Chapters 8 and 9

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genome

the sum total of the genetic material of a cell; most consists of chromosomes but genetic material can appear in non chromosomal sites too

active site/catalytic site

specificity is a function of the enzymes; the specific region or "pocket" where the substrate binds

aerobic respiration

used by bacteria, fungi, protozoa and animals; a series of reactions that converts glucose to CO2; relies on oxygen as the final acceptor for electrons and hydrogens; produces a relatively large amount of ATP; a series of 3 coupled pathways (glycolysis (breaking of glucose); Krebs cycle or citric acid cycle and electron transport chain)

anabolism

enzyme-regulated chemical reactions that require energy - simpler substances are combined to form more complex organic molecules

anaerobic respiration

involves glycolysis, Krebs cycle and electron transport chain accept uses inorganic molecules other than oxygen function as the final electron acceptor

anticodon

a 3 nucleotide sequence that designates the specificity of the tRNA and complements the mRNA codon

Be able to provide the tRNA anticodons, given a segment of mRNA codons

phosphate, ribose and uricil; DNA = a-t and c-g RNA = a-u and c-g (aaa would be paired with uuu and ccc would be paired with ggg acu would be paired with cag

Be able to transcribe a segment of mRNA from a segment of DNA.

phosphate, ribose and uricil; DNA = a-t and c-g RNA = a-u and c-g (aaa would be paired with uuu and ccc would be paired with ggg acu would be paired with cag

catabolism

enzyme-regulated chemical reactions that release energy - the breakdown of complex organic molecules into simpler substances

catalyst

chemicals that increase the rate of a chemical reaction without becoming part of the products or being consumed in the reaction

chaperone proteins

as the chain grows it folds, with the help of this, into its unique conformation of a functional protein molecule

chromosomes

large complexes of DNA and proteins; a single circular chromosome in bacteria; multiple linear chromosomes in eucaryotes, located in the nucleus

codon

triplet of nucleotides in an mRNA molecule that is the complement to the sequence of 3 nucleotides in DNA

coenzyme

organic molecules, derivatives of vitamins - assist the enzyme by accepting atoms removed from the substrate or donating atoms required by the substrate

cofactor

active enzymes - help bring the active site and substrate close together

competence

the recipient cell is in a physiological state to take up the donor DNA - results from alterations in the cell wall that make it permeable to large DNA molecules

competitive inhibitors

complete with the normal substrate for the active site of the enzyme - their shape and size similar to normal substrate - mimics the substrate

complimentary base pairs

A = T and C = G; joined by hydrogen bonds

condensation reaction

(aka dehydration synthesis reactions) are used, which require ATP and release water

conjugation

§requires the attachment of 2 related species and the formation of a bridge that can transport DNA

constitutive enzyme

-always present in relatively constant amounts regardless of the amount of substrate - enzymes involved in utilizing glucose are examples

conjugated enzyme/holoenzyme

contain protein and non-protein molecules, made up of apoenzyme (protein portion), one or more cofactors (coenzymes and metallic cofactors)

deoxyribose sugar bonds

one of the bonds is to the 5' carbon on deoxyribose, the other bond is to the 3' carbon; this specifies the order and direction of each strand

DNA replication

one "parental" double stranded DNA molecule is converted to 2 identical "daughter" molecules

endergenic reaction

cellular reactions that are driven forward with the addition of energy

endoenzyme

-retained intra-cellularly and function there - enzymes of the metabolic pathway

energy

the capaicty to do work or to cause change

energy of activation/activation energy

the amount of energy needed to initiate a reaction

enzyme

biological catalyst

enzyme induction

enzymes appear only when suitable substrates are present; if the bacterium is subsequently inoculated into a medium containing sucrose, it will cease producing lactase and strat producing sucrase

enzyme repression

a means to stop further enzme synthesis somewhere along its pathway; as the level of the end product from a given enzymatic reaction has built to excess, the genetic apparatus responsible for replacing these enzymes is automatically repressed

exergenic reaction

cellular reactions that release energy - energy of this tpe is considered free - it is available for doing cellular work

exoenzyme

-after synthesis in the cell, these enzymes are transported extra-cellularly - break down large food molecules or harmful chemicals

exons

regions of DNA that are expressed

fermentation

incomplete oxidation of glucose and other carbohydrates in the absence of oxygen; facultative & aerotolerant anaerobes use this pathway; oxygen not required; organic compounds are the final electron acceptors; a relatively small amount of ATP is produced

frameshift mutation

one or a few base pairs are deleted or added to DNA - almost always results in a long stretch of altered amino acids and production of an inactive protein

gene

a certain segment of DNA that contains the necessary code to make a protein or RNA molecule

generalized transduction

the bacterial chromosome is broken apart by phage enzymes; random fragments of disintegrating host DNA are taken up by the phage during assembly; virtually any gene from the bacterium can be transferred

genotype

an organisms's distinctive genetic makeup - the sum total of all three types of genes

helicase

prior to the start of replication, these untwist the helix and break the hydrogen bonds holding the strands together; catalyze the base pairing; can only synthesize new DNA in the 5' to 3' direction; leading strand is synthesized continuously; lagging strand is synthesized in short fragments called Okazaki fragments, DNA ligase fills in the spaces between fragments

hydrolysis reaction

catabolic reaction that require the input of water

induced mutation

result from exposure to a known mutagen

inducer

a substance that acts to induce transcription of a gene

inducible

the category each operon falls into is determined by how transcription is affected by the environment surrounding the cell; many catabolic reactions are this - the operon is turned on by the substrate of the enzyme for which the structural genes code

induction

the process that turns on transcription of a gene

introns

intervening regions of DNA that do not encode protein

Know what the degeneracy of the genetic code means.

64 different codons are possible and all of them occur in mRNA; there are only 20 amino acids to be coded for; 3 of these codons do not have corresponding tRNA; 61 different tRNA are specific for the remaining 61 codons; provides some protection against mutation

messenger RNA

a copy of a structural gene; carries coded information to the ribosomes

metabolism

the sum of all chemical reactions within a living organism

metallic cofactor

metal ions - help bring the active site and substrate close together, and participate directly in chemical reactions with the enzyme-substrate complex

missense mutation

a change in the code causes amino acid substitutions and can do one of the following: create a faulty, nonfunctional protein; produce a protein which functions in a different manner; cause no significant alteration in protein function

mutagen

physical and chemical agents in the environment that cause permanent changes in DNA - almost any agent that can chemically or physically react with DNA can potentially cause mutations

mutant strain

a microbe that bears a mutation

mutation

a permanent, inheritable change in the nitrogenous base sequence of DNA - that change may cause a change in the product coded for by the mutated gene

mutation rate

the probability that a gene will mutate when a cell divides; because mutations are very rare, the rate is expressed as 10 to a negative power

noncompetitive inhibitors

do not compete with substrate for active sites, act on the regulator site of the enzyme and decrease the enzymes abilit to combine with normal substrate

nonsense mutation

creates a stop codon, stops production of the protein wherever it occurs - almost always results in a nonfunctional protein

nucleotides

building blocks of DNA and RNA; a deoxyribose sugar, (a 5 carbon sugar), a phosphate, a nitrogen base

operon

a coordinated set of genes, all of which are regulated as a single unit

oxidation

the removal of or more electrons from a substrate - protons are often removed with the electrons (equivalent to the removal of hydrogen atoms) - the compound that loses the electrons is oxidized

peptide bonds

forms between the two amino acids and the first tRNA is released

phenotype

the expression of the genotype; all organisms contain more genes in the genotypes than are expressed as a phenotype at any given time. Can change depending on what genes are "turned on" (expressed)

plasmids

small, replicating DNA molecules found in some bacteria, protozoa and fungal cells; mitochondria & chloroplasts have their own DNA in eucaryotic cells

point mutation

addition, deletion or substituion of one base

promoter region

transcription is initiated when RNA polymerase recognizes a segment of DNA called this

purines

adenine and guanine (A & G)

pyrimidines

thymine and cytosine (T & C)

reduction

the gain of one or more electrons by a substrate - the compound that receives the electron is reduced

regulated enzyme

the production is turned on (induced) or turned off (repressed) in response to changes in concentration of substrate or product; not constantly present; present in amounts ranging from a few molecules to several thousand depending on the metabilic requirement; the level of these enzymes is controlled by the degree to which the genes for these proteins are transcribed into proteins

repressible

the category each operon falls into is determined by how transcription is affected by the environment surrounding the cell; a similar system often controls the genes coding for anabolic enzymes - with these operons several genes are turned off by the product synthesized by the enzyme

repression

the regulatory mechanism that inhibits gene expression and decreases the synthesis of enzymes; usually a response to the overabundance of an end-product of a metabolic pathway; mediated by regulatory proteins called repressors, which block the ability of RNA polymerase to initiate transcription from the repressed gene

ribosomal RNA

site of protein synthesis;

RNA polymerase

a large enzyme complex is responsible for transcription

semi-conservative replication

each new DNA molecule contains one old strand and one new strand

silent mutations

the base change causes no change in the activity of the product encoded by the gene; commonly occur when one nucleotide is substituted for another, especiall at a location corresponding to the third position of the mRNA codon - because of the degeneracy fo the gentic code, the resulting new codon might still code for the same amino acid

simple enzyme

consists of only protein

specialized transduction

a highly specific part of the host genome is regularaly incorporated into the virus; this specificity is explained by the prior existence of a temperate prophage inserted in a fixed site on the bacterial chromosome; when activated the prophage DNA separates from the bacterial chromosome and carries a segment of host genes with it.\

spliceosome

remove the intron-derived RNA and splice together the exon-derived RNA, producing mRNA

spontaneous mutation

occur without the presence of any mutagen - random changes in DNA arising from errors in replication due to unknown cause

substrate

the specific substance an enzyme acts on

transcription

the master code of DNA is first used to synthesize RNA via this process; the formation of RNA using DNA as a template

transduction

DNA transfer mediated by the action of bacterial viruses

transfer RNA

brings amino acids to the ribosome; a tRNA molecule is 70-80 nucleotides long; two distinct ends of the molecule: a specific binding site for a particular amino acid and the anticodon

transformation

small segments of DNA that can move from one region to another region of the same chromosome, or to a different chromosome or plasmid; can be beneficial or adverse depending on where the insertion occurs in a chromosome; what kinds of genes are relocated; the tpe of cell involved.

translation

the information contained in the RNA is then used to produce proteins in this process; the synthesis of proteins using RNA a a template

transposons

have the distinction of shifting from one part of the genome to another and are termed "jumping genes".

triplet code

each of the 20 different amino acids is represented by one of these (a 3 nucleotide sequence) in a DNA molecule; other sequences encode instructions for beginning or ending snthesis of a protein molecule - "start" and "stop" instructions; when transcribed it dictates the type and order of amino acids in a protein

wild strain

a microbe that exhibits a natural, non-mutated characteristic

3 basic cataboilic pathways

aerobic respiration; anaerobic respiration; fermentation

chemical mutagens

base pair mutagens; nucleoside analogs; frameshift mutagens

base pair mutagens

make a specific base-pair change in DNA

nucleoside analogs

structurally similar to normal nitrogenous bases, but have slightly altered base-pairing properties - some anti-viral and anti-tumor drugs are nucleoside analogs - AZT

frameshift mutagens

causes small deletions or insertions - benzpyrene, present in smoke and soot causes frameshift mutations

Flickr Creative Commons Images

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