Microbiology Chapter 7 Terms

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Genetics

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is the study of inheritance and inheritable traits.

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Genes

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are composed of specific sequences of nucleotides that code for polypeptides or RNA molecules.

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genome

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is the sum of all the genetic material in a cell or virus. Prokaryotic and eukaryotic cells use DNA as their genetic material; some viruses use DNA, and other viruses use RNA.

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The two strands of DNA are held together by hydrogen bonds between complementary bases of nucleic acids called

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base pairs (BP)

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One end of a DNA strand is called the ----because it terminates in a phosphate group attached to a 5' carbon;

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5' end

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the opposite end of the DNA strand is called the ----- end because it terminates with a hydroxyl group bound to a 3' carbon of deoxyribose.

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3' end

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chromosomes

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Prokaryotic genomes consist of one or two, which are typically circular molecules of DNA associated with protein and RNA molecules

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nucleoid

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localized in a region of the cytoplasm

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plasmids

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Prokaryotic cells may also contain one or more extrachromosomal DNA molecules, which contain genes that regulate nonessential life functions such as bacterial conjugation; resistance to one or more antimicrobial drugs, heavy metals, or toxins; destruction of competing bacteria; and pathogenicity.

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histones

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eukaryotic chromosomes contain proteins

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nucleosomes (beads of DNA)

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histone arrangements that clump with other proteins to form chromatin fibers. Eukaryotic cells also contain extrachromosomal DNA in mitochondria, chloroplasts, and plasmids.

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semiconservative

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A cell separates the two original strands and uses each as a template for the synthesis of a new complementary strand. The process is where each daughter DNA molecule is composed of one original strand and one new strand.

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DNA replication,

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the cell removes histones and other proteins from the DNA molecule. DNA helicase unzips the double helix, breaking hydrogen bonds between complementary base pairs, to form a replication fork.

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DNA synthesis

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always moves in the 5' to 3' direction, so the leading strand is synthesized toward the replication fork. Synthesis is mediated by enzymes that prime, join, and proofread the pairing of new nucleotides.

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lagging strand

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is synthesized in a direction away from the replication fork, and discontinuously in Okazaki fragments. It always lags behind the process occurring in the leading strand. DNA ligase seals the gaps between adjacent Okazaki fragments to form a continuous DNA strand.

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methylation

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a cell adds a methyl group to one or two bases that are part of specific nucleotide sequences. In some cases, genes that are methylated are “turned off” and are not transcribed, whereas in other cases, they are “turned on” and are transcribed. In some bacteria, methylated nucleotide sequences play a role in initiating DNA replication, repairing DNA, or recognizing and protecting against viral DNA.

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Eukaryotic DNA replication is similar to that in bacteria with a few exceptions. These are:

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Eukaryotic cells use four DNA polymerases to replicate DNA. Due to the large size of eukaryotic chromosomes there are many origins of replication. Okasaki fragments of eukaryotes are smaller than those of bacteria. Finally, plant and animal cells methylate cytosine bases exclusively.

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genotype

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is the actual set of genes in its genome,

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phenotype

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is the physical and functional traits expressed by those genes, such as the presence of flagella. Thus, genotype determines phenotype; however, not all genes are active at all times.

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central dogma of genetics

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states that DNA is transcribed to RNA, which is translated to form polypeptides.

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The transfer of genetic information begins with -------- of the genetic code from DNA to RNA,in which RNA polymerase links RNA nucleotides that are complementary to genetic sequences in DNA.

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transcription

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Transcription begins at a region of DNA called a ------- (recognized by RNA polymerase) and ends with a sequence called a ----------.

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promoter, terminator

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Cells transcribe four types of RNA from DNA. These are:

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RNA primer molecules, Messenger RNA (mRNA) molecules, Ribosomal RNA (rRNA) molecules, Transfer RNA (tRNA) molecules

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RNA primer molecules

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used for DNA polymerase to use during DNA replication.

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Messenger RNA (mRNA) molecules

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which carry genetic information from chromosomes to ribosomes

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Ribosomal RNA (rRNA) molecules

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which combine with ribosomal polypeptides to form ribosomes, the organelles that synthesize polypeptides

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Transfer RNA (tRNA) molecules

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which deliver amino acids to the ribosomes

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Eukaryotic transcription differs from bacterial transcription in several ways. These are:

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Eukaryotic cells transcribe RNA in the nucleus, while prokaryotic transcription occurs in the cytosol. Eukaryotes have three types of nuclear RNA polymerase and multiple transcription factors. Eukaryotic cells process mRNA before translation. RNA processing involves capping, polyadenylation, and splicing.

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Translation

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the sequence of genetic information carried by mRNA is used by ribosomes to construct polypeptides with specific amino acid sequences. To understand how four DNA nucleotides can specify the 20 different amino acids commonly found in proteins requires an understanding of the genetic code.

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Scientists define the genetic code as the complete set of triplets of mRNA nucleotides called ----- that code for specific amino acids.

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codons

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more than one codon is associated with all the amino acids except for

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methionine and tryptophan.

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The smaller subunit of a ribosome is shaped to accommodate three codons at one time. Each ribosome also has three binding sites that are named for their function:

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A site, P site, and E site

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A site

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accommodates a tRNA delivering an amino acid.

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P site

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holds a tRNA and the growing polypeptide.

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E site

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Discharged tRNAs exit from .

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Prokaryotic translation proceeds in three stages. These are:

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initiation, elongation, and termination

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initiation

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an initiation complex is formed

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elongation

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tRNAs sequentially deliver amino acids as directed by the codons of mRNA. Ribosomal RNA in the large ribosomal subunit catalyzes a peptide bond between the amino acid at the A site and the growing polypeptide at the P site.

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termination

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does not involve tRNA; instead, proteins called release factors halt elongation. The ribosome then disoociates into its subunits.

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riboswitch

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is a molecule of mRNA that folds in such a way as to block ribosomes and translation of the polypeptide they encode when that polypeptide is not needed.

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Translation can also be controlled by

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short interference RNA (siRNA). siRNA is an RNA molecule complementary to a portion of mRNA, tRNA, or a gene. siRNA binds to its target and renders it inactive.

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operon consists of a promoter, an adjacent regulatory element called an -----and ------

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operator, a series of genes all either repressed or induced by one regulatory gene located elsewhere.

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Inducible operons

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such as the lac operon are not usually transcribed and must be activated by inducers.

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Repressible operons

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such as the trp operon are transcribed continually until deactivated by repressors.

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mutation

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a change in the nucleotide sequence of a genome.

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point mutations

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the most common type of mutation in which just one or a few nucleotide base pairs are affected.

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Point mutations include the following:

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Substitutions, Frameshift mutations

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Substitutions

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in which a single nucleotide is substituted for another, possibly leaving the amino acid sequence unaffected because of the redundancy of the genetic code.

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Frameshift mutations

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including insertions and deletions of nucleotides, in which nucleotide triplets subsequent to an insertion or deletion are displaced, creating new sequences of codons that result in vastly altered polypeptide sequences.

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silent mutations

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Some base-pair substitutions produce them. The substitution does not change the amino acid sequence because of the redundancy of the genetic code.

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missense mutation

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A change in a nucleotide sequence resulting in a codon that specifies a different amino acid, that gets transcribed and translated makes sense, but not the right sense

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nonsense mutation

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a base-pair substitution changes an amino acid codon into a stop codon. Nearly all nonsense mutations result in nonfunctional proteins. Frameshift mutations (insertions or deletions) typically result in drastic missense and nonsense mutations.

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Mutations can be:

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spontaneous, or result from recombination

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mutagens

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Physical or chemical agents, which include radiation and several types of DNA-altering chemicals, induce mutations. Radiation in the form of X-rays and gamma rays can cause mutations.

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pyrimidine dimers

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Additionally, nonionizing radiation in the form of ultraviolet light causes adjacent pyrimidine bases to bond to one another to form. The presence of dimers prevents hydrogen bonding with the nucleotides in the complementary strand, distorts the sugar-phosphate backbone, and prevents proper replication and transcription.

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nucleotide analogs

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chemical muagens include compounds that are structurally similar to normal nucleotides but, when incorporated into DNA, cause mutations.

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base-pair substitution mutations

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nucleotide-altering chemicals alter the structure of nucleotides,

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Aflatoxins

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nucleotide-altering chemicals that result in missense mutations and cancer. Still other mutagenic chemicals insert or delete nucleotide base pairs, resulting in frameshift mutations

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How many genes contain an error?

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About one of every ten million genes contain an error. Mutagens typically increase the mutation rate by a factor of 10–1000 times.

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light repair

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cells use DNA photolyase to break the bonds between adjoining pyrimidine nucleotides

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dark repair

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enzymes repair pyrimidine dimers by cutting damaged DNA from the molecule, creating a gap that is repaired by DNA polymerase I and DNA ligase.

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base-excision repair

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an enzyme system excises the erroneous base and DNA polymerase I fills in the gap.

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mismatch repair

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enzymes scan newly synthesized unmethylated DNA looking for mismatched bases, which they remove and replace.

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Once a new DNA strand is ----- mismatch repair enzymes cannot correct any errors that remain.

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methylated

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SOS response occurs when?

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When damage is so extensive that these mechanisms are overwhelmed, bacterial cells resort by involving the production of a novel DNA polymerase capable of copying less-than-perfect DNA.

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If a cell does not repair a mutation, it and its descendents are called

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mutants

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wild type cells

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cells normally found in nature

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Positive selection

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which involves selecting a mutant by eliminating wild type phenotypes

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Negative selection (also called indirect selection)

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a process in which a researcher attempts to culture auxotrophs

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Ames test

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used to identify potential carcinogens (cancer-causing agents).

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Researchers have developed methods to recognize mutants amidst their wild type neighbors. These include:

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positive selection, negative selection, and ames test

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Genetic recombination

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refers to the exchange of nucleotide sequences between two DNA molecules often mediated by segments that are composed of identical or nearly identical nucleotide sequences called homologous sequences.

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recombinants

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DNA molecules that contain new arrangements of nucleotide sequences. Scientists first observed them in eukaryotes during crossing over, a process in which portions of homologous chromosomes are recombined during the formation of gametes (sex cells).

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Vertical gene transfer

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the transmission of genes from parents to offspring

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horizontal gene transfer

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DNA from a donor cell is transmitted to a recipient cell.

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recombinant cell

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results from genetic recombination between donated and recipient DNA.

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The types of horizontal gene transfer are:

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Transformation, transduction, and bacterial conjugation

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transformation

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a competent recipient cell takes up DNA from the environment. Competency is found naturally and can be created artificially in some cells.

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transduction

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a virus such as a bacteriophage carries DNA from a donor cell to a recipient cell. Donor DNA is accidentally incorporated in transducing phages.

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conjugation

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a bacterium containing an F fertility plasmid (factor) forms a conjugation pilus that attaches to an F– recipient bacterium. Plasmid genes are transferred to the recipient, which becomes F+ as a result.

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Hfr (high frequency of recombination) cells

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result when an F plasmid integrates into a prokaryotic chromosome. Hfr cells form conjugation pili and transfer cellular genes more frequently than normal F+ cells

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Transposons

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are DNA segments that code for the enzyme transposase and contain palindromic sequences known as inverted repeats (IR) at each end. (A palindrome is a word, phrase, or sentence that has the same sequence of letters when read backward or forward.) Transposons move among locations in chromosomes in eukaryotes and prokaryotes.

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insertion sequences (IS)

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The simplest transposons, consist only of inverted repeats and transposase.

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Complex transposons

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contain other genes as well