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Flashcards in biochem Deck (148):
1

heat energy

movement of molecules

2

potential energy

energy stored in chemical bonds

3

Gibbs free energy

^G=^H-T^S

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enthalpy

total heat content of a system

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entropy

measure of disorder

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spontaneous

^G is negative

7

nonspontaneous

^G is positive

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endergonic

energy that is absorbed

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exergonic

energy that exits the system

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exothermic

liberate heat (metabolism)

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endothermic

input of heat

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equilibrium

point where the rate of reaction in one direction equals the rate of reaction in the other

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chemical kinetics

study of reaction rates

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activation energy

the energy required to produce the transient intermediate

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catalyst

lowers the activation energy without undergoing permanent chemical changes

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photosynthesis

process by which plants store energy from the sun in the bond energy of carbohydrates

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photoautotrophs

use energy from light to make their own food

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chemoheterotrophs

use energy of chemicals produced by other living things for food

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oxidation

loss of electron
gain of oxygen
loss of hydrogen

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reduction

gain of electrons
loss of oxygen
gain of hydrogen

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is changing CH3CH3 to H2C=CH2 an oxidation, a reduction, or neither

oxidation, because hydrogens have been removed

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is changing FE3+ to FE2+ an oxidation, reduction, or neither

reduction, because an electron has been added

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is O2->H2O a oxidation, reduction, or neither

reduction, because hydrogens have been added

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is a configuration of disulfide bond and oxidation, reduction, or neither

oxidation, because they are loosing hydrogens

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redox pair

oxidizing and reducing for one happening the other occurs with something else

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catabolism

breaking down molecules

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anabolism

building-up metabolism

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oxidative catabolism

break down glucose by oxidizing

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Assuming that temperature is consistent and not so high as to denature proteins, which of the following would indicate that a chemical reaction is NOT spontaneous?

A. rx with a large + ^H and a large + ^S
B. rx with a large + ^H and a large - ^S
C. rx with a small - ^H and a large + ^S
D. rx with a small + ^H and a large + ^S

B. rx with a large +^H and a large -^S

^G=^H-T^S

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side chain

variable R-group, which gives it the physical and chemical properties that distinguish it from the other nineteen

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acidic amino acids

aspartic acid (Asp)
Glutamic acid (Glu)

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basic amino acids

Lysine (lys)
Arginine (Arg)
Histidine (His) - can go both ways

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Hydrophobic (nonpolar) Amino Acids

Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Phenylalanine (Phe)
Tryptophan (Trp)

34

Polar amino acids

Serine (Ser)
Threonine (Thr)
Tyrosine (Tyr)
Asparagine (Asn)
Glutamine (Gln)

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Sulfur-containing amino acids

Cysteine (Cys)
Methionine (Met)

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Proline

Proline (Pro)

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Which of the following amino acids is most likely to be found on the exterior of a protein at pH 7.0?

A. Leucine
B. Alanine
C. Serine
D. Isoleucine

C. Serine

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amphoteric

can act as acids or bases

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peptide bonds

is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water

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disulfide bridges

covalent bond derived from two thiol groups

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backbone

N-C-C-N-C-C pattern

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residue

individual amino acid when part of a polypeptide chain

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proteolysis or proteolytic cleavage

hydrolysis of a protein by another protein

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proteolytic enzyme or protease

protein that does the cutting

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denaturation

disruption of a protein's shape without breaking peptide bonds

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denatured

improperly folded, proteins are non-functional

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primary structure

sequence, linear ordering of amino acid residues

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secondary structure

initial folding of a polypeptide chain into shapes stabilized by hydrogen bonds between backbone NH and CO groups.
Alpha helix
Beta pleated sheet

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parallel beta pleated sheet

adjacent polypeptide strands running in the same direction

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antiparallel beta pleated sheet

polypeptide strands run in opposite directions

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tertiary structure

may include van der Waals forces between nonpolar side chains, hydrogen bonds between polar side chains, disulfide bonds between cysteine residues, and electrostatic interactions between acidic and basic side chains

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hydrophobic effect

hydrophobic R-groups tend to fold into the interior of the protein, away from the solvent, and hydrophilic R-groups tend to be exposed to water on the surface of the protein

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quaternary structure

highest level of protein structure, describes interactions between polypeptide subunits

54

subunit

is a single polypeptide chain that is part of a large complex containing many subunits

55

reaction coupling

a very favorable reaction is used to drive an unfavorable one

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active site model

referred to as the "lock and key hypothesis," states that the substrate and active site are perfectly complementary

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substrates

reactants in an enzyme-catalyzed reaction

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induced fit model

asserts that the substrate and active site differ slightly in structure and that the binding of the substrate indices a conformational change in the enzyme

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active site

the region in an enzyme's three-dimensional structure that is directly in catalysis

60

cofactors

metal ions or small molecules that are required for activity in many enzymes

61

coenzyme

when a cofactor is an organic molecule, these often bind to the substrate during the catalyzed reaction

62

regulation of enzyme activity

1. covalent modification
2. proteolytic cleavage
3. Association with other polypeptides
4. Allosteric regulation

63

negative feedback or feedback inhibitation

the diminution or counteraction of an effect by its own influence on the process giving rise to it, as when a high level of a particular hormone in the blood may inhibit further secretion of that hormone, or where the result of a certain action may inhibit further performance of that action

64

enzyme kinetics

study of the rate of formation of products from substrates in the presence of an enzyme

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reaction rate

is the amount of product formed per unit time, in moles per second

66

saturated

all active sites are occupied

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noncompetitive inhibitors

bind at an allosteric site, not at the active site, no matter how much substrate you add, the inhibitor will not be displaced from its site of action

68

uncompetitive inhibitor

if an inhibitor is only able to bind to the enzyme-substrate complex (it can not bind before the substrate has bound)

69

mixed-type inhibition

occurs when an inhibitor can bind to either the unoccupied enzyme or the enzyme-substrate complex

70

competitive inhibitors

are molecules that compete with substrate for binding at the active site

71

Lineweaver-burk plot

1/v=(Km/Vmax)(1/[S])+(1/Vmax)

72

all of the following are true of uncompetitive inhibition EXCEPT:

A. increasing inhibitor concentration decreases Vmax
B. decreasing inhibitor concentration increases Km
C. the inhibitor binds to the active site
D. inhibition results in an increase in apparent affinity of the enzyme for the substrate

B. decreasing inhibitor concentration increases Km

enzymes decrease the activation energy of a reaction by stabilizing the transition state

73

disaccharide

two monosaccharides bonded together

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monosaccharide or simple sugar

single carbohydrate molecule

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glycosidic linkage

bond between two sugar molecules

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polysaccharides

made from the disaccharides

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maltase

the enzyme that catalyzes the hydrolysis of maltose into two glucose monosaccharides

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lactase

specific enzyme that digests lactose

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lactose malabsorbers

people without lactase, any lactose they end goes to the colon

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lactose intolerant

gas and diarrhea with people who are lactose malabsorbers

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flavoprotein

FAD with a protein

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glycolysis

glucose splitting

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pyruvic acid

glucose is oxidized while it is split in half

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pyruvate dehydrogenase complex

second stage, the pyruvate produced in glycolysis is decarboxylated to form an acetyl group

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krebs cycle (tricarboxylic acid cycle TCA cycle)

the sequence of reactions by which most living cells generate energy during the process of aerobic respiration

86

electron transport chain

is a series of complexes that transfer electrons from electron donors to electron acceptors via redox

87

hexokinase

catalyzes the first step in glycolysis

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phosphofructokinase (PFK)

the transfer of a phosphate group from ATP to fructose-6-phosphate to form fructose-1,6-bisphosphate

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reducing power

reduction potential

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fermentation

the chemical breakdown of a substance by bacteria, yeasts, or other microorganisms, typically involving effervescence and the giving off of heat

91

oxidative decarboxylation

reactions are oxidation reactions in which a carboxylate group is removed, forming carbon dioxide

92

coenzyme A

is a coenzyme, notable for its role in the synthesis and oxidation of fatty acids, and the oxidation of pyruvate in the citric acid cycle

93

tricarboxylic acid cycle

krebs cycle

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citric acid cycle

also known as the tricarboxylic acid (TCA) cycle or the Krebs cycle – is a series of chemical reactions used by all aerobic organisms to release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins into carbon dioxide and chemical energy

95

oxaloacetate

is a crystalline organic compound with the chemical formula HO2CC(O)CH2CO2H. Oxaloacetic acid, in the form of its conjugate base oxaloacetate, is a metabolic intermediate in many processes that occur in animals

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citrate

a key intermediate in metabolism

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mitochondria membranes

outer membrane- composed of a lipid bilayer, smooth and contains large pores formed by porin proteins

inner membrane- composed of a lipid bilayer, impermeable, densely folded into structures called cristae that extend into the matrix (the innermost space)

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intermembrane space

the space between the two membranes

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ATP synthase

is an enzyme that creates the energy storage molecule adenosine triphosphate (ATP). ATP is the most commonly used "energy currency" of cells for most organisms

100

oxidative phosphorylation

oxidation of the high-energy electron carriers NADH and FADH2 coupled to the phosphorylation of ADP to produce ATP

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electron-transport chain

group of five electron carriers

102

cyochromes

any of a number of compounds consisting of heme bonded to a protein. Cytochromes function as electron transfer agents in many metabolic pathways, especially cellular respiration

103

NADH dehydrogenase (CoQ reductase)

is an enzyme that catalyzes the chemical reaction

104

ubiquinone

CoQ

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proton gradient

The product of the electron transport chain. A higher concentration of protons outside the inner membrane of the mitochondria than inside the membrane is the driving force behind ATP synthesis

106

gluconeogenesis

occurs when dietary sources of glucose are unavailable and when the liver has depleted its stores of glycogen and glucose

107

futile cycling

running both pathways at the same time

108

fatty acids

composed of long unsubstituted alkanes that end in a carboxylic acid

109

saturated

filled with hydrogen bonds

110

unsaturated

have one or more double bonds

111

michelle

shape fatty acids make with their polar end and nonpolar tail

112

triacylglycerol or triglyceride

fat

113

lipases

enzymes that hydrolyze fat

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amphipathic

both hydrophilic and hydrophobic regions

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hormones made from steroid cholesterol

testosterone and estradiol

116

tocopherols

methylated phenols

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fat soluble vitamids

A, D, E, K

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prostaglandins

prostaglandin A2
prostaglandin E1
prostaglandin E3alpha

119

ketogenesis

is the biochemical process by which organisms produce a group of substances collectively known as ketone bodies by the breakdown of fatty acids and ketogenic amino acids

120

nucleotides

are the building blocks of nucleic acids

contain ribose (or deoxyribose) sugar group, a purine or pyrimidine base joined to carbon number one or the ribose ring, and one, two, or three phosphate units joined to carbon five of the ribose ring

121

purines

double-ring structure (6 and 5)

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pyrimidines

single six membered ring structure

123

nucleoside

ribose with a purine or pyrimidine linked to the 1 carbon in a beta-N-glycosidic linkage

124

Watson-Crick model

cellular DNA is a right-handed double helix held together by hydrogen bonds

125

antiparallel orientation of DNA

5'end of one chain is paired with the 3'end of the other

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melting, or denaturation

separation of strands

127

annealing, or hybridization

the binding of two complementary strands of DNA into a double-stranded structure

128

right-handed double helix

corkscrews in a clockwise motion

129

histones

globular proteins

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chromatin

fully packed DNA-composed of closely stacked nucleosomes

131

heterochromatin

chromosome material of different density from normal (usually greater), in which the activity of the genes is modified or suppressed

132

euchromatin

chromosome material that does not stain strongly except during cell division. It represents the major genes and is involved in transcription

133

kinetochores

a complex of proteins associated with the centromere of a chromosome during cell division, to which the microtubules of the spindle attach

134

centromere

the region of a chromosome to which the microtubules of the spindle attach, via the kinetochore, during cell division

135

chromatids

each of the two threadlike strands into which a chromosome divides longitudinally during cell division. Each contains a double helix of DNA

136

short arms

p

137

long arms

q

138

telocentric

when the centromere is at the end

139

acrocentric

when the centromere is very near one end

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submetacentric

when the centromere is just off central location making one arm longer and one arm shorter

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metacentric

when the centromere is centrally located making all arms equal

142

telomeres

end of linear chromosomes

143

RNA

single-stranded
uracil instead of thymine
pentose ring rather than 2'deoxyribose

144

messenger RNA

only type of coding RNA

145

transfer RNA

responsible for translating the genetic code

146

ribosomal RNA

major component of the ribosome

147

small nuclear RNA

associate with proteins to form snRNP complexes in the spliceosome

148

microRNA and small interfering RNA

function in RNA interference