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93 terms

Chapters 8 and 9

STUDY
PLAY
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

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