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