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Chemotrophs

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use chemical substances as source of energy

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phototrophs

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use light as a source of energy

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autotrophs

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use CO2 as sole source of carbon

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heterotrophs

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use organic compounds as source of carbon

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organotrophs

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use organic compounds as source of carbons

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lithotrophs

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use inorganic compounds as source of electrons

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bacteria

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play critical roles in the nitrogen cycle

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nitrogen fixation

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conversion of N2 from the air into NH3

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ATP

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storage molecule for chemical energy in all cells

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catabolism

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biodegradation

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anabolism

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biosynthesis

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The energy produced in ________ provides the energy needed for ________.

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catabolism, anabolism

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ATP is hydrolyzed to

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ADP + Pi + energy in a reversible reaction

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Endergonic reactions

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would not occur in living cells, but can be effectively promoted by coupling them to ATP hydrolysis

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oxidation

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the loss of electrions

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reduction

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gain of electrons

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redox reactions

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oxidation-reduction reactions in which electrons are transferred from one substance (that becomes oxidized) to another substance that be comes reduced

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biological redox reactions

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two electrons and two hydrogen ions are transferred simultaneously

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Electron transport chains

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proteins that are imbedded in membranes that transfer electrons and hydrogen ions in such a way that a pH gradient is generated across the membrane.

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chemiosmosis

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This force drives the synthesis of ATP catalyzed by the enzyme ATP synthase when hydrogen ions pass through the the enzyme

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enzymes

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biological catalysts; most are proteins

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catalytic RNAs

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robozymes

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active site of the enzyme

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the place on it where the substrate binds

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active site of the enzyme

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the place on it where the substrate binds

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competitive inhibitors

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compounds that compete for the binding of substrate to the enzyme

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allosteric site on an enzyme

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another site to which a noncompetitive inhibitor or activator can bind thereby affecting the activity of the enzyme

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feedback inhibition

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in some anabolic (biosynthetic) pathways the final product of the pathway acts as a noncompetitive inhibitor of the first enzyme in the pathway

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enzymes

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lower the activation energy needed for catalysis

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the activity of an enzyme is influenced by

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influenced by pH, temperature and the concentration of substrate

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glycolysis

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the cleavage of glucose into two three-carbon compounds

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the Kreb's (TCA) cycle

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converts acetyl-CoA into 2 CO2

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substrate level phoshorylation

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results in 2ATP/glucose in glycolysis and 2GTP=2ATP in the Kreb's cycle

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oxidative phosphorylation

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converts NADH and FADH2 into ATP by chemiosmosis

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the maximum possible energy yield

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for one molecule of glucose in aerobic respiration is 38ATP/glucose, but the actual yield is usually 30-32 ATP/glucose

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respiration

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a series of redox reactions in which an inorganic substance is the final electron acceptor. In aerobic respiration that substance is O2

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fermentation

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a series of redox reactions in which an organic substance is the the final electron acceptor, usually a small organic acid or alcohol. A number of fermentative microbes are commerically important such as bakers' and brewers; yeast (S. cerevisiae) the yield of ATP from fermentation is 2ATP/glucose

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lipids and proteins

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can be catabolized to yield energy

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metabolism

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extensively integrated so that the same or similar pathways can be used for production of energy or production of carbon chains for biosynthesis

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photosynthesis

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results in carbon fixation powered by ATP produced from the absorption of light by chlorophylls organized into photosystems. These processes occur in chloroplasts in eukaryotes and in the plasma membranes of prokaryotes

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Photosystem I

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has cyclic electron flow and doesn't produce oxygen

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Photosystem II

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has noncyclic electron flow and does produce oxygen.

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carbon fixation

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CO2 added to carbohydrate

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_________ are __________ into polymers in anabolism of macromolecules

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monomers are polymerized. these requireenergy. most of the ATP used by cells is used in the synthesis of proteins

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amino acids form

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proteins

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nucleotides form

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nucleic acids

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monosaccharides form

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polysaccharides

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DNA

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the genetic material in all cells and many viruses

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Griffith's transformation

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this experiment was very strong evidence that DNA is the genetic material

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vertical

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transmission of DNA that occurs in cell division

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horizontal

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transmission of DNA occurs within a generation

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duplex molecule

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consistin of two strands (polymers of nucleotides attached by phosphodiester bonds. Has a 5'-->3' polarity and is antiparallel with respect to the polarity of the two strands

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the four bases in DNA

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ACGT and form base pairs AT and GC

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where sequence-specific DNA binding proteins bind

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the major groove of the double helix of duplex DNA

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DNA replication

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involves separation of the two strands of parental DNA and their copying as templates resulting in the synthesis of two new strands of daughter DNA

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polymerase

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the main enzyme in DNA replication

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primase and ligase

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important enzymes in DNA replication

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discontinuous, continuous

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DNA synthesis is ____ on the lagging strand and _____ on the leading strand

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one, many

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there is ____ origin on circular DNAS and there are ____ on large linear chromosomal DNAs

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Nucleic acid synthesis

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proceeds in the 5'-->3' direction

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telomeres

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repeated DNAs on both ends of eukaryotic chromosomes. They are generated by the action of telomerase, an enzyme that copies RNA in making DNA

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transcription

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the synthesis of RNA complementary to the template strand of DNA in the gene

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RNA polymerase

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the enzyme that catalyzes the polymerization of ribonucleotides into RNA. it binds to a sequence of DNA called the promoter. There is one RNA polymerase in E. coli that synthesizes mRNA, rRNA and tRNA. In eukaryotes there is a separate RNA polymerase for each of these

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polycistronic mRNAs

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In bacteria, related genes are clustered together and transcribed into _________ that are then translated into several proteins

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monocistronic RNAs

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In eukaryotes genes are transcribed individually into ______ that are translated into one protein

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exons

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Eukaryotic genes have coding sequences

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introns

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non coding sequences in eukaryotic genes

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heterogeneous nuclear RNA (hnRNA)

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the first product of transcription in eukaryotes that must be spliced to remove introns

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sliceosomes

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complexes of small nuclear RNAs and proteins that perform the splicing

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genetic code

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a triplet code that is nearly universal in biology. three nucleotides in mRNA encode one amino acid in the protein product of the gene. There are 20 common amino acids in proteins and 61 codons

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degenerate

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the genetic code is said to be _______, more than one codon per amino acid

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AUG

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the start codon

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UAA UAG and UGA

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stop codons

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transfer RNAS

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have an anticodon that matches the sequence in the codon

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aminoacyl-tRNA sythetases

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amino acids are attached to tRNAS by this (requires ATP)

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peptidyl transferase

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activity in protein synthesis is 23S rRNA in bacteria 28S rRNA in eukaryotes.

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catalytic RNAs

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catalyze the formation of peptide bonds between amino acids

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protein snthesis

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occurs on the ribosome 70S in bacteria 80S in eukaryotes

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protein initiation factors, elongation factors as well as GTP

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required for protein synthesis

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protein release factors

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bind to stop codons and mediate termination pfprotein synthesis

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protein folding

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may occur spontaneously or require specific proteins (chaperones)

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gene expression

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regulated at the level of transcription by proteins binding to specific sequences of DNA

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regulation

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occurs at the level of translation as well, epsecially in eukaryotes. Also, mRNA splicing can be regulated

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constitutive genes

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always expressed

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inducible genes

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function in catabolism are usually not expressed, but they can be turned on

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repressible genes

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function in anabolism are usualy expressed but they can be turned of

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the lac operon

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regulated by a repressor that binds to an operated. When the repressor is bound transcription is blocked

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lactose

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inducer, when it is present, it binds to the repressor and causes it to change shape so that it can't bind to DNA; transcritpion then occurs

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trp operon

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regulated by a repressor that binds to an operator

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tryptophan

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corepressor, when it is present, it binds to the repressor and activates it so that it binds to the operateor sequence of DNA

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negative regulation

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inhibition of transcription

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positive regulation

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stimulation of transcription

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lac operon

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exhibits both negative and positive regulation; negative by the repressor and positive by the CAP-cAMP

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adenlyl cyclase

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when glucose levels are low _______ converts ATP in to cyclic AMP (cAMP) + PPI. cAMP binds to the catabolite activator protein (CAP) to form a functional complex that binds to DNA and stimulates the binding of RNA polymerase to its promoter

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siRNAs (small nuclear RNAs)

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bind to mRNAs and cause them to be degraded by a nuclease (dicer) this eliminates the mRNAs from being translated into proteins

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novel sequences

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DNA sequences can recombine to yield these

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mutation

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achange int he sequence of nucleotides in DNA

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mutagens

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chemicals that cause mutations

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UV or x-rays

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electromagnetic radiation

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point mutations

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changes in on base pair in the DNA

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missense mutations

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change a codon into a codon for another amino acid

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nonsense mutations

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change a codon for an amino acid into a stop codon

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silent mutations

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change a codon for an amino acid into another codon for teh same amino acid

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thymine-thymine dimers

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occur when DNA obseorbs UV light

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repair enzymes

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correct damage to DNA

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excision repair

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for any DNA squence

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mismatch repair

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for newly replicated DNA only

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excision repair and mismatch repair

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involve removal of damaged DNA segment, polymerization of nucleotides to fill in the gap and DNA ligation

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carcinogens

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chemicals that cause cancer. They can be assayed as mutagens in the AMes test that measures the frequency of reversion of a his- mutation to the wild type his+

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auxotroph

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nutritional mutant

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homologous recombination

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occurs between relatied DNA sequences

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site-specific recombination

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occurs at specific sites

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plasmids

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small circular DNAs with their own origin of DNA replication. They replicate independently of the bacterial chromosomal DNA. The F factor is a plasmid that is required for conjugation. Donor E. coli are F+ and recipients are F-

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F Factor

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this itself is transfered. it can integrate into the bacterial chromosomal resulting in a high frequency of recombination cell. the high frequency recombination cell can cross with an F- cell; chromosomal genes are transferred

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transposon

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a mobile sequence of DNA some transposons harbor genes for drug resistance

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transformation

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the uptake and integration of DNA this occurs at high frequencies in bacteria

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transduction

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the uptake and incorporation of DNA mediated by a virus

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generalized transduction

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the encapsidation of a piece of bacterial DNA into a virus particle

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recombinant DNA

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DNA from two sources that is spliced together

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restriction enzymes

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cut DNA at specific sequences (palindromes) many different restriction enzymes have been isolated from different microbes

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vector

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a sequence of DNA that can be used for the formation of recombinant DNA.

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cloning vectors

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for production of DNA inserts

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expression vectors

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production of the protein product of the gene

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complementary DNA (cDNA)

answer

is produced from mRNA by reverse transcriptase

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selectable marker

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a gene for resistance to an antibiotic; such a gene can be used to ensure that transformed bacteria contain recombinant DNA desire

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libraries

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series of cloned DNAs

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DNA fragments

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can be separated by size by agarose gel electrophoresis

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Southern blot

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combines the separation of DNa by size with the detection of specific DNA sequences by hybridization

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hybridization

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allowing mixed duplexes to form between a test DNA or probe and the DNA being studied

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polymerase chain reaction

answer

a way to amplify DNA. it uses oligonucleotide primers and Taq DNA polymerase (thermostable) in a thermocycler to produce many copies of DNA in a test tube

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Sanger method

answer

DNA sequence method uses dideoxynucleotides as chain terminators. The results are analyzed by polyacrylamide gell electrophoresis. This process has ben automated. Newer sequenciing thenologies are much more powerful. Tens of billions of nucleotides of DNA sequences are availableon public data bases

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genome

answer

consists of all genes in an organism

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microarrays

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the expression of many genes can be analyzed simultaneously by using this

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proteome

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represents all proteins in an organism. They can be anaylzed using two-dimensional gell electrophoresis

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