Microbio Exam Ii

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Genetics

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The study of the structure of genes, their function, and how genes and their cumulative effects are passed between organisms (heredity)

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Genetic Material

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DNA, or RNA (viruses) where the information for life is stored in organisms.

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Heredity

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The transmission of genetic material from organism to offspring

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Chromosomes

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A circular (prokaryotes) or linear (eukaryotes) threadlike molecule of DNA and its associated proteins

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Plasmids

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an extra-chromosomal circular strand of DNA that contains genetic information which supplements information in the chromosome

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Characteristics of plasmids

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-can replicate and transcribe mRNA on its own
-may be gained or lost without harm to the cell
-may carry certain genes for activities such as: antibiotic resistance, tolerance to toxic metals, the production of toxins and the synthesis of enzymes.

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Genome

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The total sum of an organism's genetic information

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Nucleotide

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made up of sugar (5C sugar deoxyribose), Phosphate, and a base

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Bases

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A- Adenine pairs with T
G- Guanine pairs with C
C- Cytosine pairs with G
T- Thymine pairs with A

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Arrangement

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Nucleotides arranged in helix, with base pairs held together by hydrogen bonds

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Gene

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-A linear sequence of nucleotides
-contains information for structure and function of an organism

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Allele

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different molecular forms of the same gene

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Mutation

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-permanent alteration in DNA
-usually change the sequence of nucleotides in DNA and thereby change the information in DNA

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dsDNA Structure

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-antiparallel
-direction always 5'-3'
-strands are held together by hydrogen bonds between bases A&T and C&G

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5'-3'

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referes to carbon 5 and carbon 3 of the deoxyribose molecule

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antiparelel

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2 strands are parallel but oriented in opposite directions

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Helicase

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1st step in DNA replication. Splits DNA into 2 strands, creating 2 replication forks traveling in opposite direction

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DNA Polymerase

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2nd step DNA replication. Binds each strand and synthesizes a compliment strand in 5'-3' direction.
-can synthesize one continuous complimentary strand, leading strand
-The lagging strand is synthesized
discontinuously as short fragments (Okazaki fragments) and then extended by DNA polymerase

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Ligase

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3rd step DNA replication. links the Okazaki fragments making one continuous strand

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Kinda of RNA

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Ribosomal RNA
Messenger RNA
Transfer RNA

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rRNA

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- Binds closely to certain proteins to for 2 kinds (30S and 50S) of ribosome subunits. A subunit of each kind combines to form a ribosome, sites of protein synthesis
-Serve as a binding site for tRNA and some of their proteins act enzymes that control protein synthesis
-after the 2 subunits join together around the strand of mRNA, the synthesis of a peptide begins
-Serve

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mRNA

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-synthesized in units that contain sufficient information to direct the synthesis of one or more polypeptide chains
-1 mRNA transcript corresponds to one or more genes
- the information coded in the mRNA acts during translation to dictate the sequence of amino acids in the protein

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Codon

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each triplet (sequence of 3 bases) in mRNA
-each codon specifies a particular amino acid or acts as a terminator of translation

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First codon

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AUG (methionine)

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End Codons

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UAA, UAG or UGA

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tRNA

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-Transfers amino acids from the cytoplasm to the ribosomes
-consists of 75 to 80 nucleotides and is folded back on itself to form several loops that are stabilized by complementary base pairing
-each tRNA has a 3-base anticodon that is complimentary to a particular mRNA codon
-also has binding site for an amino acid (particular amino acid specified by mRNA)
-anticodon attaches by complimentary base pairing to the appropriate mRNA codon

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regulatory mechanisms

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- The mechanisms that control metabolism either regulate enzyme activity directly or regulate the synthesis of enzymes by turning on or off genes that code for particular enzymes.

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Categories of regulatory mechanisms

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-feedback inhibition
-enzyme induction
-enzyme repression

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Feedback inhibition

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-the end-product of a biosynthetic pathway directly inhibits the first enzyme in the pathway
-because feedback inhibition acts quickly and directly on a metabolic process, it allows the cell to conserve energy
-requires less energy than the more complex processes that regulate gene expression

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Constituitive Enzymes

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Enzymes that are synthesized continuously regardless of the nutrients available to the organisms
-the genes that make these enzymes are always active

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Inducible Enzymes

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Enzymes that are synthesized by genes that are sometimes active and sometimes inactive, depending on the presence or absence of substrates

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Repression

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-A regulatory mechanism that inhibits gene expression and decreases the synthesis of enzymes
-Is usually a reponse to the ocerabundace of end product of a metabolic pathway
-Mediated by regulator proteins called repressors, which block the ability of RNA polymerase to initate transcription from the repressed genes

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Induction

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-Process that turns on the transcription of gene or genes
-Substances that induce gene transcription are called inducers and the enzymes that are synthesized in the presence of inducers are called inducible enzymes

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Operon Model of Gene Expression

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-A model that explains the regulation of some protein synthesis in bacteria
-includes one or more structural genes and the operator and promoter

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Structural Genes

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carry information for the synthesis of specific proteins such as enzyme molecules

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Operator region

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a short sequence that repessor-proteins and inducer-proteins bind to in order to prevent or enhance transcription

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Promoter Region

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a common sequence that RNA polyamerase recognizes, binds and begins transcription from

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Structural Region

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the actual coding-sequence, which will represent the transcribed mRNA sequence

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Enzyme Repression

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- the structural genes are transcribed until they are turned off, or repressed
- genes for enzymes involved in the synthesis of tryptophan are regulated by this mechanism
-when excess tryptophan is present, it acts as a corepressoe binding to the repressor protein
-the repressor protein then binds to the operator and stops further tryptophan synthesis

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Genotype

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the genetic information contained in the DNA of the organism

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Phenotype

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refers to the specific characteristics displayed by the organisms

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Mutations

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always change the genotype but not necessarily be expressed in the phenotype

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Inversions

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when a segment of DNA is excised and reinserted upside down

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Transposition

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When a segment of DNA is excised and reinserted somewhere else

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Are mutations the cause of all phenotypic variations?

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no

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What else can cause a phenotypic variation?

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Environmental factors

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Spontaneous Mutations

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-occur in the absence if any agents known to cause changes in the DNA sequence
-arise during replication of DNA and appear to be errors in base pairing of nucleotides

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Induced Mutations

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produced by mutagens

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Mutagens

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-increase rate of mutation compared to spontaneous mutation rate
-include chemical agents and radiation

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light repair (photoreactivation)

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-occurs in the presence of visible light in bacteria previously exposed to UV light
-mutations that might have been passed along to daughter cells are corrected and the DNA is returned to its normal state

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Dark Repair

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occurs in some bacteria in the presence or absence of light, requires several enzyme controlled reactions

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Vertical Gene Transfer

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When genes pass from parents to offspring (asexual reproduction-binary fission in bacteria)

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Lateral Gene Transfer

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genes are passed to other microbes of the same generation (not associated with reproduction)

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Significance of Transduction

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-transfers genetic material from one bacterial cell to another and alters the genetic characteristics of the recipient cell
-The incorporation of phage DNA into a bacterial chromosome demonstrates a close evolutionary relationship between prophage and the host bacterial cell
-The discovery that a prophage can exist in a cell for a long period of time suggests a similar possible mechanism for the viral origin of cancer (how animal viruses cause malignant changes)

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Conjugation Mechanism

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- Requires contact between donor and recipient cell
- Transfers much larger quantities of DNA (occasionally whole chromosome)

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Conjugation Significance

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- contributes significantly to genetic variation.
- larger amounts of DNA are transferred in conjugation than in any other transfers

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What are Viruses?

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Obligate intracellular parasites

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Viral Components

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Nucleic acids (dna OR rna)
Capsid (protein coat)
Envelope (lipid bilayer membrane with spikes) not all viruses have envelopes

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Virion

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a complete virus particle, including its envelope

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Viral Nucleic Acids

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-either DNA or RNA
-use their genome to replicate themselves in host cells resulting in disruption of activities or host cell death
-viral replication depends on the expression of viral genome for the formation of viral proteins
-can be single or double stranded
-all genetic info in RNA is carried by RNA

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Capsids

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-protein coats that enclose and -protect the nucleic acids
-determines shape of the virus
-play an important role in attachment of some viruses to host cells
-composed of protein subunits called capsomeres

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Capsomeres

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-proteins may be of a single type or different types
-the number of proteins and the arrangements of the capsomeres are characteristics of specific proteins

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Envelopes

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-enveloped viruses have bilayer membrane outside the capsid
-such viruses acquire the envelope after they are assembled in a host cell as they bud
-composition determined by viral genome and substances from host cell membrane
-combinations of lipids, proteins and carbohydrates make up most envelopes
-viruses without envelopes are called naked viruses
-projections called spikes made of glycoproteins, may or may not extend from the viral envelope

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Spikes

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serve to attach virions to specific receptor sites on host cell surfaces

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Spikes advantages

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help viruses infect new cells by fusion of the envelope with the host’s cell membrane

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Helical

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consists of ribbon like protein that forms a spiral around the nucleic acid

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Polyhedral

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many-sided, Icosahedral viruses have 20 triangular faces

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Complex

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combination of helical and icosohedral shapes

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Viral Host Range

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refers to the spectrum of hosts that a virus can infect. Different viruses can infect bacteria, fungi, algae, plants, vertebrates. Most viruses are limited to only one host

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Viral Specificity

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refers to the specific kinds of cells a virus can infect, eg certain papillomaviruses which cause warts are so specific in their replication process that they will target only skin cells
-Determined mainly by whether a virus can attach to a cell
-Attachment depends on the presence of specific receptor sites on the host cells and attachment sites on capsids or envelopes

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enterovirus

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Polio

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Rhinovirus

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Common Cold

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Hepatovirus

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Hep A

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Rubellavirus

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Rubella

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Equine Encephalitis

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Equine Encephalitis

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Falvirus

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Yellow Fever

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HTLV-I

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Adult Leukemia, tumors

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Morbillivirus

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Measles

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Lyssavirus

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Rabies

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Influenzavirus

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Influenza A&B

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Filovirus

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Marburg, Ebola

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Hantavirus

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Respiratory Distress, Hemorrhagic Fevers

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Rotavirus

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Respiratory and Gastrointestinal Infections

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Classification if Viruses

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double stranded, single stranded, shape (linear or circular), capsid shape, and presence or absence of an envelope

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Human adenovirus

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Respiratory Infections

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Simplexvirus

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oral and genital herpes

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Varicellovirus

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Chickenpox/shingles

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Orthopoxvirus

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Smallpox/Cowpox

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Human papilloma virus

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warts, cervical cancer, penile cancer

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Hepatitus B virus

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Hep B

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B19

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Fifth Disease (erythema infectiosum) in children

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Adsorption

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Phage is adsorbed onto bacterial cell wall

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Penetration

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Phage penetrates bacterial cell wall and cell membrane, injects its DNA, bacterial DNA is disrupted

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Biosynthesis

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the phage DNA directs the cell's metabolism to produce viral components-- proteins and copies of phage DNA

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Maturation

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collars, sheaths, heads, and tails come together and are packaged

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Release

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Bacterial cell lyses, releasing mature phages

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Lytic cycle

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adsorption, penetration, biosynthesis, maturation, release

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Latent Viruses

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can lie dormant in the host organism throughout the hosts life. However, can also replicate but not show symptoms

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Cytomegalovirus

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Infections found in 1% of live births, most defects are neurological and children have mental retardation

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Herpes Simplex Virus

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Infections are acquired at or shortly after birth. In case of infections that spread through the body, some children die, others will have permanent damage to eyes and central nervous system

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Rubella Virus

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infections in the mother during early stages of pregnancy are most likely to result in fetal defects. Defects include deafness, damage to sense organs, heart and circulatory defects, and mental retardation. Some fetuses may be naturally aborted

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Viroids

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an infectious RNA particel smaller than a virus
-Have no capsids
-Infect plants

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Prions

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Infectious agent, only protein (no genetic material)
-normal proteins that get folded incorrectly, possibly as a result of mutation
-Prion Proteins are thought to stick together inside cells, forming fibers.
-Creutzfeldt-Jakob disease, kuru, scrapie(sheep), mad cow disease