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MCB Final Exam
Molecular and Cell Biology cumulative content
| Term | Definition |
|---|---|
| Archaeon | prokaryotic cell adapted to exotic environments |
| Bacterium | prokaryotic cell that is adapted to live in normal environments |
| Cell | phospholipid membrane-enclosed collection of highly organized organic molecules |
| Chloroplast | specialized organelle found only in plants that uses solar energy to convert carbon dioxide and water into glucose |
| Chromosome | eukaryotic structure composed of DNA and associated proteins that carries genetic information of an organism |
| Cytoplasm | contents of a cell between the membrane and nucleus (if it has one) |
| Cytoskeleton | collection of protein fibers inside a cell that provide structure, movement, and transport functions |
| Cytosol | aqueous gel of large and small organic molecules inside a cell |
| Deoxyribonucleic acid | double-stranded molecule made up of complementary, antiparallel nucleotides |
| DNA | deoxyribonucleic acid |
| Eukaryote | organism that keeps its genetic information separated from the cytoplasm within a double-walled nucleus; contains specialized organelles |
| Evolution | process of mutation and natural selection responsible for the diversity of life on Earth |
| Genome | collection of genetic information contained in a cell |
| Homologous | protein/nucleic acid sequences that are similar because of a common evolutionary origin |
| Mitochondrion | organelle responsible for aerobic metabolization; carries out oxidative phosphorylation, producing most of a cell's ATP |
| Nucleus | eukaryotic organelle that encloses the genome and restricts passage of molecules |
| Chromatid | one copy of a chromosome formed by DNA replication that is still joined at the centromere to the other copy during mitosis |
| Organelle | structure within a eukaryotic cell that carries out a specialized function |
| Prokaryote | simple cell without a nucleus or membranous organelles that can vary widely in chemical capabilities and adapt to extreme environments |
| Protein | one or more linear chains of amino acids linked together by peptide bonds in a specific sequence; each unique conformation determines function |
| Protozoan | free-living, unicellular, non-photosynthetic, motile eukaryotic organism |
| Ribosome | ribozyme that reads from an mRNA and catalyzes protein synthesis |
| Ribonucleic acid | single strand of nucleic acids that serves diverse functions in the cell, including transcription, translation, catalysis, and defense |
| RNA | ribonucleic acid |
| Specialization | division of labor among cells in a multicellular organism, leading to differentiated gene expression between tissues |
| Conformation | three-dimensional shape of a protein |
| Difference in size between prokaryotic and eukaryotic cells | eukaryotic cells are at least ten times larger than prokaryotic cells |
| Endosymbiotic theory | hypothesis that mitochondria and chloroplasts originated as bacteria that were engulfed by other cells |
| Types of filaments in the cytoskeleton | actin, intermediate filaments, microtubules |
| Cell cycle | the process of duplication and division in cells |
| DNA interoperability | one organism can read and produce proteins from another's genes |
| Acid | molecule with a tendency to release protons when dissolved in water |
| Amino acid | molecule consisting of a central carbon atom, a carboxyl and an amine group, and a residue; component of proteins |
| Adenosine triphosphate | carrier molecule most commonly used in reactions within cells |
| ATP | adenosine triphosphate |
| Base | molecule with a tendency to release hydroxyl ions when dissolved in water |
| Buffer | weak acid or base that can be used to stabilize the pH of a solution |
| Covalent bond | very strong, stable bond between atoms that requires catalysis to separate |
| Condensation reaction | anabolic reaction that joins two molecules and releases a water molecule |
| Electrostatic attraction | attractive force between two atoms with opposite electrical charge |
| Fatty acid | carboxyl group attached to a long hydrocarbon chain |
| Hydrogen bond | electrostatic attraction between the hydrogen atoms of one water molecule and the oxygen atom of another |
| Hydrolysis | catabolic reaction that uses a water molecule to break apart a molecule |
| Hydronium ion | single proton |
| Hydrophilic | substance that dissolves in water; contains mostly polar covalent bonds |
| Hydrophobic | substance that does not dissolve in water; contains mostly non-polar covalent bonds |
| Ion | atom with more or fewer electrons than protons |
| Ionic bond | strong, stable bond between atoms that weakens significantly in water |
| Macromolecule | organic molecule with a weight in excess of 1,000 daltons |
| Molecular weight | sum of the weights of the constituent atoms of a molecule |
| Monomer | single unit of a complex organic molecule |
| Noncovalent bond | one of several relatively weak types of atomic bond, important in cellular function |
| Types of noncovalent bonds | hydrogen bond, electrostatic, van der Waals |
| Nucleotide | nucleoside with one or more phosphate groups attached to the sugar subunit |
| Polar covalent bond | an atomic bond in which the electrons are unequally shared; important in organic chemistry because they allow molecules to interact by electrostatic attraction |
| Polymer | organic molecule consisting of many monomers |
| Sequence | linear order of monomers in a large molecule that specifies its precise biological function |
| Sugar | molecule consisting of one or more saccharides |
| Saccharide | molecule with the general formula (CH2O)n |
| Subunit | either a monomer or a complete molecule that forms part of a larger polymer |
| Most common elements in organic chemistry | hydrogen, carbon, oxygen, phosphorus, nitrogen, and sulfur |
| Nonpolar covalent bond | bond between atoms where electrons are equally shared |
| Four major families of small organic molecules | sugars, amino acids, fatty acids, nucleotides |
| Function of sugars in the cell | provide an energy source, polymerize to store energy, or form mechanical supports |
| Phospholipid | molecule composed of a head and two fatty acid tails |
| Composition of the phospholipid head | polar group, phosphate, glycerol |
| Function of fatty acids in the cell | form phospholipid membranes, serve as a concentrated food reserve |
| Lipid | a class of organic molecules that is insoluble in water, but soluble in fats or organic solvents |
| Amphipathic | containing both polar and nonpolar subunits; both hydrophilic and hydrophobic |
| Peptide bond | bond between amino acids that is formed by a condensation reaction between the amine and carboxyl groups |
| Number of different amino acids found in proteins | twenty |
| Chiral molecule | cannot be superposed on its mirror-image; has the property of being "left-handed" or "right-handed" |
| Nucleoside | a nitrogen-containing ring compound attached to a 5-carbon sugar |
| Phosphoanhydride bond | bond between two phosphate groups |
| Nucleosides used in RNA | adenine, cytosine, guanine, uracil |
| Nucleosides used in DNA | adenine, cytosine, guanine, thymine |
| Pyrimidine | nucleotide with a six-member pyrimidine ring as the nitrogenous subunit; cytosine, thymine, uracil |
| Purine | nucleotide with a five-membered ring attached to the six-member ring in its nitrogenous subunit; adenine and guanine |
| Nucleic acid | long polymer of nucleotides |
| Electrical charge of nucleic acids | negative due to the phosphate groups |
| Phosphodiester bond | covalent bond between the phosphate group of one nucleotide and the sugar subunit of another |
| Number of hydrogen bonds between adenine and thymine/uracil | two hydrogen bonds; relatively weaker bond |
| Number of hydrogen bonds between cytosine and guanine | three hydrogen bonds; relatively stronger bond |
| Interactions between macromolecules | mediated by noncovalent bonds |
| Steroid | lipid with a multiple-ring structure; does not require active transport to enter the cell |
| Micelle | small sphere of phospholipids |
| Triacylglycerol | glycerol with ester linkages to three fatty acids; energy storage molecule |
| Four families of amino acids | acidic, basic, uncharged polar, nonpolar |
| Hydrophobic bond | two hydrophobic groups held together in water by the water's electrostatic repulsion |
| Acetyl CoA | acetyl group linked to coenzyme A by an easily hydrolyzed thioester bond |
| Activated carrier | carrier molecule in its high-energy state |
| Activation energy | the amount of energy required to carry out a chemical reaction |
| Carrier molecule | small molecule used to carry energy or chemical groups in many different metabolic reactions |
| Anabolism | reaction pathways by which large molecules are made from smaller ones |
| Catabolism | reaction pathways by which large molecules are broken down into smaller ones |
| Catalysis | acceleration of a chemical reaction due to the presence of a molecule which is itself unchanged by the reaction |
| Coupled reaction | link between an exothermic chemical reaction and an endothermic one which accelerates the rate of the endothermic reaction |
| Diffusion | random, thermally-driven movement of molecules from one place to another |
| Entropy | a closed system always increases in disorder |
| Enzyme | protein that catalyzes chemical reactions |
| Equilibrium | state in which two chemical reactions are proceeding at a rate that creates no net chemical change |
| Free-energy change | the increase or decrease in free energy associated with a single chemical reaction; chemical reactions that increase free energy are more likely to occur spontaneously |
| Metabolism | all of the chemical reactions going on within a cell |
| Oxidation | loss of electron density from an atom, as when an oxygen is added to a carbon atom |
| Reduction | gain of electron density in an atom, as when an oxygen is removed from a carbon atom, or a hydrogen atom is added |
| Respiration | process in a cell where uptake of molecular oxygen is coupled to the production of CO2 |
| Photosynthesis | process in a cell that drives synthesis of saccharides from water and carbon dioxide |
| Substrate | molecule on which an enzyme acts |
| Turnover number | number of substrate molecules converted to product per one second by one enzyme |
| V-max | the maximum rate of an enzymatic reaction |
| Biosynthesis | process by which cells create more order in their internal environment, increasing the entropy of their external environment |
| Metabolic pathway | a long linear pathway of chemical reactions that a cell can modulate to control the turnover number of the enzymes involved |
| Carbon fixation | the non-light-dependent stage of photosynthesis, where activated carrier molecules are used to convert carbon dioxide and water to sugar |
| Unsaturated fatty acid | fatty acid that contains double bonds between carbon atoms in the hydrocarbon chain |
| Saturated fatty acid | fatty acid that contains no double bonds between carbon atoms in the hydrocarbon chain |
| Active site | a subunit of an enzyme into which only particular substrates will fit |
| Chemical disequilibrium | the state of living cells where chemical reactions occur at unequal rates |
| Binding energy | the energy released in a binding interaction between two molecules |
| Scaffold proteins | draw together sets of interacting proteins at specific locations in the cell |
| Common carrier molecules in cells | ATP, NADH, NADPH, acetyl CoA |
| NADH | carrier molecule used in cells as an oxidizing agent |
| NADPH | carrier molecule used in cells as a reducing agent |
| Carrier molecules in an RNA world | hypothesis that many carrier molecules contain nucleotides because RNA molecules were the main catalysts for early life forms on Earth, so the carrier molecule nucleotides would bind readily to ribozymes |
| Allosteric | protein that can exist in two or more conformations depending on the binding of a ligand at a site other than the catalytic site |
| Alpha-helix | a structural motif in proteins where a chain of amino acids form a right-handed helix stabilized by hydrogen bonds between backbone atoms |
| Amino acid sequence | the order of amino acid residues in a protein chain |
| Antibody | protein that binds tightly to foreign molecules or cells, inactivating them or marking them for destruction |
| Antigen | molecule that stimulates the production of specific antibodies in an immune response |
| Beta-sheet | folding pattern of proteins in which neighboring regions of the polypeptide chain form a rigid, flattened structure |
| Binding site | region on the surface of a protein that is complementary in shape to a ligand |
| Coiled-coil | two or more alpha-helices coiled around each other, forming a very stable rod |
| Conformation | unique shape of a protein that determines its function; usually the shape in which free energy is minimized |
| Disulfide bond | a covalent bond between cysteine residues that often joins two proteins |
| Feedback inhibition | end product of a chain of enzymatic reactions reduces activity of an enzyme earlier in the pathway |
| Fibrous protein | protein with an elongated shape |
| Globular protein | protein with a rounded, spherical shape |
| GTP-binding protein | allosteric protein whose conformation and activity are modulated by the presence of GDP or GTP; used frequently in cell signaling |
| Ligand | molecule that binds to a specific site on a protein |
| Motor protein | protein that uses energy from ATP hydrolysis to propel itself along a protein filament or polymeric molecule |
| Polypeptide backbone | the chain of atoms containing repeating peptide bonds to which the amino acid side chains are attached; not to be confused with DNA/RNA backbone, which consists of repeated phosphodiester bonds between phosphates and pentoses |
| Domain | small discrete region of a protein or membrane |
| Protein family | a group of proteins in an organism with similar amino acid sequences, which usually perform related but distinct functions |
| Protein kinase | enzyme that adds a phosphate group to a protein |
| Protein machine | set of proteins that bind together and use concerted movements to carry out a sequence of reactions quickly and effectively |
| Protein phosphatase | enzyme that removes a phosphate group from a protein |
| Regulatory protein code | the set of covalent modifications that a protein has at any given time, which controls the behavior of the protein inside the cell |
| Secondary structure | formation of alpha helices and beta sheets |
| Side chain | the residue of an amino acid |
| Transition state | chemical structure that forms transiently in the course of a reaction and has the highest energy state of any reaction intermediate |
| X-ray crystallography | determining the structure of a protein by analyzing the diffraction pattern of a beam of X-rays passed through a crystal of the protein |
| Examples of general protein functions | catalysis, structural support, transport, movement, storage, signaling, reception, gene regulation, or highly specific purposes |
| Types of noncovalent bonds involved in protein folding | electrostatic attractions, hydrogen bonds, van der Waals attractions, hydrophobic interaction |
| Denaturation | disruption of the noncovalent interactions that help a protein keep its conformation, through heat, pH, or solvents |
| Renaturation | spontaneous refolding of a denatured protein into its original conformation |
| Molecular chaperones | molecules that assist protein folding and make it more efficient/reliable |
| Prion diseases | diseases caused by a "contagious" misfolded protein that converts normally-conformed proteins into the misfolded shape and form aggregates |
| Protein subunit | a complete protein joined to other complete proteins in a larger structure |
| Specificity | each protein can only bind to one or a few molecules due to the shape of active sites, which form more noncovalent bonds with ligands than with other molecules |
| Structure of antibodies | Y-shaped protein with two identical and highly mutable binding sites |
| Immunoglobulin | antibody |
| Protein phosphorylation | change in conformation triggered by the addition or removal of a phosphate group |
| Cell homogenate | slurry of cell contents ready for purification via chromatography |
| Chromatography | process that separates individual components of a complex mixture into different portions; used to purify proteins for study |
| Base pair | two complementary nucleotides connected by hydrogen bonds |
| Centromere | complex of DNA and proteins at the center of a chromosome that holds sister chromatids together and forms the kinetochore |
| Kinetochore | structure on a chromosome that captures microtubules extending from the mitotic spindle |
| Chromatin | complex of DNA, histones, and nonhistone proteins found in the nucleus of a eukaryotic cell |
| Chromatin-remodeling complex | enzyme that alters histone-DNA interactions, making nucleotide sequences more or less available for transcription |
| Double helix | structure of DNA that completes a full turn every 10 nucleotides, or 3.9 nm |
| Epigenetic inheritance | preservation of information superimposed on the information inherited on the DNA sequence itself |
| Euchromatin | loosely wound chromatin that can be easily transcribed |
| Gene | nucleotide sequence that codes for a protein or RNA molecule |
| Genome | totality of heritable information contained in a cell |
| Heterochromatin | tightly wound chromatin that cannot be transcribed |
| Histone | small protein with a strong positive charge on it that attracts and winds up DNA to form nucleosomes |
| Karyotype | mitotic chromosomes from an organism arranged by size, shape, and number |
| Nucleolus | highly active subregion of the nucleus where the genes for ribosomal RNA are transcribed and ribosomal subunits are assembled |
| Nucleosome | unit of chromatin formed of one histone and its associated DNA base pairs |
| Replication origin | DNA sequence rich in adenine-thymine pairs (and thus, fewer hydrogen bonds) where helicase binds and opens the DNA strand for replication |
| Telomere | repetitive DNA sequences at the ends of a chromosome that ensure full replication of the genome and prevent the end of the chromosome from being mistaken for broken DNA in need of repair |
| Transforming principle | the substance isolated by Fred Griffith in the 1920s, ultimately identified as DNA |
| Nucleic acid polarity | directionality of a nucleic acid due to the chemical difference between the groups attached to the 5' and 3' carbons in the pentose |
| Homologous chromosomes | two copies of each chromosome in organisms that reproduce sexually; each copy in a pair is donated by a different parent |
| Sex chromosomes | a pair of chromosomes that determine physical sex of an organism; the only chromosomes that can be nonhomologous |
| Chromosome numbers | can vary widely among closely related species |
| Nuclear pore | small opening in the wall of the nucleus which allows molecules in and out |
| Nuclear envelope | two concentric membranes that enclose the nucleus |
| Nuclear lamina | network of protein filaments that form a thin layer underlying the inner nuclear membrane |
| Rate of compaction in interphase DNA | 500x compaction |
| Rate of compaction in mitotic DNA | 10,000x compaction |
| Structure of histone | octameric core formed from two subunits each of four separate proteins; a ninth histone protein pulls nucleosomes together into the 30-nm fiber |
| 30-nm chromatin | secondary structure of chromatin, consisting of tightly packed nucleosomes |
| 300-nm fiber | tertiary structure of chromatin formed by loops of 30-nm fiber |
| Barr body | in human females, the spare X chromosome, which is condensed into heterochromatin early in development |
| DNA polymerase | enzyme that polymerizes DNA nucleotide triphosphates into a nucleic acid |
| DNA repair | enzymatic processes that correct harmful changes affecting the continuity or sequence of a DNA strand |
| DNA replication | the process by which a copy of a DNA molecule is made |
| Homologous recombination | genetic exchange between identical or very similar sequences of DNA during meiosis and DNA repair |
| Lagging strand | the DNA strand at a replication fork that is replicated discontinuously |
| Leading strand | the DNA strand at a replication fork that is replicated continuously |
| Direction of DNA polymerization | 5'-3' |
| Direction of DNA "reading" | 3'-5' |
| Mobile genetic element | short segment of DNA that can move, sometimes using an RNA intermediate, to another location in the genome; important source of genetic variation |
| Fully mobile genetic element | a virus |
| Mutation | alteration in the DNA sequence |
| Nonhomologous end-joining | mechanism for repairing double-strand DNA breaks in which the broken ends are joined without needing to be sequence-homologous |
| Okazaki fragment | discontinuously replicated DNA fragments that are later joined covalently by DNA ligase |
| Proofreading | enzymatic function of DNA polymerase that can correct errors in replication |
| Replication fork | point at which DNA replication is occurring |
| Retrotransposon | type of mobile genetic element that moves by being transcribed into RNA and then reverse transcribed elsewhere in the chromosomes |
| Retrovirus | virus that carries its genetic information as RNA, which it reverse transcribes into the host's DNA |
| Reverse transcriptase | enzyme that creates a double-stranded DNA copy of a single-stranded RNA molecule |
| Telomerase | enzyme that uses a short strand of RNA to add many repetitive sequences to the ends of chromosomes |
| Template | molecular structure that serves as a pattern for the production of other molecules |
| Transposon | mobile genetic element |
| Virus | particle consisting of a nucleic acid enclosed in a protein coat, capable of replicating within a host and spreading from cell to cell |
| Rate of mutations in un-proofread DNA | 1 every 10^7 base pairs |
| Rate of mutations in proofread DNA | 1 every 10^9 base pairs |
| Replication machine | protein complex that carries out DNA replication |
| Semiconservative | the style of DNA replication, where each old strand of DNA serves as the template for a new strand |
| Cesium chloride gradient | centrifugation method that permits separation of molecules by weight; Meselson and Stahl used it to establish that DNA replicates semiconservatively |
| Bidirectional DNA replication | simultaneous replication in both directions |
| Pyrophosphate | two phosphate groups joined together; one product of DNA polymerization |
| Primase | enzyme that adds RNA nucleotides to the DNA strand in order to allow discontinuous replication on the lagging strand |
| Repair polymerase | enzyme that replaces RNA primers with DNA during replication |
| Single-strand binding protein | protein that attaches to a newly opened DNA strand and prevents it from annealing to itself |
| Helicase | enzyme that breaks the hydrogen bonds between base pairs to allow replication |
| Sliding clamp | protein that prevents DNA polymerase from falling off the strand |
| Sickle-cell anemia | disease caused by a SNP in the beta-globin gene, which directs the ribosome to insert a valine instead of a glutamic acid at the sixth position and causing malformation of red blood cells |
| DNA mismatch repair protein | an enzyme that removes all the newly synthesized nucleotides between the error and the nearest nick in the DNA backbone, allowing the mistake to be repaired |
| Common types of DNA damage | depurination, deamination, thymidine dimerization |
| Depurination | DNA damage where a guanine loses its nitrogenous base, giving rise to a lesion in the strand |
| Deamination | DNA damage where a cytosine loses an amine group, becoming a uracil |
| Thymidine dimerization | DNA damage where ultraviolet photons provide sufficient activation energy to bond adjacent thymine bases |
| Branch point | during homologous recombination, the point at which two DNA strands cross and one strand is used as a template to elongate the other |
| Horizontal gene transfer | process by which bacteria pass homologous chromosomes to one another |
| Percentage of human DNA made up of mobile genetic elements | ~50% |
| Alternative splicing | method by which spliceosomes can create different combinations of exons from the same gene, creating protein isoforms |
| Aminoacyl-tRNA synthetase | enzyme that adds an amino acid to a tRNA molecule with the corresponding anticodon sequence |
| Anticodon | sequence of 3 nucleotides on a tRNA molecule that match up to the corresponding mRNA sequence in the ribosome |
| Codon | sequence of 3 nucleotides on an mRNA molecule that specify which amino acid should be polymerized onto the polypeptide chain |
| Exon | in eukaryotes, a stretch of mRNA that codes for an amino acid sequence |
| Gene expression | process by which a gene makes its effect on a cell or an organism, by directing the synthesis of a protein or RNA sequence with a characteristic activity |
| Genetic code | set of rules specifying the correspondence between nucleotide triplets and amino acids |
| General transcription factors | in eukaryotes, a group of proteins that assemble on the promoter sequence of a gene and load RNA polymerase at the correct position |
| Initiator tRNA | methionine-carrying tRNA that binds to the small subunit of the ribosome at the P-site before translation begins |
| Intron | noncoding region of a eukaryotic gene that is transcribed by RNA polymerase but later spliced out |
| Messenger RNA | RNA molecule that contains the genetic code for a protein |
| Promoter | DNA sequence upstream of a gene that marks the coding strand and where RNA polymerase attaches to the strand to transcribe |
| Protease | an enzyme that degrades other proteins |
| Proteasome | large protein complex in the cytosol responsible for degrading proteins that have been marked for destruction |
| Reading frame | set of successive triplets in which a string of nucleotides is translated into protein |
| Open reading frame | an RNA sequence in which the starting point of translation is unknown; can be one of three possibilities |
| Ribosomal RNA | specific RNA molecules that form part of the ribosome and participate in protein synthesis |
| Ribosome | large molecule composed of RNA and protein that synthesizes polypeptide chains from mRNA |
| Ribozyme | strand of RNA folded into a unique conformation that can catalyze reactions |
| RNA processing | modifications that a eukaryotic mRNA molecule undergoes during maturation; include capping, splicing, and polyadenylation |
| mRNA capping | processing step where a 7'-methylguanosine is added via a triphosphate bridge to the 5' end of a maturing mRNA strand |
| mRNA splicing | processing step where introns are removed from a maturing mRNA strand |
| mRNA polyadenylation | processing step where a sequence of 150-300 adenosines are added to the 3' end of a maturing mRNA strand, protecting it from degradation |
| Small nuclear RNA | RNA molecule approximately 200 nucleotides long that forms the core of the spliceosome |
| Spliceosome | large assembly of RNA and proteins that splices introns out of pre-mRNA strands |
| Transcription | process of creating an RNA molecule from DNA |
| Transfer RNA | RNA molecule that contains an anticodon and carries a specific amino acid; if it encounters a matching codon on an mRNA strand in a ribosome, it releases its amino acid for polymerization |
| Translation | process of creating a protein from an mRNA molecule |
| Translation initiation factor | protein that promotes proper association of mRNA with ribosomes, and is necessary for protein synthesis |
| Central dogma of molecular biology | DNA replication -> RNA transcription -> protein translation |
| Types of RNA produced in cells | messenger, transfer, small nuclear (snRNA), ribosomal, small interfering (siRNA) |
| Rate of errors in RNA polymerase transcription | 1 every 10^4 base pairs |
| Sigma factor | in prokaryotes, a protein attached to RNA polymerase that finds the promoter site, loads the RNA polymerase, and falls off during transcription, reattaching to another polymerase at the end of transcription |
| RNA polymerase I | in eukaryotes, transcribes most rRNA genes |
| RNA polymerase II | in eukaryotes, transcribes protein-coding genes, miRNA genes, plus genes for some small RNAs |
| RNA polymerase III | transcribes tRNA genes, one rRNA gene, and genes for many other small RNAs |
| TATA box | DNA sequence where TFIID transcription factor attaches, bending the DNA helix 80 degrees and serving as a landmark for other general transcription factors to attach |
| Typical location of TATA box | 25 nucleotides upstream of the transcription start site |
| TFIIH | general transcription factor that adds phosphate groups to RNA polymerase, helping transcription to commence |
| 3' untranslated region | in eukaryotic mRNA, the region that lies between the 3' end of the coding sequence and the poly-A tail and controls the lifetime of a mature mRNA strand |
| Wobble base-pairing | tRNA construction that allows for a mismatch in the third position of the anti-codon; cell requires fewer different tRNA molecules as a result |
| Ribosome binding sites | E-site, P-site, A-site |
| A-site | active site on the ribosome where aminoacyl-tRNAs bind |
| P-site | active site on the ribosome where the peptide bond between amino acids is catalyzed |
| E-site | active site on the ribosome that carries used tRNA molecules out of the structure |
| Antibiotic | compound that inhibits prokaryotic protein synthesis |
| Stop codon | one of three codes that signal to the ribosome to stop translation |
| Release factor | protein that attaches to a stop codon that reaches the A site, causing peptidyl transferase to add a water molecule instead of another amino acid to the polypeptide chain |
| Polyribosome | a large cytoplasmic assembly of multiple ribosomes attached to a single mRNA molecule |
| Ubiquitin | 75-amino-acid, 8.5 kilo-Dalton protein covalently attached to a protein, marking it for destruction |
| Activator | protein that binds to a specific regulatory region of DNA to permit transcription of an adjacent gene |
| Combinatorial control | the way groups of proteins work together to control the expression of a single gene |
| Differentiation | process by which a cell undergoes a progressive change to a more specific type |
| DNA methylation | type of epigenetic marker that discourages gene expression by attracting proteins that block transcription |
| MicroRNA | small, non-coding RNA strand that regulates gene expression by binding to a specific mRNA and controlling its stability and translation |
| Positive feedback loop | the end product of a reaction stimulates its own production |
| Post-transcriptional control | regulation of gene expression that occurs after the start of transcription |
| Regulatory DNA sequence | DNA sequence to which a transcription regulator binds to determine when, where, and in what quantity a gene will be transcribed to RNA |
| Reporter gene | a gene encoding a protein that is easy to monitor experimentally; introduced artificially between the promoter sequence and transcription start of the gene of interest |
| Repressor | protein that inhibits RNA transcription |
| Riboswitch | short sequences within some RNAs that change their conformation when specifically bound to certain chemicals, regulating transcription/translation |
| RNA interference (RNAi) | cellular mechanism activated by the presence of double-stranded RNA molecules that results in the destruction of RNA strands containing a similar nucleotide sequence |
| Experimental use of RNAi | gene silencing |
| Small interfering RNA | short lengths of RNA produced from double-stranded RNA during RNA interference |
| Transcription regulator | protein that binds specifically to a regulatory DNA sequence and helps control whether a gene is turned off or on |
| Housekeeping proteins | proteins common to all the cells of a multicellular organism |
| Number of genes expressed by a differentiated human cell | 5,000 - 15,000 genes |
| Steps at which gene expression can be controlled | transcription, RNA processing, RNA transport and localization, mRNA degradation, translation, protein activity |
| DNA-binding motifs | common domains of transcription regulators that bind to the DNA strand |
| Types of DNA-binding motifs | homeodomain, leucine zipper, zinc finger |
| Homeodomain | type of DNA-binding motif consisting of 3 alpha-helices in a row |
| Leucine zipper | type of DNA-binding motif that binds to DNA as a dimer |
| Zinc finger | type of DNA-binding motif composed of an alpha-helix and beta-sheet held together by a zinc molecule; often clusters together |
| Operon | a group of genes in a prokaryote that are expressed together |
| Constitutive gene expression | continuous transcription of an operon at a low level |
| Catabolite activator protein (CAP) | bacterial activator protein that relies on the presence of cyclic AMP to bind to DNA |
| Lac operon | operon that digests lactose; in the presence of lactose, the repressor is modified and falls off, and in the absence of glucose, CAP binds to the promoter and begins transcription of the operon |
| Histone deacetylase | enzyme attracted by eukaryotic repressor protein that removes acetyl groups from histones, discouraging gene transcription |
| Cell memory | remembering changes in gene expression triggered by a transient signal |
| Coordinating gene expression in eukaryotes | accomplished by using the same protein to regulate several different genes |
| RNA-induced silencing complex (RISC) | protein and RNA complex that seeks out and destroys RNA sequences matching the one contained in the RISC |
| Complementary DNA | DNA synthesized from a messenger RNA that assists in identifying genes; used to produce eukaryotic proteins in prokaryotes because prokaryotes can't splice out introns |
| Dideoxy DNA sequencing | sequencing a PCRed DNA fragment by adding it to four separate tubes, each containing DNA polymerase and a specific dideoxynucleotide, and subsequently running the products through polyacrylamide gel electrophoresis |
| DNA cloning | making many identical copies of a DNA molecule |
| DNA library | collection of cloned DNA molecules that represent either an entire genome, or cDNA copies of mRNA |
| DNA microarray | a glass side on which a large number of short DNA molecules have been immobilized, acting as probes for a large number of genes simultaneously |
| Gene knockout | inactivating a specific gene by one of several methods, such as introducing a deletion in its sequence |
| Gene replacement | replacement of a normal gene in an organism with one that has been mutated in vitro |
| Genotype | set of genes carried by an organism |
| Green fluorescent protein | jellyfish protein used as a marker for the movement of other proteins in living cells |
| Hybridization | technique for detecting specific DNA sequences |
| In situ hybridization | technique in which an RNA or DNA molecule is used to locate a gene or mRNA molecule in tissue |
| Phenotype | observable character of a cell/organism |
| Plasmid | small extragenomic DNA strand found in bacteria; commonly used to transform DNA sequences of interest into bacteria |
| Polymerase chain reaction | technique for amplifying specific DNA regions by multiple cycles of DNA synthesis, each followed by heat treatment to separate complementary DNA strands |
| Recombinant DNA | DNA molecule that is composed of DNA from multiple sources |
| Recombinant DNA technology | collection of techniques used to create recombinant DNA |
| Restriction enzyme | type of prokaryotic enzyme that cleaves DNA molecules at a specific recognition sequence |
| Site-directed mutagenesis | makes a mutation at a particular site in DNA |
| Transgenic organism | organism in which a gene has been artificially introduced |
| Southern blot | separate DNA by electrophoresis, denature DNA by drawing an alkali solution through the gel, transfer to a nitrocellulose sheet by blotting, sheet exposed to radioactive DNA probe, wash off non-hybridized DNA, visualize bands with autoradiography |
| Next-generation sequencing | DNA sequencing carried out using capillary electrophoresis and fluorescent dyes |
| Expression vector | vector containing transcription and translation sequences as well as gene of interest, ensuring high expression of the gene |
| Hybridization | joining of complementary DNA sequences; used frequently in molecular biology to probe for sequences of interest |
| Adaptation | adjustment of sensitivity of a cell or organism following repeated stimulation that can allow a response even when there is a high background level of stimulation |
| Adenylyl cyclase | enzyme that produces cyclic AMP |
| Calmodulin-dependent kinase | enzyme that phosphorylates target proteins in response to an increase in Ca2+ concentration in the cell |
| Calmodulin | small Ca2+-binding protein that modifies the activity of many target enzymes and membrane transport proteins in response to changes in Ca2+ concentration |
| Cell signaling | molecular mechanisms by which cells detect and respond to external stimuli and send messages to other cells |
| Cyclic AMP (cAMP) | nucleotide generated from ATP in response to hormonal stimulation of cell-surface receptors; acts as a signaling molecule by activating protein kinase A; activates the lac operon in E. coli in absence of glucose; degraded to AMP by a phosphodiesterase |
| Protein kinase A (PKA) | enzyme that responds to cAMP |
| Cytokine | local signaling molecule that acts on neighboring cells via cell-surface receptors |
| Diacylglycerol (DAG) | lipid produced by cleaving membrane inositol phospholipids in response to extracellular signals; serves as a membrane-located signaling molecule for protein kinase C |
| Enzyme-coupled receptor | transmembrane receptor protein that activates an intracellular enzyme in response to ligand binding to extracellular portion |
| Extracellular signal molecule | messenger compound that acts on a cell by binding to the extracellular portion of transmembrane receptors |
| G protein | one of many GTP-binding proteins composed of three different subunits that are important intermediaries in intracellular signaling pathways; usually activated by extracellular signaling |
| Heterotrimetric GTP-binding protein | signaling protein that binds GTP and is composed of three different subunits |
| G-protein-coupled receptor | sevenpass transmembrane protein that associates with a G-protein after activation |
| GTP-binding protein | allosteric protein whose conformation and activity are determined by association with GTP or GDP; includes G-proteins and Ras |
| Guanosine 5'-triphosphate | molecule involved in many cellular pathways, including RNA synthesis, energy-transfer reactions, microtubule assembly, protein synthesis, and cell signaling |
| Hormone | chemical substance produced by one set of cells in a multicellular organism and transported via body fluids to target tissues on which it exerts a specific effect |
| Inositol | six-carbon saccharide with six hydroxyl groups |
| Inositol phospholipid | lipid component of plasma membranes found in cytosolic half of bilayer, which contains phosphorylated inositol derivatives; distinguish different intracellular membranes and perform signal transduction in eukaryotes |
| Inositol 1,4,5-triphosphate (IP3) | intracellular signaling molecule produced during activation of the inositol phospholipid signaling pathway |
| Ion-channel-coupled receptor | transmembrane receptor protein or protein complex that forms a water-filled channel across the lipid bilayer, through which specific inorganic ions can diffuse down their electrochemical gradients |
| Intracellular signaling molecule | molecule that is part of the mechanism for transducing and transmitting signals inside a cell |
| Intracellular signaling pathway | set of proteins and small-molecule second messengers that interact with each other to relay a signal from the cell membrane to its final destination in the cytoplasm or nucleus |
| Local mediator | secreted signal molecule that acts at a short range on adjacent cells |
| Mitogen-activated protein (MAP) kinase | kinase that performs a crucial step in relaying signals from cell-surface receptors to the nucleus |
| MAP-kinase signaling module | three-kinase sequence that ends in activation of MAP kinase; also known as MAP kinase cascade |
| Molecular switch | protein or protein complex that operates in an intracellular signaling pathway and can reversibly switch between an active and inactive state |
| Monomeric GTPase | Single-subunit GTP-binding protein; proteins in this family are part of many different signaling pathways |
| Neurotransmitter | small signaling molecule secreted by a nerve cell at a chemical synapse to signal to the postsynaptic cell |
| Nitric oxide (NO) | small highly-diffusable molecule widely used as an intracellular signal |
| Nuclear receptor | receptor protein resent inside a eukaryotic cell that can bind to signal molecules that enter the cell and form a transcription-regulation complex |
| Phosphoinositide 3-kinase | enzyme that phosphorylates inositol phospholipids in the plasma membrane in response to signals received by a cell; the phosphorylated lipids become docking sites for intracellular signaling proteins |
| Phospholipase C | enzyme that performs a crucial step in inositol phospholipid signaling pathways |
| Protein kinase C | enzyme that responds to DAG and Ca2+ concentration |
| Ras | one of a large family of monomeric GTPases that help relay signals from cell-surface receptors to the nucleus; initiates MAPK cascade; named for the gene first identified in viruses that causes rat sarcomas |
| Receptor serine/threonine kinase | enzyme-coupled receptor with an extracellular signal-binding domain and an intracellular kinase domain that phosphorylates signaling proteins on serine or threonine |
| Receptor tyrosine kinase | enzyme-coupled receptor that phosphorylates signaling proteins on tyrosine in response to ligand binding to the extracellular domain |
| Second messenger | small molecule formed in or relesased into the cytosol in response to an extracellular signal that helps to relay the signal to the interior of the cell |
| Examples of second messengers | cAMP, IP3, Ca2+ |
| Serine/threonine kinase | enzyme that phosphorylates specific proteins on serines or threonines; includes protein kinases A and C, MAP kinase, and Ca2+/calmodulin-dependent kinases |
| Signal transduction | conversion of a signal from one form to another |
| Steroid hormone | lipophilic molecule related to cholesterol that acts as a hormone |
| Types of cell signaling | endocrine, paracrine, autocrine, neuronal, contact dependent |
| Endocrine signaling | hormones produced by specialized tissue travel through body fluids to target cells |
| Paracrine signaling | one cell releases local mediators, which are taken up by nearby cells |
| Autocrine signaling | signaling that occurs within the cell |
| Neuronal signaling | signals are transduced from an electrical impulse to the release of neurotransmitters across a small synapse, where they are again transduced to electricity by the target cell |
| Contact-dependent signaling | membrane-bound signal molecule in the signaling cell attaches to a receptor on the target cell |
| NO signaling chain | nitric oxide activates guanylyl cyclase, which forms cyclic GMP, a second messenger |
| Nitroglycerine | compound that is readily converted to NO in the body, causing relaxation of blood vessel walls |
| Functions of cell-signaling pathways | relay signals, amplify signal received, integrate signals from multiple pathways, distribute signals to multiple pathways |
| Three classes of cell-surface receptors | ion-channel-coupled, G-protein-coupled, enzyme-coupled |
| Pathophysiology of cholera | cholera toxin enters intestine epithelial cells and modifies Gs protein so that it cannot hydrolyze the bound GTP and stop signaling; signal to release Cl- and H2O into the gut becomes too strong, causing diarrhea and dehydration |
| Pathophysiology of pertussis | bacterium colonizes the lung and produces pertussis toxin, which binds to cAMP-inhibiting Gi protein and prevents it from activating; subsequent prolonged, inappropriate signal stimulates excessive coughing |
| Target proteins recognized by G-proteins | either membrane-bound enzymes or ion channels |
| Transduction of GPCR signaling | mainly into cAMP production via activation of adenylyl cyclase |
| Cell-signaling effect of caffeine | inhibits cAMP phosphodiesterase, prolonging and increasing signals modulated by cAMP |
| cAMP phosphodiesterase | enzyme that degrades cAMP to AMP, reducing the level of reaction along cAMP-modulated pathways |
| Cell-signaling effect of adrenaline | binds to adrenergic receptors (type of GPCR) and stimulates cAMP production |
| Inositol phospholipid pathway | causes Ca2+ release from endoplasmic reticulum, increasing concentration of ions within the cell |
| GPCR activation of adenylyl cyclase vs. phospholipase C | former triggers cAMP-mediated pathways; latter triggers inositol-phospholipid-mediated pathways |
| Structure of inositol phospholipid | consists of a diacylglycerol moiety and an IP3 moiety; split by phospholipase C |
| Photoreceptor signaling cascade | rhodopsin, a light-activated GPCR, activates the G-protein transducin; transducin alpha subunit induces closure of cation channels, changing voltage across the cell membrane and ultimately producing a nerve impulse |
| Role of enzyme-coupled receptors | respond to signals at very low concentrations (10^-11 to 10^-9 M); also can mediate direct, rapid reconfigurations of the cytoskeleton in response to signal proteins attached to the surface over which the cell is moving |
| Modulation of RTK pathways | different RTKs recruit different sets of intracellular signaling proteins |
| PI-3-kinase-Akt signaling pathway | RTK-activated pathway beginning with Akt (protein kinase B), which phosphorylates and inactivates apoptotic enzymes and indirectly activates Tor, a growth enzyme that promotes protein synthesis and inhibits protein degradation |
| Effect of rapamycin | inactivates Tor, part of the PI-3-kinase-Akt signaling pathway, preventing cell growth |
| Interferon | cytokine produced by infected cells that instruct other cells to produce proteins that make them more resistant to viral infection |
| Signal transducer and activator of transcription (STAT) | regulatory protein mediated by cytokines that stimulates gene transcription in the nucleus |
| Effect of prolactin on breast cells | binds to an enzyme-coupled receptor that activates a STAT involved in the transcription of milk protein genes |
| Notch pathway | contact-dependent signaling pathway that cleaves the receptor, allowing the cytosolic tail to travel to the nucleus and activate Notch-reponsive genes |
| Ethylene pathway in plants | dimeric ethylene receptors remain active in the absence of ethylene and inhibit transcription of ethylene-responsive genes; presence of ethylene disables the receptors, disinhibiting transcription |
| Differences between cell signaling in animals and plants | occur due to the unicellularity of the common ancestor of plants/animals; plants do not use RTKs, steroid-type nuclear receptors, or cAMP, and only a few GPCRs; animals use fewer enzyme-coupled receptors and structurally different S/T kinases |
| Estimated number of human genes that encode kinases | 400 (consider that eukaryotic genes can also produce protein isoforms!...) |
| Relative amount of DNA per cell | doubles between G1 and G2; can be used to determine how many cells in a culture are in which stage of the cell cycle |
| Drug that inhibits cells at G2-M transition | more cells in a culture will be found in G2 than G1 |
| Cyclin-dependent kinases (Cdk) | enzymes modified by the presence of the protein cyclin that drive cell cycle processes |
| M-cyclin | protein that activates M-Cdk when it passes a concentration threshold |
| Cyclin | proteins with no enzymatic activity whose concentration in a cell varies through the cell cycle; modify cyclin-dependent kinases (Cdk) to activate or deactivate them |
| Anaphase-promoting complex (APC) | protein that ubiquitylates cyclins to mark them for proteolysis |
| Wee1 | kinase that phosphorylates cyclin-Cdk complexes to prevent them from activating |
| Cdc25 | phosphatase that dephosphorylates cyclin-Cdk complex and activates it |
| P21 | inhibitory protein that attaches to active cyclin-Cdk complexes and prevent them from acting |
| G1 phase | Cdks stably inactivated; mitogens promote production of cyclins; if there is DNA damage, G1 progression can be temporarily halted |
| G0 phase | specialized nondividing state that cells can enter if there are insufficient resources in the environment, or if it stops receiving mitogenic signals |
| G1 checkpoint | cell can commit to S phase, pause, withdraw to G0, or withdraw permanently and terminally differentiate |
| Terminal differentiation | cell cycle stage that permanently removes the cell from division cycle, while differentiating it to express highly-specialized functions |
| Disease process of retinoblastoma-protein-based tumors | RTK inappropriately activates Ras, initiating the MAPK cascade; activated G-Cdk and G1/S-Cdk phosphorylate Rb protein; Rb-inhibited transcription regulator begins to cause cell proliferation |
| P53 | tumor suppressor protein that is mutated in 50% of cancers; induces P21 expression, inhibiting G1/S-Cdk and S-Cdk |
| S-Cdk | protein complex that interacts with proteins on DNA ORIs, triggering synthesis |
| M-Cdk mitosis involvement | produces positive feedback loop where more and more M-Cdk is produced |
| Cohesin | holds sister chromatids together in early mitosis |
| Condensin | protein that enables high compactification of DNA during mitosis |
| Role of apoptosis in digit formation | cells between digits die, leaving gaps |
| Only cells that do not undergo apoptosis | cancer cells |
| Necrosis | unprogrammed cell death that spreads cell contents into the interstitial environment |
| Apoptosis | benign programmed cell death that contains cell contents as they are lysed; dead cell subsequently engulfed by a macrophage |
| Caspase | suicide protease, normally paired, activated through cleavage by procaspase |
| Amplifying caspase cascade | positive feedback loop that creates many copies of active executioner caspases, which cleave the nuclear lamina and degrade cytosolic proteins |
| Bax/Bak | death-promoting proteins that move cytochrome C molecules from the mitochondrion into the cytoplasm, where they activate adaptor proteins and assemble into large apoptosomes, recruiting procaspase-9 and beginning the caspase cascade |
| Bcl2 family | family of proteins which regulate Bax/Bak/Bad activity, promoting or preventing apoptosis |
| Anaphase | third stage of mitosis, when duplicated chromatids separate and move apart; in anaphase A, chromosomes move toward spindle poles; in anaphase B, spindle poles move apart |
| Aster | star-shaped system of microtubules emanating from a centrosome/pole of mitotic spindle |
| Bi-orientation | alignment of sister chromatids on the mitotic spindle such that each chromatid is attached to opposite mitotic spindles |
| Cell cycle control system | network of regulatory proteins that governs progression of a eukaryotic cell through the cell cycle |
| Centrosome | centrally located organelle of animal cells that is the primary microtubule-organizing center and separates to form the two spindle poles during mitosis; in most animal cells it contains a pair of centrioles |
| Centrosome cycle | duplication of the centrosome during interphase, and separation of the two new centrosomes at the beginning of mitosis |
| Growth factor | extracellular polypeptide signaling molecule that stimulates a cell to grow or proliferate |
| Metaphase | stage of mitosis at which chromosomes are firmly attached to the mitotic spindle at its equator but have not yet segregated |
| Mitogen | extracellular signal molecule that stimulates cell proliferation |
| Mitotic spindle | array of microtubules and associated molecules that forms between the opposite poles of a eukaryotic cell during mitosis; during the separation of the duplicated chromosomes, the spindle serves to move the two chromosome sets apart |
| Origin recognition complex (ORC) | large protein complex that is bound to the DNA at origins of replication in eukaryotic chromosomes throughout the cell cycle |
| Phragmoplast | structure made of microtubules and membrane vesicles that fors in the equatorial region of a dividing plant cell and from which the membrane that divides the daughter cells will be made |
| Spindle pole | one of two centrosomes in a cell undergoing mitosis; microtubules radiating from the spindle poles become the mitotic spindle |
| Survival factor | extracellular signaling molecule that prevents apoptosis |
| Telophase | stage of mitosis when separated chromosomes decondense and become enclosed by nuclear envelopes |
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