Biochemistry Flashcards
(217 cards)
1
Q
Amino Acids
A
molecule with 4 groups attached to the central carbon (alpha carbon).
1) amino group
2) carboxylic acid group
3) hydrogen atom
4) R group
the r group determines the function of the amino acid.
2
Q
Amino group
A
a functional group composed of NH3+
3
Q
Carboxylic acid
A
a functional group composed of COOH
4
Q
Zwitterions
A
molecules that contain both positive and negative charges on the same molecule
5
Q
Alpha carbon
A
central carbon atom of an amino acid, bonded to the amino group, carboxyl group, and R group
6
Q
Peptide bond
A
bond between each amino acid in a protein; catalyzed by the ribosome; forms primary structure of a protein
7
Q
Amide bond
A
another term for peptide bond; has partial double bond character which limits rotation of the constituent groups
8
Q
Primary structure
A
the string of amino acids connected by peptide bonds, and is defined solely by the identity of amino acids within it
9
Q
secondary structure
A
formed through the hydrogen bonding interactions between atoms forming the backbone of the protein chain; includes alpha helices and beta sheets
10
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tertiary structure
A
structure that arises from interactions between the side chains of different amino acids
11
Q
quaternary structure
A
interactions between different protein subunits that make up a protein with more than one subunit
12
Q
hydrophobic affect
A
a consequence of nonpolar and polar interactions; in an aqueous environment, hydrophobic residues will be attracted to each other, while they will also be repelled by the polar aqueous environment
13
Q
protein folding
A
the process through which a protein is organized (or folded) into its proper secondary and tertiary structures
14
Q
denaturing
A
the process through which a protein is unfolded or loses its proper 3D structure
15
Q
chaperones
A
helper proteins that assist in folding denatured proteins back into their native state
16
Q
Cytoskeleton
A
composition of proteins and macromolecules that provides structure for the cell; primarily composed of actin and tubulin
17
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Extracellular matrix
A
composition of proteins and macromolecules that provide structure for tissue; primarily composed of collagen, elastin, and keratin
18
Q
Actin
A
the most abundant protein in eukaryotic cells; actin monomers assemble into long polymers known as microfilaments that possess positive and negative polarity
19
Q
Myosin
A
a motor protein that works with actin in a crossbridge cycle to contract muscle cells
20
Q
Tubulin
A
structural monomer that assembles into heterodimers of alpha-tubulin and beta-tubulin to form microtubules
21
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Collagen
A
helical fiber made of three interwoven strands and composes a large portion of the extracellular matrix in connective tissue
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Elastin
A
provides structure to the rest of our body; when stretched, elastin fibers become more linear in shape while still preserving the cross-linked structure of the extracellular matrix
23
Q
Keratin
A
not directly localized in the extracellular matrix, but provides cells with needed structure and stability to protect our bodies, and acts as a hard barrier from the outside world
24
Q
Kinesin
A
a motor protein that travels towards the positive end of microtubules (towards the periphery of the cell)
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Dynein
a motor protein that travels towards the negative end of microtubules (towards the nucleus of the cell)
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GPCR
G-protein coupled receptor; a transmembrane signal-transducing protein system
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G-protein
a trimeric protein, consisting of an alpha, beta, and gamma subunit. The alpha subunit is responsible for hydrolyzing GTP in the G-protein, while the beta and gamma subunits can have other functions in the cell
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Pores
transmembrane structures embedded within the cell membrane that allows small, polar molecules to move down their respective gradients; one such example is aquaporin, which facilitates the diffusion of water
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Ion channels
allows charged ions to diffuse through the cell membrane; some ion channels can be gated with ligand- or voltage-dependent sensors
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Active transporters
proteins that can move ions and large molecule against their concentration gradient; rely on ATP hydrolysis for energy to move cargo
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Peptide hormones
hormones that are peptides or proteins (shown below); transduce signals between organ systems and circulate in the bloodstream
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HPG axis
hypothalamic-pituitary-gonadal axis; describes the sequential stimulation of hormones from the hypothalamus to the reproductive gonads
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Innate immune system
nonspecific defenses against pathogens and foreign material our bodies encounter
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Adaptive immune system
provides us more specific defenses against particular antigens; antibodies are key to this adaptive response
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Variable region
includes paratopes on an antibody; sequences of polypeptide that provide the ability to recognize foreign substances and flag them as invasive
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Constant region
region on an antibody important for recruiting other antibodies or immune system cells to help destroy the antigens
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Catalyst
a substance that speeds up the rate of a reaction without being consumed itself
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Biological catalyst
a molecule (can be protein or nucleic acid) that speeds up the rate of a biochemical reaction without being consumed itself
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Activation energy
the input energy required to initiate a chemical reaction
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Kinetics
how quickly a reaction converts reactants to products
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Reaction rate
the rate at which reactants are consumed OR the rate at which products are formed
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Regeneration
the ability of enzymes to reform and engage in multiple catalytic cycles
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Lock-and-key model
an enzyme-substrate binding theory that poses the substrate as a “key” that fits perfectly into the enzymatic “lock” without changing conformations
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Induced fit model
an enzyme-substrate binding theory that poses the substrate and enzyme undergo slight conformational changes upon binding to one another
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One-letter amino acid code
a one-letter code that defines an amino acid (e.g., K is lysine)
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Three-letter amino acid code
a three-letter code that defines an amino acid (e.g., Lys is lysine)
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Michaelis-Menten
a plot that measures reaction velocity versus an increasing concentration of substrate while holding the enzyme concentration constant
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Reaction velocity
the speed at which a certain concentration of enzymes convert substrate to product
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Vmax
the maximum speed at which a certain concentration of enzymes can convert substrate to product
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Km
the substrate concentration at ½ vmax and also corresponds to affinity between the enzyme and substrate
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Saturation
the point at which additional substrate does not produce an increase in reaction velocity because the enzymes are already working as fast as they can
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Catalytic efficiency
describes the efficiency of an enzyme by incorporating how fast the enzyme is working (kcat) and how well the enzyme can bind substrate (Km) using the following expression: kcat / Km
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Lineweaver-Burk
a double reciprocal of the Michaelis-Menten plot in which (1/reaction velocity) is plotted against 1/[S]
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Competitive inhibition
an inhibitor competes with substrate binding to the active site, resulting in an unchanged vmax and an increased Km
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Uncompetitive inhibition
an inhibitor binds to the enzyme-substrate complex, resulting in a decreased vmax and a decreased Km
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Mixed inhibition
an inhibitor binds to both the enzyme alone and the enzyme-substrate complex, resulting in a decreased vmax and an increased or decreased Km
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Noncompetitive inhibition
a subclass of mixed inhibition in which an inhibitor binds to the enzyme alone 50% of the time and the enzyme-substrate complex 50% of the time, resulting in a decreased vmax and an unchanged Km
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Cofactor/coenzyme
binds to the enzyme’s active site and assists in catalyzing the reaction
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Prosthetic group
a cofactor or coenzyme that binds extremely tightly to the enzyme
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Holoenzyme
an enzyme with its cofactors and/or coenzymes
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Apoenzyme
an enzyme without its cofactors and/or coenzymes
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Post-translational modification
the covalent addition of a functional group or atom to an enzyme
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Allosteric sites
a site distant from the active site that can be used as a point of regulation
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Allosteric activators
binds to an enzyme’s allosteric site and activates the enzyme
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Allosteric inhibitors
binds to an enzyme’s allosteric site and inhibits the enzyme
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Zymogens
inactive enzyme forms that must be cleaved in order to be activated
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Feedback regulation
the control of flux through biological pathways by using positive and negative regulation
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Negative regulation
the enzyme’s product or a product further down the pathway can inhibit the enzyme and decrease flux through the pathway
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Feed-forward (positive) regulation
an enzyme’s substrate or a product upstream in the enzyme’s pathway can activate the enzyme to increase flux through the pathway
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Cooperativity
the binding of substrate to a multi-subunit protein affects the binding of subsequent substrates
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Hill’s coefficient
a term that describes whether a multi-subunit protein is not cooperative (=1), positively cooperative (>1), or negatively cooperative (<1)
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Sigmoidal
an S-shaped curve that is characteristic of cooperative behavior
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Double helix
structure of DNA; two strands of DNA wrap around each other and form a twisted ladder pattern
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Nucleotides
bonded DNA pairs that include adenine, guanine, cytosine, and thymine
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Purines
aromatic nitrogenous bases with two rings; include adenine and guanine
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Pyrimidines
aromatic nitrogenous bases with one ring; include cytosine and thymine
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Watson-Crick base pairing
bonding rules under which adenine exclusively bonds with thymine and cytosine exclusively bonds with guanine
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Sugar phosphate backbone
a repeating pattern of pentose sugar and phosphate groups bonded together; in DNA, the sugar is deoxyribose
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G-C content
a measure of the percentage of nucleotide bases that contain guanine or cytosine in a fragment of DNA; high G-C content indicates higher melting point
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Melting point
the temperature at which hydrogen bonds between base pairs are disrupted and the two strands of DNA are dissociated
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Chargaff’s rules
state that the ratio of purine nucleotides to pyrimidine nucleotides in DNA is 1 to 1. In fact, the ratio of guanine nucleotides to cytosine nucleotides and the ratio of adenine nucleotides to thymine nucleotides are also each 1 to 1
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Antiparallel
describes the two strands of DNA that run in opposite directions (5’ to 3’ and 3’ to 5’)
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Origin of replication
a sequence rich in adenine-thymine bonds at which the replisome is initially formed
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Helicase
an enzyme that unzips DNA strands during replication
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DNA topoisomerase
an enzyme that relaxes the coiling in DNA by making selective cuts in the phosphate backbone and repairing them
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DNA primase
an enzyme that creates a short strand of RNA that is complementary to DNA
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DNA polymerase
an enzyme that replaces RNA primers, continuously adds nucleotides to the daughter strand, and conducts proofreading during DNA synthesis
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Ligase
an enzyme that seals sequences of nucleotides together during DNA synthesis
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Leading strand
the template strand used during DNA synthesis, running in the 3’ to 5’ direction
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Lagging strand
the strand complementary to the lagging strand; runs in the 5’ to 3’ direction
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Okazaki fragments
short sequences of DNA that are produced in spurts along the lagging strand
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Mismatch repair
occurs in the G2 phase of the cell cycle to correct any leftover errors from synthesis
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Transcription
the process by which an RNA transcript is created from existing DNA; RNA polymerase creates RNA strands that are complementary to the template strand of DNA
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Translation
describes how proteins are created from synthesized RNA transcripts; occurs in ribosomes
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Retroviruses
RNA viruses that use a special enzyme known as a reverse transcriptase to create a double-stranded DNA molecule out of the RNA they possess
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Epigenetic modifications
physical changes on DNA that amplify or silence the expression of certain genes; include histone acetylation and deacetylation and DNA methylation and demethylation
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Imprinting
occurs when an inherited copy of a gene is silenced due to epigenetic modifications passed on from parent to offspring
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Nucleosome
a protein octamer known as a histone, and DNA
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Histone acetyltransferases (HATs)
enzymes that transfer acetyl groups to histones and function in the upregulation of gene expression
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DNA methyltransferases
enzymes that add methyl groups to DNA and function in the deactivation of genes
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Euchromatin
chromatin that is relatively relaxed and can easily be read
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Heterochromatin
chromatin that is relatively dense and cannot easily be read
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X inactivation
involves cells randomly silencing an X-chromosome, either from the mother or father, during early female development
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Cancer
characterized by uncontrolled cell proliferation, lack of response to apoptotic signals (e.g. immunity to programmed cell death), and migration to different tissues in the body
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Oncogene
a gene that causes cancer when mutated
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Tumor suppressor gene
a gene that inhibits cell cycle progression and marks cells for apoptosis
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Nondisjunction
failure of pairs of chromosomes to separate during meiosis; can result in chromosomal disorders such as trisomy 21 and Klinefelter syndrome
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Ribonucleic acid (RNA)
a form of nucleic acid that typically exists in single-stranded form; contains ribose in its phosphate backbone
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Nucleic acid
molecules composed of nucleotides, chained together by a sugar phosphate backbone
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Nucleotides
the basic building blocks of nucleic acids; includes adenine, guanine, cytosine, thymine, and uracil
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Uracil
uridine monophosphate; a nucleotide taking the place of thymine in RNA
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Transcription:
the first step of the Central Dogma; results in the transcription of genetic information from DNA’s nucleotides to RNA nucleotides
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RNA polymerase
an enzyme that serves as a translator to synthesize an RNA transcript
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Splicing
a form of posttranscriptional processing in which introns are removed and exons are ligated together
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mRNA
messenger RNA; carries information from the nuclear DNA to ribosomes for translation
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Alternative splicing
a phenomenon in which one gene can give rise to multiple proteins by retaining different combinations of RNA exons
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Translation
the second step of the Central Dogma; occurs in ribosomes and results in the translation of RNA nucleotides into polypeptides
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Codons
sequences of three nucleotides; complementary to anticodons
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tRNA
transfer RNA; each tRNA contains a unique anticodon loop and an amino acid it is charged with
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Degeneracy
a phenomenon that results in multiple nucleotide codons encoding the same amino acid
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Wobble effect
non-Watson Crick base pairing that allows for weak binding between the third nucleotide of the codon in mRNA and anticodon in tRNA
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rRNA
ribosomal RNA; main component of ribosomes; combines with special proteins to create the small and large subunits of the ribosome
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snRNPs
small nuclear ribonucleoproteins; complexes of small nuclear RNA (snRNA) and proteins that combine with pre-mRNA to form a spliceosome
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Fischer projection
a two-dimensional representation of a molecule that gives three-dimensional information; represents sugars in D- and L-configurations
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Haworth projection
a representation of the cyclic forms of sugars; represents sugar in their ⍺-anomer or β-anomer form
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Aldose
a sugar with an aldehyde group (-CHO); cyclization forms a hemiacetal
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Ketose
a sugar with a ketone group (-CO); cyclization forms a hemiketal
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Mutarotation
the ability of monosaccharides in aqueous solution to undergo spontaneous cyclization
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Pyranose
a sugar that contains a six-membered ring; e.g., glucose
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Furanose
a sugar that contains a five-membered ring; e.g., fructose
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Benedict’s reagent
reacts in the presence of aldoses to form a red copper precipitate
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Tollen’s reagent
reacts in the presence of aldehydes to form a silver, mirrorlike precipitate
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Glycogen
a polysaccharide used by the body as its primary form of carbohydrate-based energy storage
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Signaling lipids
specialized lipids involved in signal transduction pathways, or the passing of information between and within cells; include steroids and fat-soluble vitamins
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Amphipathic
referring to the presence of both hydrophobic and hydrophilic regions on the same molecule
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Phospholipids
the primary component of the phospholipid bilayer of the cell; contain a hydrophilic, polar phosphate head group joined through an ester linkage to a hydrophobic nonpolar fatty acid tail
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Triglycerides
lipids composed of a glycerol head group and three fatty acid tails; primarily used for energy storage and feature prominently in metabolism.
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Micelles
spherical structures composed of a single layer of fatty acids arranged in their lowest energy state
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Liposome
an empty spherical vesicle enclosed by a bilayer
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Fluid mosaic model
describes the structure of cell membrane components within the “sea” of relatively fluid phospholipids that make up the bilayer
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Passive transport
occurs when a molecule moves from an area of high concentration to an area of low concentration and no energy is required
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Active transport
occurs when a molecule is moving from an area of low concentration to an area of high concentration and the process requires energy; can be further categorized into primary and secondary active transport
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Amylase
an enzyme that begins to hydrolyze large polymeric carbohydrates into monosaccharides and disaccharides
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Glucagon
hormone secreted by α-cells when blood glucose levels are low
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Insulin
hormone released by β-cells when blood glucose levels are high
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Glycogenesis
pathway through which glucose is polymerized into glycogen
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Glycogenolysis
pathway through which glycogen is deconstructed into glucose monomers
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Glycolysis
metabolic process by which a glucose molecule is converted into two molecules of pyruvate
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Phosphofructokinase 1
catalyzes the rate-limiting step of glycolysis
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G3P dehydrogenase
an enzyme that catalyzes the reversible conversion of glyceraldehyde 3-phosphate into 1,3-bisphosphoglycerate, which yields two molecules of NADH per glucose molecule
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Phosphoglycerate kinase
an enzyme that catalyzes the reversible conversion of 1,3-bisphosphoglycerate into 3-phosphoglycerate; generates one ATP per molecule of phosphoglycerate
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Pyruvate kinase
an enzyme that catalyzes the irreversible conversion of phosphoenolpyruvate into pyruvate; generates one ATP per molecule of phosphoenolpyruvate
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Lactic acid cycle
serves to regenerate NAD⁺ under anaerobic conditions, so glycolysis can continue
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Pyruvate dehydrogenase
an enzyme catalyzes the irreversible conversion of pyruvate into acetyl-CoA and generates NADH and carbon dioxide as byproducts
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Citric acid cycle
pathway that takes place in the mitochondrial matrix and produces NADH and FADH2 from one molecule of acetyl-CoA
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Isocitrate dehydrogenase
an enzyme that catalyzes the rate-limiting step of the TCA cycle
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Electron transport chain
consists of the reactions catalyzed by four membrane-bound complexes located in the mitochondrion's inner membrane; serves to transfer electron equivalents from NADH and FADH2 to oxygen and create a proton gradient
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Proton-motive force
the proton gradient established between the intermembrane space and the mitochondrial matrix
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Oxidative phosphorylation
a process that transfers energy that was released through the oxidation of NADH and FADH2 into a new bond: one between ADP and an inorganic phosphate molecule, resulting in the production of ATP
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Chemiosmosis
the spontaneous flow of hydrogen ions through the F₀ component of ATP synthase
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Decoupling agents
molecules that inhibit the synthesis of ATP by destroying the proton gradient present in the mitochondrion
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Pentose phosphate pathway
produces NADPH that can be used in fatty acid synthesis and carbohydrate products that can be used in glycolysis or nucleotide synthesis
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Palmitic acid
a 16-carbon saturated fatty acid
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Citrate shuttle
a shuttle that moves citrate to the cytoplasm from the mitochondrion
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Oxaloacetate shuttle
a shuttle that moves oxaloacetate to the mitochondrion from the cytoplasm
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Beta oxidation
the breakdown of fatty acids into acetyl-CoA
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Carnitine acyltransferase I
an enzyme in the carnitine shuttle that adds carnitine to fatty acids before entry into the mitochondria
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Biotin
vitamin B₇; an essential cofactor for fatty acid breakdown
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Ketone bodies
small, water-soluble compounds that can be dissolved in the bloodstream; used by the brain during ketogenesis
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Urea cycle
converts ammonium into urea, a compound that can be safely transported to the kidneys for excretion through urine
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Gel electrophoresis
an experiment used to separate different components of a mixture based on their size and charge
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Cathode
negatively charged side of a gel
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Anode
positively charged side of a gel
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PAGE (polyacrylamide gel electrophoresis)
the material that often makes up the gel in gel electrophoresis
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Charge density
the amount of charge per area of a molecule
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SDS-PAGE
a specific type of gel electrophoresis where sodium dodecyl sulfate (SDS) is used to denature proteins and add a constant distribution of negative charges
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Denature
to unfold a protein
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Reducing SDS-PAGE
similar to SDS-PAGE although a reducing agent is used to break disulfide bridges
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Disulfide bond
a covalent bond formed between two cysteine residues
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Native-PAGE
a type of gel electrophoresis that does not denature the proteins, which will retain their secondary, tertiary, and quaternary structure
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Isoelectric focusing
a type of gel electrophoresis used to separate proteins by their isoelectric point (pI)
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Isoelectric point (pI)
the pH at which the net charge of a protein is zero
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Northern blot:
a technique used after gel electrophoresis to identify a specific RNA strand
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Reporter
an enzyme, fluorescent or radioactive compound, or other substance that sends a readily observed or measurable signal that is used to report the presence of another substance that is difficult to visualize
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Southern blot
a technique used after gel electrophoresis to identify a specific DNA strand
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Western blot
a technique used after gel electrophoresis to identify a specific protein
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Primary antibody
the first antibody that binds a target protein
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Secondary antibody
an antibody with a fluorescent label or conjugated enzyme that binds to the primary antibody
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Sanger method
a technique used to determine the sequence an of DNA strand
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Primer
a small, single-stranded piece of DNA or RNA that binds to the 3’ end of a piece of DNA and is necessary for the initiation of DNA replication by DNA polymerase
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Reverse transcriptase
an enzyme that produces a strand of DNA that is complementary to an RNA strand
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Polymerase chain reaction (PCR)
a method used to generate a large number of copies of a piece of DNA
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cDNA library
a collection of host cells, usually bacteria, that is used to store genes of interest
194
Indirect ELISA
a type of ELISA where you immobilize an antigen and determine if an antibody binds to it, followed by a secondary antibody linked to a reporter enzyme to determine if binding has occurred
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Direct ELISA
a type of ELISA where you immobilize an antigen and determine if an antibody binds to it, and a reporter enzyme linked to the antibody tells you if binding has occurred
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Sandwich ELISA
a type of ELISA where you determine the concentration of an antigen in solution by immobilizing an antibody, adding the antigen, and then adding additional antibody that is linked to a reporter enzyme
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Bacterial transformation
the process of a bacteria absorbing genetic information from its surroundings and inserting it into its genome
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Plasmids
circular pieces of DNA
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Restriction enzymes/endonucleases
enzymes that cut specific palindromic sequences of DNA
200
Centrifugation
separating substances by spinning them at high speeds
201
Pellet
the solid region at the bottom of a centrifuged tube containing dense substances
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Supernatant
the liquid region at the top of a centrifuged tube containing less dense substances
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Chromatography
a technique used to isolate a substance of interest from a larger mixture of molecules
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Mobile phase
the liquid containing your substance of interest in chromatography
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Stationary phase
the immobilized part of the column that will attract your substance of interest in chromatography
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Gel filtration (size exclusion) chromatography
a type of chromatography where you use beads with many small paths as your stationary phase to separate contents of a mobile phase by size
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Ion-exchange chromatography
a type of chromatography where you use a positively or negatively charged stationary phase to separate contents of a mobile phase by charge
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Anion-exchange chromatography
a form of ion-exchange chromatography that attracts negatively charged molecules
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Cation-exchange chromatography
a form of ion-exchange chromatography that attracts positively charged molecules
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Elute
breaking the interaction between your substance of interest and the stationary phase so that your substance of interest exits the column
211
Affinity chromatography
a type of chromatography where you isolate a specific substance from the mobile phase by using a stationary phase that contains something with a high affinity for your substance of interest
212
Isomerase
Catalyzes an isomerization reaction, which is an intramolecular rearrangement of bonds in a molecule.
example: An enzyme that converts a cis double bond into a trans double bond
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Ligase
Catalyzes the joining of two molecules.
example: An enzyme that seals the gap between two adjacent Okazaki fragments
214
Transferase
Catalyzes the transfer of a functional group from one molecule to another molecule.
example: A kinase that adds a phosphate group from ATP to a protein substrate
215
Lyase
Catalyzes the breaking of a molecule without the use of water.
example: An enzyme that breaks a bond between two nucleotides without using water
216
Hydrolase
Catalyzes the breaking of a molecule by adding water.
example: An enzyme that breaks a bond between two nucleotides by adding water.
217
Oxidoreductase
Catalyzes the transfer of electrons between molecules.
example: An enzyme that transfers extra electrons from an NADH electron carrier to a protein substrate.
