Molecular Biology Of The Gene

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Virus

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--A microscopic particle capable of infecting cells of living organisms and inserting its genetic material
--Viruses are invaders that sabotage our cells
--Viruses have genetic material surrounded by a protein coat and, in some cases, a membranous envelope
--Viral proteins bind to receptors on a host’s target cell
--Viral nucleic acid enters the cell
-It may remain dormant by integrating into a host chromosome
-When activated, viral DNA triggers viral duplication, using the host’s molecules and organelles
-The host cell is destroyed, and newly replicated viruses are released to continue the infection
--Generally Viruses are not considered to be alive because they do not display all of the characteristics associated with life

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Molecular Biology

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--The study of Heredity at the molecular level

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Hershey and Chase

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--1952 they performed a very convincing set of experiments that showed DNA to be the genetic material of T2 (a virus that infects the bacterium Esherichia Coli)
--Used Bacteriophages to show that DNA is the genetic material
--Phages were labeled with radioactive sulfur to detect proteins or radioactive phosphorus to detect DNA
--Bacteria were infected with either type of labeled phage to determine which substance was injected into cells and which remained outside
--The sulfur-labeled protein stayed with the phages outside the bacterial cell, while the phosphorus-labeled DNA was detected inside cells
--Cells with phosphorus-labeled DNA produced new bacteriophages with radioactivity in DNA but not in protein

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Frederick Giffith

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--Discovered that a “transforming factor” could be transferred into a bacterial cell
--Disease-causing bacteria were killed by heat
--Harmless bacteria were incubated with heat-killed bacteria
--Some harmless cells were converted to disease-causing bacteria, a process called transformation
--The disease-causing characteristic was inherited by descendants of the transformed cells

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Bacteriophages

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--Viruses that infect bacterial cells
--AKA Phages

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Nucleotide

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--The monomer unit of DNA and RNA
--Contains:
-Nitrogenous base
-5-carbon sugar called Ribose in RNA and Deoxyribose in DNA
-Phosphate group

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Polymers

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--Long chains of monomers
--A large molecule consisting of many identical or similar monomers linked together by covalent bonds

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Monomers

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--Subunit that serves as a building block for Polymers
--Chemical Units

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Polynucleotide

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--A polymer made up of many nucleotide monomers covalently bonded together
--DNA or RNA Strands

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Sugar-Phosphate Backbone

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--In a polynucleotide (DNA or RNA strands), the alternating chain of sugar-phosphate-sugar-phosphate to which the nitrogenous bases are attached

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Nitrogenous Base

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•DNA nitrogenous bases are adenine (A), thymine (T), cytosine (C), and guanine (G)
•RNA also has A, C, and G, but instead of T, it has uracil (U)

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Phosphate Group

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--A chemical group consisting of a phosphorus atom bonded to 4 oxygen atoms

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Covalent Bonds

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-A strong chemical bond in which two atoms share one or more pairs of outer shell electrons

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DNA

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--DNA is composed of two polynucleotide chains joined together by hydrogen bonding between bases, twisted into a helical shape
--The sugar-phosphate backbone is on the outside
--The nitrogenous bases are perpendicular to the backbone in the interior
--Deoxy means Without oxygen
--Nucleic portion refers to DNA's location in the nuclei of Eukaryotic Cells
--A double stranded helical nucleic acid molecule consisting of nucleotide monomers with deoxyribose sugar and the nitrogenous bases (A) Adenine, (C) Cytosine, (G) Guanine, and (T) Thymine
•Capable of replicating
•An organism's genetic material

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Pyrimidines

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--Single Ring structures
--Thymine (T) and Cytosine (C)

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Purines

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--Larger Double Ring structures
--Adenine (A) and Guanine (G)

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RNA

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--A type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases (A) Adenine, (C) Cytosine, (G) Guanine, and (U) Uracil
•Usually single stranded
•Functions in protein synthesis, gene regulation, and as a genome of some viruses

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Hydrogen Bonding

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--A type of weak chemical bond formed when the partially positive hydrogen atom participating in a polar covalent bond in one molecule is attracted to the partially negative atom participating in a polar covalent bond in another molecule (or in another region of the same molecule)
--Bases Hydrogen Bond to other Bases A-C-G-G
--Single Ring structure pair with Double Ring Structures
--A bonds best with T --> 2 HBs
--G bonds best with C --> 3 HBs

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Difference Between DNA and RNA

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--Deoxyribose and Ribose
--The sugar in RNA has an -OH group attached to the C atom in the lower right hand corner
--RNA has a nitrogenous base called Uracil (U) instead of Thymine (T) in DNA
--RNA is usually single stranded

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Complimentary

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-- A bonds best with T
--A is complimentary to T
-- G bonds best with C
--G is complimentary to C

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Chargaff's Rules

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--He discovered that the amount of Adenine in the DNA of any one species was equal to the amount of Thymine and that the amount of Guanine was equal to that of Cytosine
--A always pairs with T and G on one chain only pairs with C on the other chain
--Imagine a Ladder and the steps are Hydrogen Bonds

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Sequence of DNA

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--Watson and Crick
--G and C Bonds are stronger because they have 3 Hydrogen Bonds between them
--A and T have 2 Hydrogen Bonds between them
--The 2 Sugar Phosphate Backbones of the Double Helix are oriented in opposite directions
--No Restrictions on the sequence of the Nucleotides along the length of a DNA strand
--The sequence of bases can vary in countless ways and each gene has a unique order of nucleotides or base sequence

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Semiconservative Model

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--DNA Replication--half of parental molecule is maintained (conserved) in each daughter molecule
--The two DNA strands separate
--Each strand is used as a pattern to produce a complementary strand, using specific base pairing
--Each new DNA helix has one old strand with one new strand

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DNA Replication

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--DNA replication begins at the origins of replication
--DNA unwinds at the origin to produce a “bubble”
--Replication proceeds in both directions from the origin
--Replication ends when products from the bubbles merge with each other
--DNA replication occurs in the 5’---> 3’ direction
--Replication is continuous on the 3’ -- 5’ template
--Replication is discontinuous on the 5’ -- 3’ template, forming short segments

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Watson and Crick's Template Hypothesis

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--DNA replication takes half of the strand and looks at the sequence of bases and then make a complentary strand from the free nucleotides that are always available

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3' Three Prime

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--On one end of each DNA strand the sugar's 3' Carbon Atom is attached to an -OH group

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5' Five Prime

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--On one end of each DNA strand the sugar's 5' Carbon is attached to a phosphate group

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DNA Polymerase

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--Adds nucleotides to a growing chain
--Carry out the proofreading step that quickly removes nucleotides that have base-paired during Replication

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DNA Ligase

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--Joins small fragments (Okazaki Fragments) into a continuous chain

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Genotype

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--An organism's genetic makeup
--An organism's heritable information contained in its DNA

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Phenotype

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--An organism's physical traits

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Transcription

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--The synthesis of RNA under the direction of DNA
--The transfer of information from DNA to RNA
--DNA is transcribed into RNA
--Use U bases instead of T bases complementary to A bases in the strand of DNA this puts it in RNA's Nucleic Acid language -- the linear sequence of the nucleotides of the DNA molecule dictates the sequence of the nucleotides of RNA

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Translation

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--The synthesis of protein under the direction of RNA
--The use of the information in RNA to make a Polypeptide
--RNA is translated into protein
--The conversion of the Nucleic Acid language to the Polypeptide Language -- the Linear sequence of the nucleotides of the RNA molecule dictates the sequence of the amino acids of the polypeptide
--The 4 Bases of RNA must somehow specify ALL 20 amino acids -- they do this with A Triplet Code AGU specify one amino acid-- AGA specifies another

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Protein

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--The presence and action of proteins determine the phenotype of an organism

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Molecular Chain of Command

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--From DNA in the nucleus to RNA to Protein Synthesis in the Cytoplasm

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Gene

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--A sequence of DNA that directs (provides instructions for) the synthesis of a specific protein
--Consists of hundreds of thousands of nucleotides in a specific sequence

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One Gene -- One Enzyme Hypothesis

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--Was based on studies of inherited metabolic diseases
--The idea that the function of a gene is to dictate the production of a specific enzyme

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One Gene -- One Protein Hypothesis

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--Expands the relationship to proteins other than enzymes

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One Gene -- One Polypeptide Hypothesis

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--Recognizes that some proteins are composed of multiple polypeptides
--The function of a gene is to dictate the production of a polypeptide

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Triplet Code

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--A set of 3 nucleotide long "words" (3 Bases AGU AUU) that specify the amino acids for polypeptide chains
--64 codons are possible
--Some amino acids have more than one possible codon
--61 codons correspond to amino acids
--AUG codes for methionine and signals the start of transcription
--3 “stop” codons signal the end of translation

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Codon

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--The basic unit of the genetic code
--A 3 Nucelotide Sequence in mRNA that specifies a particular amino acid or polypeptide termination signal
--64 codons are possible
--Some amino acids have more than one possible codon

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Genetic Code

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--The set of rules that dictates the correspondence between RNA codons in an mRNA molecule and amino acids in protein

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Redundancy

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--More than one triplet code can represent the same amino acid
--EX) Codons UUU and UUC both specify Phenylalanine

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No Ambiguity

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--The triplet code represents ONLY one amino acid
--EX) Codons UUU and UUC ONLY specify Phenylalanine

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AUG

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--Met or Start Codon
--It is the first amino acid in the polypeptide

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Stop Codon

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-- UAA or UAG or UGA
--Continue translation until you reach one of these Codons

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Process of Transcription

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--The two DNA strands separate
--One strand is used as a pattern to produce an RNA chain, using specific base pairing
--For A in DNA, U is placed in RNA
--FIRST PHASE: Initiation: the attachment of RNA Polymerase to the Promotor and the start of RNA Synthesis
--SECOND PHASE: Elongation: the RNA grows; as RNA synthesis continues the RNA strand peels away from its DNA template, allowing the 2 seperated DNA strands to come back together in the region already transcribed
--THIRD PHASE: Termination: the RNA Polymerase reaches a sequence of bases in the DNA template called Terminator which signals the end of the gene-- the Polymerase detaches from the RNA molecule and the gene

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RNA Polymerase

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--Transcription Enzyme
--A large molecular complex that links together the growing chain of RNA nucleotides during transcription, using a DNA strand as a template

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Promoter

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--A specific nucleotide sequence in DNA located near the start of the gene that is the binding site for RNA Polymerase and the place where transcription begins

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Terminator

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--A special sequence of nucleotides in DNA that marks the end of a gene
--It signals RNA Polymerase to release the newly made RNA molecule and then to depart from the gene

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mRNA

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--Messenger RNA
--The kind of RNA that encodes amino acid sequences
--It conveys genetic messages from DNA to the translation machinery of the cell
--mRNA is TRANSCRIBED from DNA and the information in the mRNA is then TRANSLATED into polypeptides
--In Prokaryotic Cells: Transcription and Translation occur in the Cytoplasm
--In Eukaryotic Cells: the mRNA must exit the nucleus via the nuclear pores and enter the Cytoplasm (where the machinery for polypeptide synthesis is located)
--Before leaving the nucleus as mRNA... Eukaryotic transcripts are modified or processed in several ways: Cap and Tail, Introns and Extrons, RNA Slicing

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Cap

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--A single G Nucleotide
--Facilitates the export of the mRNA from the nucleus
--Protects the mRNA from attack by cellular enzymes
--Helps Ribosomes bind to the mRNA
--Not translated into protein

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Tail

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--A chain of 50 to 250 A nucleotides
--Facilitates the export of the mRNA from the nucleus
--Protects the mRNA from attack by cellular enzymes
--Helps Ribosomes bind to the mRNA
--Not translated into protein

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Introns

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--"Intervening Sequences"
--Interrupting Sequences
--Internal Noncoding Stretches (Regions) of nucleotides that interrupt the nucleotides that actually code for amino acids (unitelligible sequences)
--Removed when RNA leaves the nucleus so that the Exons can join together to produce an mRNA molecule with a continuous coding sequence
--Found in most genes of plants and animals

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Exons

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--The Coding Regions
--The parts of a gene that are expressed
--Transcribed from DNA to RNA
--Before the RNA leaves the nucleus, the exons are joined (after the introns are removed) to produce an mRNA molecule with a continuous coding sequence

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RNA Slicing

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--The removal of introns and joining of exons to produce and mRNA molecule with a continuous coding sequence
--Catalyzed by a complex of proteins and small RNA molecules
--RNA can sometimes act as an enzyme that removes its own introns
--Provides a means to produce multiple polypeptides from a single gene

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tRNA

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--Transfer RNA
--Serve as Interpreters during Translation
--Translates a genetic message carried in mRNA into the amino acid language of proteins
--Translates from Nucelic Acid Language (Codons) to Amino Acid Language
--Structure allows tRNA to Perform 2 Tasks:
-Picking up the appropriate amino acids
-Recognizing the appropriate codons in the mRNA
Structure: Twists and Folds itself, RNA Polypeptide Chain, Hydrogen Bonding Attachment Site on one end and Anticodon on the other

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Attachment Site on tRNA

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--An amino acid attachment site allows each tRNA to carry a specific amino acid

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Anticodon

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--On tRNA-- A specific sequence of 3 nucleotides that is complimentary to a codon triplet on mRNA
--Allows the tRNA to bind to a specific mRNA codon, complementary in sequence
--A pairs with U, G pairs with C

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Ribosomes

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--Structures in the cytoplasm that position mRNA and tRNA close together and catalyze the synthesis of polypeptides
--Translation occurs on the surface of the ribosome
--Ribosomes have two subunits: small and large
--Each subunit is composed of ribosomal RNAs and proteins
--Ribosomal subunits come together during translation
--Ribosomes have binding sites for mRNA and tRNAs

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rRNA

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--Ribosomal RNA
--The type of RNA that together with Proteins makes up Ribosomes
--The most abundant type of RNA in most cells

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P Site

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--A binding site for amino acids bearing tRNA on Ribosomes
--tRNA gives up the polypeptide to the tRNA that follows it

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A Site

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--A binding site for amino acids bearing tRNA on Ribosomes
--tRNA's amino acid receives the growing polypeptide from the tRNA that precedes it

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Codon Recognition

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--The anticodon of an incoming tRNA binds to the mRNA at the A site of the ribosome

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Peptide Bond Formation

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--The polypeptide seperates from the tRNA in the P Site and attaches by a new peptide bond to the amino acid carried by the tRNA in the A Site
--The Ribosome catalyzes formation of the peptide bond by adding one more amino acid to the growing polypeptide chain

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Translocation

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--tRNA is released from the P site and the ribosome moves the remaining tRNA from the A site into the P site
--The codon and the anticodon remain hydrogen bonded and the mRNA and tRNA moves as a unit (this movement brings in the next mRNA codon to be translated and the process starts over again at step 1)
--Elongation continues until a Stop Codon

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DNA--RNA--Protein

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--Transcription DNA --> RNA
--Translation RNA --> Protein

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Mutation

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--A change in the nucleotide sequence of DNA
--The ultimate source of genetic diversity
--They can be Spontaneous: due to errors in DNA replication or recombination
--They can be Induced by mutagens

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Base Substitutions

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--Reeplacement of one nucleotide with another
--Effect depends on whether there is an amino acid change that alters the function of the protein

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Base Insertions or Deletions

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--Usually have disastrous effects!
--Alter the reading frame of the mRNA, so that nucleotides are grouped into different codons
--Lead to significant changes in amino acid sequence downstream of mutation
--Cause a nonfunctional polypeptide to be produced

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Reading Frame

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--The way a cell's mRNA translating machinery groups the mRNA nucleotides into codons

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Mutagenesis

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--The creation of a change in the nucleotide sequence of an organism's DNA

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Mutagen

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--A chemical or physical agent that interacts with DNA and causes a mutation
--Example: High Energy Radiation

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Missense Mutations

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--Substitutions that change the amino acid coding
--Ex) Change from GGC to AGC

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Nonsense Mutations

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--Substitutions that change an amino acid codon into a STOP codon

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Silent Mutations

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--Mutations that have no effect at all
--Ex) GAA to GAG no effect because they both code for the same amino acid

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Microbial Genetics

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--Studies the genetics of very small (micro) organisms
--Involves the study of the genotype of microbial species and also the expression system in the form of phenotypes
--It also involves the study of genetic processes taking place in these micro organisms

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Microbes

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--Tiny organisms—too tiny to see without a microscope, yet they are abundant on Earth. They live everywhere—in air, soil, rock, and water

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Virus

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--An infectious particle consisting of a bit of nucleic acid wrapped in a protein coat (Capsid) and in some cases a membrane envelope
--They can replicate only inside cells
--A typical animal virus has Glycoproteins (protein molecules with sugar) projecting out of it

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Capsid

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--The protein coat of a Virus

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Lytic Cycle

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--Viral particles are produced using host cell components
--The host cell lyses, and viruses are released

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Lysogenic Cycle

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--Viral DNA Relication occurs without destroying the host cell
--Viral DNA is inserted into the host chromosome by recombination
--Viral DNA is duplicated along with the host chromosome during each cell division
--The inserted phage DNA is called a prophage
--Most prophage genes are inactive
--Sometime Environmental Signals can cause a switch to the lytic cycle

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Prophage

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--Phage DNA that has inserted by genetic recombination into the DNA of a bacterial chromosome
--Most Prophage Genes are Inactive

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Phage

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--A virus that infects bacteria

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Emerging Virus

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--A virus that has appeared suddenly or has recently come to the attention of medical scientists
--RNA viruses mutate rapidly
--Contact between species
--Viruses from other animals spread to humans
--Spread from isolated populations

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Reverse Transcriptase

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--An enzyme used by retroviruses (like HIV) that catalyzes the synthesis of DNA on an RNA template

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Reproductive Cycle of a Virus

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--Both DNA viruses and RNA viruses cause disease in animals
--Reproductive cycle of an RNA virus
--Entry
--Glycoprotein spikes contact host cell receptors
--Viral envelope fuses with host plasma membrane
--Uncoating of viral particle to release the RNA genome
--mRNA synthesis using a viral enzyme
--Protein synthesis
--RNA synthesis of new viral genome
--Assembly of viral particles

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Retrovirus

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--An RNA virus that reproduces by means of a DNA molecule
--It reverse-transcribes its RNA into DNA, inserts the DNA into a cellular chromosome and then transcribes more copies of the RNA from the viral DNA
--Example) HIV

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HIV Duplication

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--Reverse transcriptase uses RNA to produce one DNA strand
--Reverse transcriptase produces the complementary DNA strand
--Viral DNA enters the nucleus and integrates into the chromosome, becoming a provirus
--Provirus DNA is used to produce mRNA
--mRNA is translated to produce viral proteins
--Viral particles are assembled and leave the host cell

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Provirus

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--The genome of an animal virus integrated (by crossing over) into the chromosome of the host cell, and thus replicated in all of its daughter cells
--Can be activated to produce a complete virus
--Can cause transformation of the host cell.

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Viroids

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--Circular RNA molecules that infect plants
--Replicate within host cells without producing proteins
--Interfere with plant growth

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Prions

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--Infectious proteins that cause brain diseases in animals
--Misfolded forms of normal brain proteins
--Convert normal protein to misfolded form

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Transformation

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--The uptake of foreign DNA from the surrounding environment

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Transduction

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--Gene transfer through bacteriophages

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Conjugation

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--The transfer of DNA from a donor to a recipient bacterial cell through a cytoplasmic bridge

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Plasmid

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--Small circular DNA molecules that are separate from the bacterial chromosome

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F Factor

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--Involved in conjugation
--When integrated into the chromosome, transfers bacterial genes from donor to recipient
--When separate, transfers F-factor plasmid

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R Plasmid

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--Transfer genes for antibiotic resistance by conjugation