q

Peptidyl transferase

A

Ribozyme in the large subunit that catalyzes peptide bond formation during translation elongation (passing of the polypeptide from the tRNA in the P site to the tRNA in the A site). GTP is used for energy during peptide bond formation

219
Q

E site

A

Where the inactivated (uncharged) tRNA pauses before exiting the ribosome. The tRNA unbinds from the mRNA as it enters the E site

220
Q

RNA polymerase I

A

located in the nucleolus and synthesizes rRNA

221
Q

RNA polymerase II

A

located in the nucleus and synthesizes pre-processed mRNA (hnRNA). It binds to the TATA box promotor region

222
Q

RNA polymerase III

A

located in the nucleus and synthesizes tRNA

223
Q

Translocation mutation

A

When a segment of DNA from one chromosome is swapped with another. This can lead to either partial trisomy in some chromosomes or monosomy in others

224
Q

Saturated fatty acid

A

Only single bonds. More stable because they have greater Van der Waals forces. Solids at room temperature

225
Q

Unsaturated fatty acid

A

Includes one or more double bonds. More difficult to stack so they are liquids at room temperature. Make up the more fluid areas of membranes

226
Q

Phospholipids

A

Contain a phosphate and alcohol that make up the polar head group, joined to a hydrophobic fatty acid tail by phosphodiester linkages (distinguishing part of phospholipids)

227
Q

Ceramide

A

Simplest sphingolipid. Has a single H as its head group

228
Q

Sphingomyelins

A

Sphingophospholipids that are the component in the plasma membrane of cells producing myelin. Head group is either a phosphatidylcholine or phosphatidylethanolamine with no net charge.

229
Q

Cerebrosides

A

Glycosphingolipids with a single sugar head group

230
Q

Globosides

A

Glycosphingolipids with two or more sugar head groups

231
Q

Steroids

A

4 cycloalkane rings (3 cyclohexane, 1 cyclopentane)

232
Q

Glutathione

A

Reducing agent that helps reverse free radical formation before damage is done to the cell. Needs NADPH to be formed

233
Q

Free radicals

A

When atoms lose one of their electrons. These radicals are dangerous because the look for electrons to rip away. They attack lipids (weaken cell membrane/lysis), RBC, and DNA. Ex/ H2O2 (byproduct in aerobic metabolism)

234
Q

GLUT 2

A

Low affinity transporter in hepatocytes and pancreatic cells. Captures excess glucose mainly for storage. Activity is lowest when the blood and liver have low [glucose]

235
Q

GLUT 4

A

Transporter in adipose tissue and muscle. Responds to glucose in peripheral blood

236
Q

Glucokinase

A

Phosphorylates glucose only in liver cells and pancreatic B islet cells. High Km and induced by insulin

237
Q

Rate limiting enzyme of glycolysis

A

PFK-1

238
Q

Rate limiting enzyme of fermentation

A

lactate dehydrogenase

239
Q

Rate limiting enzyme of glycogenesis

A

glycogen synthase

240
Q

Rate limiting enzyme of glycogenolysis

A

glycogen phosphatase

241
Q

Rate limiting enzyme of gluconeogenesis

A

fructose 1,6-bisphosphatase

242
Q

Rate limiting enzyme of PPP

A

glucose-6-phosphate dehydrogenase

243
Q

G protein coupled receptors (GPCR)

A

Heterotrimeric proteins that bind GDP and GTP. In the inactive form, the α subunit binds GDP in complex with the β and γ subunits. In the active form, GDP is replaced with GTP and the α subunit dissociates from the β and γ subunits. Ex ligands/ hormones

244
Q

G𝑠

A

Stimulates adenylate cyclase -> increases cAMP levels

245
Q

Gᵢ

A

Inhibits adenylate cyclase -> decreases cAMP levels

246
Q

G𝑞

A

Activates phospholipase C -> opening of Ca channels in the endoplasmic reticulum -> increases intracellular Ca levels

247
Q

Lactose

A

Glucose and galactose

248
Q

Sucrose

A

Glucose and fructose

249
Q

Goldman-Hodgkin-Katz equation

A

Used to determine the membrane potential taking into account the contribution of each major ion

V𝑚 = 61.5 log ( 𝔭Na+[Na+]out + 𝔭K+[K+]out + 𝔭Cl-[Cl-]in / 𝔭Na+[Na+]in + 𝔭K+[K+]in + 𝔭Cl-[Cl-]out )

250
Q

Nerst equation

A

Used to determine the membrane potential of various ions

E = 61.5/z log ( [ion outside] / [ion inside] )

251
Q

NADPH

A

Reducing agent that is involved in the biosynthesis of fatty acids and cholesterol, production of glutathione, and cellular bleach production of WBC (bactericidal activity)

252
Q

Primer

A

Runs before DNA polymerase from the 3’ to 5’ end during replication. It must be complementary to the 3’ end of DNA

253
Q

Glycogen phosphorylase

A

Breaks α-1,4-glycosidic bonds (glycogen) in order to release glucose 1 phosphate. Does not break 1,6 links. Activated by glucagon, AMP, epinephrine

254
Q

Debranching enzyme

A

Hydrolyzes α-1,4 and α-1,6 glycosidic bonds. Hydrolyzing 1,6 releases glucose while hydrolyzing the 1,4 transfers the oligoglucose unit to the end of another chain

255
Q

Insertion mutation

A

A segment of DNA is moved from one chromosome to another

256
Q

Inversion mutation

A

When a single chromosome undergoes breakages and rearrangement within itself

257
Q

Chylomicrons

A

Lipoprotein rich in triacylglycerol. Originate from ingested food and formed in the small intestines. Deliver fat to liver and tissues

258
Q

Genomic DNA library

A

Represent the entire genome of an organism. Generated from clones DNA fragments that have been digested by restriction enzymes

259
Q

cDNA (complementary DNA) library

A

Generated from reverse transcribed mRNA sequences and only contains coding regions of DNA

260
Q

Lecithin-cholesterol acetyltransferase (LCAT)

A

Esterifies cholesterol and allows it to be soluble in HDL

261
Q

Fluid mosaic model

A

Describes the phospholipid bilayer as fluid in motion. Ex/ consistency like vegetable oil

262
Q

Oncogenes

A

Mutated genes that cause cancer. Primarily encode cell cycle related proteins

263
Q

Proto-oncogenes

A

Oncogenes before mutations occur

264
Q

Tumor suppressor genes

A

Encode proteins that inhibit the cell cycle or participate in the DNA repair process. Mutations of these cause cancer, but inactivation of both alleles is necessary for the loss of function. Ex/ p53, Rb (retinoblastoma)

265
Q

Proofreading

A

Function of DNA polymerase during synthesis. It is the detection of incorrect base pairs due to the instability of H bonds. The mutations on the daughter (lagging) strand are identified due to less methylation than the template strand

266
Q

2,3-bisphosphoglycerate (2,3-BPG)

A

Present in RBC and binds allosterically to B chains of hemoglobin to decrease affinity for oxygen. Allows for oxygen unloading in tissues.
*1,3-BPG -> 2,3-BPG by bisphosphoglycerate mutase

267
Q

Lipase

A

Enzyme that hydrolyzes fatty acids

268
Q

UDP glucose

A

Uridine diphosphate glucose. The glycosyl moity from UDP glucose is transferred to glycogen polymers. Contains uridine which is a nucleic acid in RNA (ribose)

269
Q

3 irreversible enzymes of glycolysis

A

Hexokinase (glucokinase), PFK-1, and pyruvate kinase

270
Q

ATP production in RBC

A

2 ATP per glucose

271
Q

Chemiosmotic coupling

A

Allows the chemical energy of the electrochemical proton gradient of the mitochondria to phosphorylate ADP to ATP

272
Q

Aminopeptidase

A

Released from the small intestine to digest proteins

273
Q

α-amylase vs. β-amylase

A

Cutting polysaccharides randomly to yield shorter polysaccharides VS. cleaving polysaccharides at the acetal end to produce maltose

274
Q

Malate-aspartate shuttle

A

Since cytosolic OAA can not cross the inner mitochondrial membrane by itself, it is reduced to malate (NADH is oxidized) which can pass. NADH is reformed when malate reforms OAA inside the mitochondria

275
Q

Blunt vs. sticky ends of enzymes

A

No overhanging DNA sequences VS. overhanging DNA sequences. Separately they create bidirectional sequences but when used together they create palindromic sequences (restriction enzymes)

276
Q

Rate limiting enzyme of TCA

A

isocitrate dehydrogenase

MCAT (7 decks)

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