Biochemistry Flashcards
a-Helix
An element of polypeptide secondary structure, marked by clockwise coiling of amino acids around a central axis.
Activation
Conversion of a biomolecule to its active or usable form, such as activating tRNA with an amino acid or activating a fatty acid with CoA to form fatty acyl-CoA.
Active Site
The catalytically active portion of an enzyme.
Active Transport
The movement of a molecule against its concentration gradient with energy investment; primary active transport uses ATP, whereas secondary active transport couples energetically costly movement to that of a favorable transport gradient of a different molecule.
Activity (Vmax)
Also sometimes called velocity or rate, this is a measure of the catalytic activity of an enzyme. Vmax is the measurement by which activity is often assessed, and may be analyzed after protein isolation.
Adenosine Triphosphate (ATP)
The primary energy molecule of the body; energy is released by breaking the molecule’s bond with the terminal phosphate to form ADP and an organic phosphate.
Aerobic Respiration
Energy-producing metabolic processes that require oxygen. These include the citric acid cycle, electron transport chain, and oxidative phosphorylation.
Allosteric Enzymes
Enzymes that experience changes in their conformation as a result of interactions at sites other than the active site (allosteric sites); the conformational changes that result may increase or decrease enzyme activity.
Amino Acid
A dipolar compound containing an amino group (-NH2) and a carboxyl group (-COOH).
Amplification
Increased transcription (and translation) of a gene in response to hormones, growth factors, and other intracellular conditions.
Anabolism
Metabolic processes that result in the consumption of energy and the synthesis of molecules. Contrast with catabolism.
Anaerobic Respiration
Energy-producing metabolic processes that do not require oxygen, including glycolysis and fermentation.
Anticodon
A three-nucleotide sequence on a tRNA molecule that pairs with a corresponding mRNA codon during translation.
Apolipoprotein
Protein component of lipoprotein complexes. Responsible for the interactions of the resultant lipoproteins with cells and the transfer of lipid molecules. Also called apoproteins.
B-pleated Sheet
An element of polypeptide secondary structure characterized by peptide chains lying alongside one another, forming rows and strands.
Basal Metabolic Rate
The amount of energy consumed in a given period of time by an organism while in a resting, nonmobile state.
Bradford Protein Assay
A colorimetric method of determining the concentration of protein in a sample as compared to a protein standard; relies on a transition of absorption between bound and unbound Coomassie Brilliant Blue dye.
Catabolism
Metabolic processes that result in the release of energy and the breakdown of molecules. Contrast with anabolism.
Cell Adhesion Molecules (CAMs)
Specialized structural proteins that are involved in cell-to-cell junctions as well as transient cellular interactions; common cell adhesion molecules include cadherins, integrins, and selectins.
Central Dogma of Molecular Biology
The major steps in the transfer of genetic information, from transcription of DNA to RNA and resultant translation of that RNA to protein.
Centrifugation
The process of separating components on the basis of their density and resistance to flow by spinning a sample at very high speeds; the most dense components form a solid pellet and the least dense components remain in the supernatant (liquid portion).
Chaperones
Proteins that assist in protein folding during posttranslation processing.
Chemiosmotic Coupling
A more widely accepted method of ATP synthase activity. Utilization of the proton-motive force generated by the electron transport chain to drive ATP synthesis in oxidative phosphorylation.
Cholesterol
A molecule containing four linked rings; cholesterol provides both fluidity and stability to cell membranes and is the precursor for steroid hormones.
Citric Acid Cycle
A metabolic pathway that produces GTP, energy carriers, and carbon dioxide as it burns acetyl-CoA; also called the Kreb’s cycle or tricarboxylic acid (TCA) cycle; can share intermediates with many other metabolic processes including fatty acid and cholesterol synthesis, gluconeogenesis, amino acid metabolism, and others.
Coding Strand
The strand of DNA that is used as a template during transcription; also called the sense strand.
Codon
A three-nucleotide sequence in an mRNA molecule that pairs with an appropriate tRNA anticodon during translation.
Coenzyme
An organic molecule that helps an enzyme carry out its function.
Cofactor
An inorganic molecule or ion that helps an enzyme carry our its function.
Competitive Inhibition
A decrease in enzyme activity that results from the interaction of an inhibitor with the active site of an enzyme; competitive inhibition can be overcome by addition of excess substrate.
Cooperativity
The interaction between subunits of a multisubunit protein in which binding of substrate to one subunit increases the affinity of other subunits for the substrate; unbinding of substrate from one subunit decreases the affinity of other subunits for the substrate.
Corepressor
A species that binds with a repressor, allowing the complex to bind to the operator region of an operon, stopping transcription of the relevant gene.
Cristae
Infoldings of the inner mitochondrial membrane that increases the surface area available for electron transport chain complexes
Denaturation
The loss of tertiary structure in a protein, leading to loss of function.
Deoxyribonucleic Acid (DNA)
A nucleic acid found exclusivity in the nucleus that codes for all of the genes necessary for life; transcribed to mRNA and always read 5’ to 3’.
Desmosomes
Cell-to-cell junctions that anchor layers of epithelial cells to one another.
Disulfide Bond
A covalent interaction between the -SH groups of two cysteine residues; an element of tertiary and quaternary structure in proteins.
Electrochemical Gradient
An uneven separation of ions across a biological membrane, resulting in electrical potential across the membrane.
Electrophoresis
The process of separating compounds on the basis of size and charge using a porous gel and an electric field; protein electrophoresis generally uses polyacrylamide; while nucleic acid electrophoresis generally uses agarose.
Elongation
The three-step cycle repeated for each amino acid being added to a protein during translation.
Endocytosis
The transport of molecules into a cell through invagination of the cell membrane and the formation of a vesicle; phagocytosis (“cell eating”) is the endocytosis of solids, pinocytosis (“cell drinking”) is the endocytosis of liquids.
Enhancer
Portion of DNA that can be bound by transcription factors to increase transcription of a gene.
Enzyme
A biological molecule with catalytic activity; includes many proteins and some RNA molecules.
Epimers
A subtype of diastereomers that differ in absolute configuration at exactly one chiral carbon.
Euchromatin
Loose, less dense collections of DNA that appear light-colored under the microscope; transcriptionally active.
Exocytosis
The transport of molecules out of a cell by release from a transport vesicles; the vesicle fuses to the cell membrane during secretion.
Exon
A portion of hnRNA that is spliced together with other exons to form mature mRNA. Contrast with introns.
Facilitated Diffusion
The movement of solute molecules through the cell membrane down their concentration gradient via a transport protein or channel; used for ions and large or polar molecules.
Fatty Acid
A monocarboxylic acid without additional substituents; fatty acids may be saturated (all single bonds) or unsaturated (contain at least one double bond); natural unsaturated fatty acids are in the cis conformation.
Feedback Inhibition
The inhibition of an enzyme by its product (or a product further down in a metabolic pathway); used to maintain homeostasis.
Feed-forward Activation
The stimulation of an enzyme by an intermediate that precedes the enzyme in a metabolic pathway.
Fermentation
The conversion of pyruvate to either ethanol and carbon dioxide (yeast) or lactic acid (animal cells); does not require oxygen.
Fischer Projection
A method of drawing organic molecules in which horizontal lines are coming out of the page (wedges) and vertical lines are going into the page (dashes).
Flavin Adenine Dinucleotide (FAD)
An energy carrier that participates as an electron acceptor and donor in the electron transport chain.
Fluid Mosaic Model
The representation of the plasma membrane as a dynamic phospholipid bilayer that interacts with cholesterol and proteins.
G protein-coupled receptors
A special class of membrane receptors with an associated GTP binding protein; activation of a G protein-coupled receptor involves dissociation and GTP hydrolysis.
Gap Junctions
Cell-to-cell junctions that allow the passage of small molecules between adjacent cells.
Globoside
A sphingolipid with multiple carbohydrate groups attached as a head group.
Gluconeogenesis
The production of glucose from other biomolecules; carried out by the liver and kidneys.
Glucose
The primary monosaccharide used for fuel by all cells of the body; has the formula C6H12O6.
Glycerol
A three-carbon alcohol that serves as the backbone for glycerophospholipids, sphingolipids, and triacylglycerols.
Glycerophospholipid
A lipid containing a glycerol backbone with a phosphate group; bound by ester linkages to two fatty acids.
Glycogen
A branched polymer of glucose that represents a storage form of glucose
Glycolysis
The breakdown of glucose into two molecules of pyruvate with the formation of energy carriers (NADH); occurs under both aerobic and anaerobic conditions.
Glycosidic Linkage
The bond between the anomeric carbon of a sugar and another molecule
Glycosphingolipid
A sphingolipid with a head group composed of sugars; includes cerebrosides and globosides.
Helicase
An enzyme that unwinds the double helix of a DNA molecule, allowing replication to take place.
Heterochromatin
Dense, tightly coiled DNA that appears dark colored under the microscope; transcriptionally inactive.
Heterogenous Nuclear RNA (hnRNA)
Preprocessed mRNA; converted to mRNA by adding a poly-A tail and 5’cap and splicing out introns.
Histone
A structural protein around which DNA is coiled in eukaryotic cells.
Holoenzyme
An enzyme that has already bound a required prosthetic group, coenzyme, or cofactor. Contrast with apoenzyme.
Hydrophilic
Being attracted to water; describes polar and charged compounds and those that can participate in hydrogen bonding.
Hydrophobic
Being repelled by water; describes nonpolar, uncharged compounds (usually lipids or certain R groups of amino acids).
Hypertonic
A solution that has a greater concentration than the one to which it is being compared. Contrast with hypotonic and isotonic.
Hypotonic
A solution that has a lower concentration that the one to which it is being compared. Contrast with hypertonic and isotonic.
Induced Fit Model
The best supported of the most prominent theories of enzyme specificity; states that the enzyme and substrate experience a change in conformation during binding to increase complementarity. Usually contrasted with the lock and key theory.
Initiation
The state of translation, in which the small subunit of the ribosome binds to the mRNA molecule and the first tRNA (methionine or N-formylmethionine) is bound to the start codon (AUG).
Intron
A portion of hnRNA that is spliced out to form mRNA; remains in the nucleus during processing. Contrast with exon.
Irreversible Inhibition
A decrease in enzymes activity that results from the interaction of an inhibitor that binds permanently at either the active site or an allosteric site; in laboratory settings, irreversible inhibitors are sometimes called suicide substrates.
Isoelectric Point (pI)
The pH at which an amino acid is predominantly in zwitterionic form.
Isoform
A slightly different version of the same protein, often to a given tissue.
Isotonic
A solution that has the same concentration as the one to which it is being compared. Contrast with hypertonic and hypotonic.
Ketogenesis
The synthesis of ketone bodies from the metabolic products of B-oxidation or amino acid metabolism occurs under conditions of starvation.
Ketogenic
Describes amino acids that can be converted into intermediates that feed into ketogenesis.
Kinase
A specific transferase enzyme that catalyzes the movement of a phosphate group, generally from ATP, to a molecule of interest.
Lagging Strand
The strand of DNA that is synthesized in small fragments, called Okazaki fragments, and then ligated together. The Okazaki fragments are synthesized in the 5’ to 3’ direction, but the overall synthesis is in the 3’ to 5’ direction.
Leading Strand
The strand of DNA that is continuously synthesized in the 5’ to 3’ direction. The template strand is read in the 3’ to 5’ direction.
Ligase
An enzyme that catalyzes the joining of large polymeric biomolecules, most commonly nucleic acids.
Lipoprotein
The transport mechanism for lipids within the circulatory and lymphatic systems; includes chylomicrons and VLDL, which transport mostly triacylglycerols, and HDL, IDL, and LDL, which transport mostly cholesterol and cholesteryl esters.
Lock and Key Theory
One of the two most prominent theories of enzyme specificity; states that the enzyme and the substrate have a static but complementary state. Less supported than the induced fit model.
Lyase
An enzyme that catalyzes the cleavage or synthesis of a molecule without the addition or loss of water.
Matrix
Contents of the inner mitochondrial membrane; includes soluble enzymes of the electron transport chain and mitochondrial DNA.
Membrane Receptors
Transmembrane protein molecules that act enzymatically or as ion channels to participate in signal transduction.
Messenger RNA (mRNA)
The strand of RNA formed after transcription of DNA; moves to the cytoplasm to be translated.
Micelle
A collection of fatty acid or phospholipid molecules oriented to minimize free energy through hydrophobic and hydrophilic interactions; generally a sphere with a hydrophobic core and hydrophilic exterior.
Mixed Inhibition
A decrease in enzyme activity that results from the interaction of an inhibitor with an allosteric site; mixed inhibitors bind to the free enzyme and to the substrate-bound enzyme with different affinities. They cannot be overcome by addition of substrate and impact both Km and Vmax.
Monocistronic
The coding pattern seen in the vast majority of eukaryotic proteins in which one mRNA molecule codes for only one protein. Contrast with polycistronic.
Motor Proteins
Proteins that are involved in cell motility through interactions with structural proteins; motor proteins have ATPase activity and include myosin, kinesin, and dynein.
Nicotinamide Adenine Dinucleotide (NAD+)
An energy carrier that accepts electrons through various processes and feeds them into the electron transport chain.
Nicotinamide Adenine Dinucleotide Phosphate (NADP+)
An electron acceptor important in the pentose phosphate pathway that is involved in biosynthesis, oxidative stress, and immune function.
Operator Site
A component of the person in prokaryotes; a nontranscribable region of DNA that is capable of binding a repressor protein.
Operon
In prokaryotes, a cluster of genes transcribed as a single mRNA that can be regulated by repressors or inducers, depending on the system.
Osmosis
The simple diffusion of water.
Osmotic Pressure
The pressure necessary to counteract the effect of an osmotic gradient against pure water; one of the colligative properties; can be thought of as a “sucking” pressure created by solutes drawing in water.
Oxidative Phosphorylation
The transfer of a phosphate group, generally to ATP, which is powered by a gradient formed by oxidation-reduction reactions; occurs in the mitochondria.
Pancreatic Proteases
The enzymes that are primarily responsible for the digestion of proteins in the small intestine; they include trypsin, chymotrypsin, and carboxypeptidases A and B, all of which are secreted as zymogens.
Paracellular Transport
Transport of materials through the interstitial space without interactions with the cytoplasm or cell membrane.
Passive Transport
The movement of a molecule down its concentration gradient without energy investment; includes simple and facilitated diffusion and osmosis.
Pentose Phosphate Pathway
A metabolic process that produces NADPH and ribose 5-phosphate for nucleotide synthesis.
Peptide
A molecule composed of more than one amino acid; can be subdivided into dipeptides (two amino acids), tripeptides (three), oligopeptides (up to 20), and polypeptides (more than 20).
Peptide Bond
An amide bond between the carboxyl group of one amino acid and the amino group of another amino acid.
Phospholipid
A lipid containing a phosphate and an alcohol (glycerol or sphingosine) joined to hydrophilic fatty acid tails.
Polycistronic
The coding pattern or prokaryotes, in which one mRNA may code for multiple proteins. Contrast with monocistronic.
Polysaccharide
A long chain of monosaccharides linked by glycosidic bonds; can be divided into homopolysaccharides (only one type of monosaccharides is used) and hertopolysaccharides (more than one type of monosaccharide is used).
Primary Structure
The linear sequence of amino acids in a polypeptide.
Prosthetic Group
A cofactor or coenzyme that is covalently bonded to a protein to permit its function
Proton-Motive Force
The proton concentration gradient across the inner mitochondrial membrane, which is created by the electron transport chain and used in oxidative phosphorylation.
Pyranose
A six-membered ring sugar.
Pyruvate
An important metabolic intermediate that can feed into the citric acid cycle, fermentation, or gluconeogenesis.
Quaternary Structure
The interaction between different subunits of a multisubunit protein; stabilized by R group interactions.
Reaction Coupling
The tendency of energetically unfavorable biological reactions to occur concurrently with favorable reactions, often catalyzed by single enzyme.
Reducing Sugar
A sugar that can reduce other compounds and that can be picked up by Tollens’ and Benedict’s reagent
Release Factor
The protein that binds to the stop codon during termination of translation
Renaturation
Regaining the correct tertiary structure after denaturation of a protein.
Repressible System
An operon that requires a repressor to bind to a corepressor before binding to the operator sire to stop transcription of the relevant gene; also called a negative control system.
Resting Membrane Potential
The electrical potential that results from the unequal distribution of charge around the cell membrane; resting membrane potential characterizes a cell that has not been stimulated.
Ribosomal RNA (rRNA)
The structural and enzymatic RNA found in ribosomes that takes part in translation.
Ribozyme
An RNA molecule with enzymatic activity.
Saponification
The reaction between a fatty acid and a strong base, resulting in a negatively charged fatty acid anion bound to a metal ion; creates soap.
Saturation
Refers to the presence or absence of double bonds in a fatty acid; saturated fatty acids have only single bonds, whereas unsaturated fatty acids have at least one double bond.
Secondary Structure
The local structure of neighboring amino acids in a polypeptide or protein; most common are a-helics and B-pleated sheets
Shuttle Mechanism
A method of functionally transferring a compound across a membrane without the actual molecule crossing; common examples are the glycerol 3-phosphate shuttle and the malate-aspartate shuttle
Side Chain
The variable component of an amino acid that gives it its identity and chemical properties; also called an R group
Simple Diffusion
The movement of solute molecules through the cell membrane down their concentration gradient without a transport protein; used for small, nonpolar, lipophilic molecules and water
Sphingolipid
A lipid containing a sphingosine or sphingoid backbone bound to fatty acid tails; includes ceramide, sphingomyelins, glycosphingolipids, and gangliosides.
Spliceosome
The apparatus used for slicing out introns and bringing exons together during mRNA processing.
Start Codon
The first codon in an mRNA molecule that codes for an amino acid (AUG for methionine or N-formylmethionine).
Stop Codon
The last codon of translation (UAA, UGA, or UAG); release factor binds here, terminating translation.
Structural Proteins
Proteins that are involved in the cytoskeleton and extracellular matrix; they are generally fibrous in nature and include collagen, elastin, keratin, actin, and tubulin.
Substrate
The molecule upon which an enzyme acts.
Substrate-level Phosphorylation
The transfer of a phosphate group from a high-energy compound to ATP or another compound; occurs in glycolysis.
Surfactant
A compound that lowers surface tension by acting as a detergent or emulsifier.
TATA Box
The site of binding for RNA polymerase II during transcription; named for its high concentration of thymine and adenine bases.
Template Strand
The strand of DNA that is transcribed to form mRNA; also called the antisense strand.
Termination
The end of translation, in which the ribosome finds a stop codon and release factor binds to it, allowing the peptide to be freed from the ribosome.
Terpene
A class of lipids built from isoprene moieties; have carbon groups in multiples of five.
Tertiary Structure
The three-dimensional shape of a polypeptide, stabilized by numerous interactions between R groups.
Tight Junctions
Cell-to-cell junction that prevent the paracellular transport of materials; tight junctions form a collar around cells and link cells within a single layer.
Transcellular Transport
Transport of materials through the cell; requires interaction with the cytoplasm and may require transport proteins.
Transcription
Production of an mRNA molecule from a strand of DNA
Transcription Factors
Proteins that help RNA polymerase II locate and bind to the promoter region of DNA
Transfer RNA (tRNA)
A folded strand of RNA that contains a three-nucleotide anticodon that pairs with an appropriate mRNA codon during translation and is charged with the corresponding amino acid.
Transferase
An enzyme that catalyzes the transfer of a functional group
Translation
Production of a protein from an mRNA molecule.
Triacylglycerol
A glycerol molecule esterified to three fatty acid molecules; the most common form of fat storage within the body.
Uncompetitive Inhibition
A decrease in enzyme activity that results from the interaction with an inhibitor at the allosteric site; uncompetitive inhibitors bind only to the substrate-bound enzyme and cannot be overcome by additition of substrate. Uncompetitive inhibitors functionally increase affinity (Km), but decrease maximum velocity (Vmax).
Vitamin
An essential organic coenzyme that assists an enzyme in carrying out its action.
Wax
A lipid with a high melting point that is composed of a very long chain alcohol and a very long chain fatty acid.
Wobble Hypothesis
Hypothesis describing the binding of the third nucleotide of a codon to an anticodon, which is not specific and can occur with mismatched bases. In the genetic code, the third nucleotide often plays no role in specifying an amino acid. This is theorized to be an evolutionary development designed to protect against mutations.
Zwitterion
A molecule that contains charges, but is neutral overall. Most often used to describe amino acids.
Zymogen
An enzyme that is secreted in an inactive form and must be activated by cleavage; common examples are digestive enzymes.
Acetyl-CoA
An important metabolic intermediate that links glycolysis and B-oxidation to the citric acid cycle; can also be converted into ketone bodies.
Cerebroside
A sphingolipid containing a carbohydrate as a head group.
Conformational Coupling
A less-accepted mechanism of ATP synthase activity in which the protons cause a conformational change that releases ATP from ATP synthase.
Conjugated Protein
A protein that derives part of its function from covalently attached molecules (prosthetic groups).
Inducible System
An operon that requires an inducer to remove a repressor protein from the operator site to begin transcription of the relevant gene; also called a positive control system.
Jacob-Monod Model
The description of the structure and function of operons in prokaryotes, in which operons have structural genes, an operator site, a promoter site, and a regulator gene.
Alternative Splicing
The production of multiple different but related mRNA molecules from a single primary transcript of hnRNA.
Km
The concentration of substrate at which an enzyme runs at half its maximal velocity; a measure of enzyme affinity (the higher the Km, the lower the affinity).
Mutarotation
The rapid interconversion between different anomers of a sugar.
Noncompetitive Inhibition
A decrease in enzyme activity that results from the interaction of an inhibitor with an allosteric site; noncompetitive inhibitors bind equally well to free enzymes and to substrate-bound enzymes. They cannot be overcome by addition of substrate.
Promoter Region
Portion of DNA upstream from a gene; contains that TATA box, which is the site where RNA polymerase II binds to start transcription
Sphingomyelin
A sphingophospholipid containing a sphingosine backbone and a phosphate head group
Anomers
A subtype of epimers in which the chiral carbon with inverted configuration is the carbonyl carbon (anomeric carbon).
Apoenzyme
An enzyme devoid of the prosthetic group, coenzyme, or cofactor necessary for normal activity. Contrast with holoenzyme.
Ceramide
The simplest sphingolipid, with a single hydrogen as its head group.
Furanose
A five-membered ring sugar
Ganglioside
A sphingolipid with a head group containing an oligosaccharide and one or more N-acetylneuraminic acid (NANA) molecules.
Glucogenic
Describes amino acids that can be converted into intermediates that feed into gluconeogenesis; all amino acids except leucine and lysine.
Isoelectric Focusing
A specialized method of separating proteins by their isoelectric point using electrophoresis; the gel is modified to possess a pH gradient.
Lariat
The lasso-shaped structure formed during the removal of introns in mRNA processing.
Nontemplate Synthesis
The method of de novo synthesis of lipids and carbohydrates that relies on gene expression and enzyme specificity rather than the genetic template of DNA or RNA.
Prostaglandins
A group of 20-carbon molecules that are unsaturated carboxylic acids derived from arachidonic acid; act as paracrine or autocrine hormones.
Respiratory Quotient
A numerical representation that can be used to determine the prevalent type of biomolecule being used in metabolism; the ratio of carbon dioxide produced to oxygen consumed.
Shine-Dalgarno Sequence
The site of initiation of translation in prokaryotes.
Degenerate
Description of an aspect of the genetic code; specifically, that more than one codon can specify a single amino acid.
B-oxidation
The catabolism of fatty acids to acetyl-CoA.
