Three components of nucleic acid: phosphate group bonded to sugar, 5 carbon sugar bonded to phos. and nitro base, nitrogenous base; they always contain a carb. Nonpolar covalent : a chemical bond from sharing electrons between two elements with similar electronegativity. Proteins: polymers composed of amino acids. Carboxyl Group: always acidic. RNA: monomers made up of nucleotides, in translation it reads 5’­3’. Allosteric Regulators: change the shape of the enzyme. Gene expression: regulated through chromatin modification, during RNA splicing and processing, during and after translation, first step in the control is chromatin remodeling, different regulatory proteins. Lac Operon of E.coli: a segment of DNA, a promoter, an operator, and three structural genes. Leading Strand: synthesized continuously 5’­3’, only needs one primer, made continuously, daughter strand elongates toward replication fork. Lagging Strand: synthesized discontinuously 5’­3’, multiple primers needed, made in segments, daughter strand elongates away from the replication fork. Deoxyribonucleotide triphosphate substrate: provides energy for polymerization reactions in DNA synthesis. Segregation: separation of the alleles of a gene into different gametes. Photosynthesis and Respiration: in eukaryotes, both processes reside in specialized organelles, ATP synthesis in both processes relies on the chemiosmotic mechanism, both use electron transport. Processes before transcripts can be translated: splicing, capping, addition of a poly A tail. Promoter: region of the gene(nontranscribed) that binds RNA polymerase, in eukaryotes it is found upstream of the gene and contains the TATA box. Control: test for factors other than the one being investigated. Prokaryotic cell domain: bacteria and archaea. Ionic bonds: sodium chloride is held by this. Polar covalent
: water is held together by this bond. Alternative splicing: helps explain the small number of genes in the human genome, the differences in complexity among organisms, why there are more mRNA’s than human genes, the great variety in proteins. Sexual reproduction: segregation of homologous chromosomes during gamete formation, fusion of haploid cells to form a diploid zygote, reduction in chromosome number during meiosis, production of genetically distinct gametes during meiosis. Chlorophyll: certain wavelengths of light raise it to an excited state, in its excited state it gives off electrons, structure allows it to attach to thylakoid membranes, it can transfer absorbed energy to another molecule. Homologous chromosome pairs: usually contain slightly different versions of the same genetic information, they separate from each other during meiosis I, they synapse during meiosis I, each contains two sister chromatids at the beginning of meiosis I. Sister Chromatids: arise by replication during S phase, separate from each other during each mitotic anaphase, usually contain identical versions of the same genetic information, joined during prophase I and metaphase I at their centromere. Eukaryotic Chromosome: telomere sequences are found at the ends of chromosomes, remodeling of chromatin structure can alter gene expression, a chromosome has a single DNA molecule, short tandem repeats are an example of noncoding DNA. Signal Transduction:1. A signal molecule binds to a receptor 2. A conformational change in the signal­receptor complex activates an enzyme 3. Protein kinases are activated 4. Target proteins are phosphorylated. Cofactor example: the nonprotein heme group in a hemoglobin molecule. Central Dogma: DNA is transcribed into RNA; RNA is translated into protein. When two nucleotides polymerize, the hydroxyl group attached to the 3’ carbon attacks the phosphate group to the 5’ carbon in a condensation reaction. RNA,DNA, and protein structure: RNA is intermediate between the complexity of proteins and the simplicity of DNA. Nucelotide: visible structures are the sugar and the base. Gel electrophoresis: technique to separate nucleotides by size using an electrical current, DNA moves toward the positive electrode because it has a negative charge. Genetic code: information is propagates from RNA to protein and then catalyzed by ribosomes., the redundancy is the consequences for having more codons than amino acids. Ribozymes: catalyze the chemistry of translation. Protein Enzymes: catalyzes the chemistry of transcription, this is evidence RNA may be first molecule of life. Frameshift Mutation: results in an early stop codon. Silent: does not change the amino acid specified by a codon. Monosaccharides: number of carbon atoms can vary. A and B forms of glucose: different ring structure in the location of a hydroxyl group. Enzymes that readily break starch apart cannot hydrolyze the glycosidic linkages in cellulose because the geometry of the bonds is different and the shapes of the enzyme active sites are highly specific. Peptidoglycan: forms sheets that stiffen the cell walls of bacteria because individual strands are joined by peptide bonds­a type of covalent bond. Carbon­Hydrogen: most free energy per gram because electronegativity is similar atoms and share their electrons nearly equally­no polarity. Carbohydrates: attached to proteins known as glycoproteins and display information in order to bond substrates and catalyze reactions. Phospholipids and Triglyceride: both have a glycerol backbone. Osmosis: water moves from areas of low solute concentration to areas of high solute concentration. Phospholipid: bilayers are more permeable as well as more fluid when they consist of shorter unsaturated hydrocarbon tails. Cell crawling is due to actin and myosin. Cross­talk: occurs when signaling pathways interact, the more steps in the pathways in more opportunity for cross­talk. Collagen: most abundant protein in the extracellular matrix of an animal cell. Plasmodesmata: allow passage of proteins and small molecules between adjacent cells. Nondisjunction: produce aneuploids and trisomy 21 in meiosis. Karyotyping: enable you to detect aneuploidy. Complementary: relationship between a newly synthesized RNA molecule and the DNA template strand. Population thinking: variation among individuals in a species is real and important. Vestigial Traits: similar to functional traits in closely related species. Natural Selection: results in adaptation.Disruptive selection: increases genetic variation, most likely to play a role in speciation. Directional Selection: drives the average of the population in one direction. Stabilizing Selection: causes no change in the average of the population; extreme phenotypes become less common, reduces variation in population. Genetic Drift: produces changes in allele frequencies that are not adaptive. Founder Effect: change in allele frequencies that occurs when a new population is established. Gene Flow: when increased between two populations the outcome is decreased genetic difference between the two populations. Mutation: increases genetic variation. Biological: not applicable for extinct species, used by scientists in classification. Morphological: relies on similarities in structures, used by scientists in classification, accommodates asexual reproduction, species criteria can be subjective. Phylogenetic: based on evolutionary history, accommodates asexual reproduction, species acceptance criteria can be subjective. Paleozoic: reptiles first appeared during this era, amphibians were the dominant vertebrate life form, seed plants first appeared, most modern animal phyla evolved, bony fish. Cenozoic: era we live in. Mesozoic: era dinosaurs went extinct, flowering plants first appeared, began 251 mil years ago. Precambrian: life arose, began 4600 mil years ago, first prokaryotic cells, animals first appeared. Histone Deacetylases: negative control, they make DNA less accessible for transcription. Epigenetic Inheritance: mechanism that does not depend on differences in DNA sequence. Histones: positively charged. Activators: type of transcription factor that bind to DNA enhancer regions, not composed of DNA sequences. Enhancer: located thousands of nucelotides away from the transcription start site of a gene. Operons: lack enhancers and introns, arranged sequentially after the promoter, a set of bacterial genes that are regulated together and transcribed into a single RNA. Basal Transcription factor: example is the TATA­binding protein. Regulatory Transcription Factors: influence the assembly of the basal transcription complex. Proteasomes: enzyme complex that breaks down proteins. Spliceosome: RNA processing, catalyzes removal of introns from primary RNA transcripts. Protein­phosphorylating: role in the regulation of gene expression involves protein activation. Proto­oncogenes: promote progression through the cell cycle when conditions are right for growth. Lac operon: occurs when lactose levels are high and glucose levels are low. Genes of an operon: stretch of DNA consisting of an operon, promoter, and genes for a regulatory set of proteins, usually makeup an entire metabolic pathway. Repressor: codes for protein, such as a repressor that controls the transcription of another gene or group of genes. Operator: regulatory proteins bind to this to control expression of the operon. Inducer: protein that inhibits gene transcription, in prokaryotes, this protein binds to the DNA in or near the promoter. Regulatory Gene: specific small molecule that binds to a bacterial regulatory protein and changes its shape so it cannot bind to an operator, thus switching an operon on. Trp Operon: regulated through negative control only, when tryptophan is present, the operon genes are not transcribed. Lac Operon: regulated through both positive and negative control. Negative control: when lactose is absent the repressor protein is active, and transcription is turned off, if present then repressor protein is inactivated and transcription is turned on. Positive Control: when glucose is absent another regulatory protein (CAP) binds to the promoter of the lac operon increasing the rate of transcription if lactose is present. RNA Polymerase: binds to promoters in bacteria and bacteria and transcribes the coding regions of the genes. LacZ gene: encodes an enzyme, b­galactosidase, which cleaves lactose into glucose and galactase. Adenylyl cyclase: converts ATP to cAMP. CAP protein: works in the positive regulation of the lac operon, controlled by cAMP at the post­translational level. Okazaki Fragments: short sections of DNA that are synthesized on the lagging strand of the replicating DNA. Replication Fork: during DNA replication, an open section of DNA in which a DNA polymerase can replicate DNA. Nucleotide excision repair: recognized and repairs thymine dimers in DNA., the system detects mutations because they produe an irregularity in the DNA molecule. Polyribosomes: increase the rate of polypeptide synthesis from a single mRNA. The anticodon of a properly formed aminoacyl tRNA ensures that the correct amino acid is added with reading of a specific codon during translation. tRNA: contains an anticodon, has amino acids covalently attached., first plays a role in translation, move through in A­P­E sequence, prior to the formation of a peptide bond is occupies the P site. mRNA: specifies the amino acid sequence for a protein, contains exons, first plays a role in transcription/RNA processing, is translated to make a protein. rRNA: a component of ribosomes, is the most abundant form of RNA, first plays a role in translation. Phosphorylation: example of a post­translational modification. The last step of the initiation phase of translation is the large ribosomal subunit joins the complex. A­site: new aminoacyl tRNA’s enter the ribosome during elongation. Translocation: the ribosome slides one codon down the mRNA. The bacterial ribosome knows where to start translation because the small ribosomal subunit binds to a sequence in the mRNA just upstream of the start codon. Initiation of prokaryotic translation: binding of the mRNA with small ribosomal subunit, recognition of initiation codon, complementary base pairing between initiator codon and anticodon of initiator tRNA, attachment of the large subunit, base pairing of the mRNA codon following the initiator codon with its complementary tRNA. Shine­Dalgarno sequence: ribosome­binding site of prokaryotics. Cadherins: mediate intracellular binding interactions. Wobble Hypothesis: more than one codon specifies for an amino acid and they all have the same nucleotides in the first two positions. Desmosomes: bind animal cells together, protect against pulling forces, (animal). Gap (Communicating) Junctions: aid in the coordination of the activities of adjacent animal cells. Tight junctions: membrane proteins that create a watertight seal between cells,(animal). Plasmodesmata: small channels between cells that are otherwise surrounded by walls; enable movement of water and solutes between cells, (plant). Cellulose: a polysaccharide that is used to synthesize cell walls, which protect cells and help maintain their shape, (plants). Collagen: long fibers of protein found in the extracellular matrix that provide structural support for cells, (animal). G protein coupled receptors: interact directly with G proteins. Receptor tyrosine kinases: catalyze the transfer of a phosphate group to the receptor, binding of the signaling molecule forms a dimer. Both receptors: binding site for signaling molecule is located on the extracellular site of the cell, receptor is located in the plasma membrane. Signal Molecule(ligand): signal transduction pathway is initiated when it binds to a receptor. Paralog: homologous genes in the same genome. Homolog: of common ancestry. Ortholog: homologous genes in different genomes. Syntelog: homologous genes derived from an ancestral genomic region. Homeolog: duplicated chromosomes within the same genome. Recombinant: possessing a new combination of alleles. Ligase: enzyme that joins pieces of DNA by catalyzing formation of a phosphodiester bond between the pieces. Hox genes: A class of homeotic genes found in several animal phyla, including vertebrates, that are expressed in a distinctive pattern along the anterior­posterior axis in early embryos and control formation of segment­specific structures. Exon: region of gene that is translated into a peptide or protein. Intron: region that is transcribed into RNA but is later removed, so it is not translated into a peptide. Reverse Transcriptase: an enzyme of RNA viruses that can synthesized double stranded DNA from a single stranded RNA template. Missense: mutation causing change in the amino acid sequence of a protein.