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132 Cards in this Set
- Front
- Back
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Fredrick Griffith
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- two strains of bacterium
- dead pathogenic bacteria and harmless bacteria - "transforming factor" that brings about heritable change |
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Hershey and Chase
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- DNA is th genetic material of a virus called T2 which infects bacterium E coli
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bacteriophages
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- virus that infect bacterium
- T2 virus reprogram hosts to produce new phages - |
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T2 Virus
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- consisting of a heal and tail
- protein and DNA - Hershey and Chase which molecule was responsible |
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Hershey and Chase
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- radioactive isotope, blender, centrifuge
- radioactively labeled phage DNA, but not labeled protein, entered the host cell during infection and directed the synthesis of new viruses |
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what happened in the Hershey Chase experiments?
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- T2 phages containing labeled protein, the radioactivity ended up mainly in the liquid, which contained phages but not bacteria
- phage protein did not enter cell - but when bacteria had been infected with phages whose DNA was tagger, the most of the radioactivity was in the bacterial pellet (when returned to growth medium they would lyse with phages containing radioactive phages in their DNA) |
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Conclusions from the Chase and Hershey experiments?
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- T2 injects DNA
- DNA causes cell to create new phages (DNA and protein) - DNA contained instructions for making new phages |
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Hershey and Chase added to earlier evidence that ...
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- DNA is the hereditary material
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what did scientist understand up to the point the Chase and Hershey discovery?
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- DNA passed on heritable material
- atoms were covalently bonded to one another |
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What did they not know?
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- the exact arrangement of atoms that gave DNA its unique properties (copy, store and pass on genetic information)
- 1 year later after the Hershey and Chase discovery the structure was identified |
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DNA and RNA are?
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- long chains (polymers) of chemical units (monomers) called nucleotides
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How many different types of polynucleotides?
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- four types each with a different nitrogenous base
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sugar phosphate backbone
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- repeating pattern of sugar phosphate sugar phosphate
- the nitrogenous bases are arranged as appendages all along this backbone - |
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Each nucleotide
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- phosphate group has P in center and is responsible for the "acid" part
- sugar has five carbon atoms - deoxyribose missing oxygen atom |
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ribonucleic vs deoxy
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- ribose contains an extra oxygen
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James D Watson and Francis Crick
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- explained the three 3D structure of DNA as a double helix accounts for its function
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what James D Watson and Francis Crick know
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- Chargaff data of base pairing
- x crystography image (helix structure) |
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who did watson and Crick beat out with their data...?
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- Roslain; died before the nobel prizes were handed out by
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Watson and Crick
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- helix
- complementary base pairing - nitrogenous bases in interior of moecule |
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two sugar phosphate backbone of the double helix are oriented in opposite directions
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- sugars on the two strands are upside down with respect to each other
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double helix makes evident what property of biology
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- relationship between structure and function
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Watson and Crick predicted what about gene replication?
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- helix structured and complimentary base pairing
- two daughter molecules will have one old strand, which was part of the parental molecule, and one newly created strand |
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semiconservative model
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- half of the parental molecule is maintained (conserved) in each daughter molecule
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DNA replication
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- each strand of DNA provides template for the assembly of a complementary strand
- line up according to base pairing rules - enzymes link the nucleotides to form new DNA strands |
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Origins of Replication
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- stretches of DNA having a specific sequence of nucleotides where proteins attach to the DNA and separate the strands
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Replication Bubble
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- Replication proceeds in both directions
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DNA has many
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... origins where replication can start simultaneously
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sugar phosphate backbones are in...
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...opposite directions
- each strand has opposite 3prime and 5prime end |
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Primed ends
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- 3 and 5 prime end on each sugar phosphate backbone
- prime numbers refer to the carbon atom of the nucleotide sugars - sugar 3 carbon attached OH - sugar 5 carbon attached phosphate group |
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Enzymes that link DNA nucleotides to a growing daughter strand
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- DNA polymerases
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DNA polymerase add in what order?
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- from 5 end to 3 end
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Replication Bubble
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- enzymes specificity of DNA polymerase causes forked structure
- one of the daughter strands can be synthesized in one continuous piece by a DNA polymerase working toward the forking point of the parental DNA - daughter strands must work outward from the forking point |
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DNA ligase
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- then links (ligates) the pieces together into a single DNA strand
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DNA polymerase also
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- carries proof reading step that quickly removes nucleotides that have base paired incorrectly during replication
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life relies on a process called ___ __________ to assure successful regeneration and reproduction using mitosis and meiosis, parental DNA has to be copied into two new strands of daughter DNA
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DNA replication
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E coli
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- common intestinal bacteria of mamals
- attacked by T2 viruses in Hershey and Chase experiments - turns into phage producing factory |
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Erwin Chargaff
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- developed a series of rules based on survey of DNA composition in organisms
- new about nitrogenous bases - A/T/G/C characteristic but not necessarily equal ratios |
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Chargafs Rule
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- regularity in the ratios of nucleotide bases which are known
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backbone of DNA consists of ...
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- alternating phosphates and sugars, from which bases project
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After seeing the x - ray crystallograpphy by Maurice Wilkins ... diffraction pattern can be used to deduce the three dimensional shape of molecules ... James Watson leaned..
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- DNA was helical in shape and he deduced the width of the helix and the spacing of bases
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DNA ladder forms a twist every...
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ten bases
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base pairing with Watson and Crick
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Based on details of their structure, adenine would form 2 hydrogen bonds only with thymine and guanine would form 3 hydrogen bonds only with cytosine.
- explains to Chargaffs rule |
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The DNA Molecule
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-Polymer of nucleotides: Adenine, thymine, cytosine, and guanine
Two polynucleotide strands form double helix associated with proteins "Backbone" is deoxyribose-phosphate Center contains the nitrogenous bases - two strands held together by hydrogen bonds - anti parallel on 5' and 3' ends |
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double helix of parental DNA separates weak hydrogen bonds
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between the nucleotides on opposite strands break in response to the action of replication enzymes
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H bonds form between...
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complementary nucleotides and each strand of the parental template to form new base pairs
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enzymes catalyze the formation of sugar phosphate bonds
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... between sequential nucleotides on each resulting daughter strand
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When a cell copies a DNA molecule, each parental strand serves as a template for
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ordering nucleotides into a new complimentary strand.
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the first step in DNA replication is....
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separation
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Semiconservative
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- daughter molecules will have one parental strand
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Matthew Meselson & Franklin Stahl supported the...
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- semiconservative model, proposed by Watson and Crick
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C-G are _____ H bonded
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triple
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A - T are ____ H bonded
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double
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Anti Parallel
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- the sugar phosphate backbone of one strand is upside down relative to the backbone of the other strand
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Semi-conservative DNA Replication (step 1)
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- parental DNA separates
- Weak H bonds break |
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Semi-conservative DNA Replication (step 2)
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- H bond form between new complementary nucleotides and each strand of the parental template to form new base pairs
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Semi-conservative DNA Replication (step 3)
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- enzymes catalyze the formation of sugar- phosphate bonds between sequential nucleotides on each resulting daughter strand
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DNA polymerase
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- add nucleotides only to the 3' end and never to the 5' end
- daughter strand can only grow from 3' to 5' |
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What functions as the link between genotype and phenotype?
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- proteins
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Proteins (genotype/phenotype)
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-DNA inherited specifies traits by building proteins
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Two main stages of protein synthesis are...
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- transcription and translation
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Transcription
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- the transfer of genetic information from DNA into a RNA molecule
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Translation
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- transfer of information from RNA into protein
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metabolic pathways are catalyzed by...
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specific enzymes
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Archibald Garrod
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- genes dictate phenotypes through enzymes
- black urine hypothesis |
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Genes code for:
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- all varieties of proteins not just enzymes
- code for polypeptides |
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molecular change of command for protein synthesis
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DNA -> RNA -> protein
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what is DNA and RNA (both polymers) made up of?
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- nucleotide monomers
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Transcription
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- nucleic acid language of DNA has been rewritten as a sequence of bases on RNA
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Translation
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- the conversion of nucleic acid language into the polypeptide language
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nucleic acids and polypeptides are both...
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- polymers
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how many amono acids are made by translation?
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- 20
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how many triplets are possible
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4^3
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Triplet Code
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- the genetic instructions for the amino acid sequence of a polypeptide chain written on DNA and RNA
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Codon
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- a series of three base words coding for polypeptide chain
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Codon experiments
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- mix codons with test tube containing ribosomes
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Genetic code
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is the set of rules giving correspondence between codons in RNA and amino acids in proteins
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RNA molecules are linked by a transcription enzyme called...
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RNA polymerase
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What is the name of the "start transcribing" signal
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promoter
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Promoter
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- nucleotide sequence that provides a specific binding site for RNA polymerase and determines which of the two strands of DNA double helix is used as as the template in transcription
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Promoters are found ....
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along DNA; provides site RNA polymerase
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Phases of Transcription (initiation)
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- attachment of RNA polymerase to promoter sequence to start RNA synthesis
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Phases of Transcription (elongation)
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- as RNA synthesis continues RNA strand peels away from DNA template allowing DNA strands to come together again
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Phases of Transcription (termination)
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- RNA reached terminator sequence which signals the end of the gene
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RNA polymerase
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separates the DNA strands at the appropriate point and bonds the RNA nucleotides as they base-pair along the DNA template.
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Like DNA polymerases, RNA polymerases can add nucleotides only to the
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3’ end of the growing polymer.
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Genes are read 3’->5’, creating
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a 5’->3’ RNA molecule.
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intrinsic 3’-exonuclease
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(“proof reading”) activity of DNA polymerase reduces this low error rate to one mistake per every 10^9 nucleotides added
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RNA polymerase II is used for
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- mRNA
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In a eukaryotic cell, almost all transcription occurs in the ______ and translation occurs mainly at _______ in the cytoplasm.
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- nucleus
- ribosomes |
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The kind of RNA that encodes amino acids sequences and convey genetic information to translation systems of the cell is called
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- mRNA
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mRNA is translated into ...
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- polypeptides
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Before the primary transcript leaves the nucleus ...
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its modified to with a singe G- nucleotide cap and a adenine- nucleotide tail (these mods are not translated)
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RNA Polymerase
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Adds new nucleotides to growing RNA strand during DNA transcription
Synthesizes RNA in 5’ 3’ direction) Requires Mg and Zn as cofactors |
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DNA transcription can be separated into three stages
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1. Initiation, 2. Elongation, and 3. Termination.
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Initiation of Eukaryotic DNA Transcription
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1. RNA polymerase I, II or III (= POL) - RNA POL II synthesizes mRNA - large multi-protein complex with about 500,000 Da - inhibited by mushroom poison alpha-amanitin; - RNA POL I and RNA POL III synthesize rRNA and tRNA
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Initiation of Eukaryotic DNA Transcription
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2. TBP (= TATA box-binding protein) - binds to the TATA box of the promoter region
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Initiation of Eukaryotic DNA Transcription
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3. Many Transcription factors, e.g. TFII F, TFII E, TFII H and TFII D - important for regulation of transcription
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transcriptome
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Activated transcription factors plus RNA polymerase II assemble and form the transcription-initiation complex
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behind the point of RNA synthesis the double helix...
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reforms
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Terminator sequence
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- poly U stop signals (no protein factor UUUUUU
- Rho-dependent termination - lacks a poly-U region, and often the hairpin loop; - requires the protein factor "rho" |
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the 5’ cap
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At the 5’ end of the pre-mRNA molecule, a modified form of guanine is added
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poly (A) tail
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- At the 3’ end, an enzyme adds 50 to 250 adenine nucleotides
- inhibits hydrolysis - facilitate the export of mRNA |
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RNA splicing
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- removal of introns
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mRNA transcript includes...
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coding regions, exons, that are translated into amino acid sequences, plus the leader and trailer sequences.
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Two different splicing mechanisms
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1. protein-independent self-splicing - requires catalytically active snRNA
2. spliceosome-dependent splicing - requires several RNA and protein components, e.g. U1, U2, U4, U5, U6 snRNA and hnRNPs - most introns are spliced by this mechanism |
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tRNA
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- converts the 3 letter words (codons) of nucleic acids to the one letter amino acid words of proteins
- attach amino acids to the appropriate codons to form the new polypeptide |
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Two tasks of tRNA
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- picking up appropriate molecules
- recognizing appropriate codons in the mRNA |
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3 major mRNA processing steps have been identified in cells
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1. CAPing of the 5’-end of the pre-pro-mRNA - covalent attachment of a chemical group(m7GpppNmpN)
- done by capping enzyme and methyl transferase 2. Attachment of Poly-A tail to 3’ end of mRNA 3. Splicing of introns (eukaryotic mRNA only) - ATP-dep. polymerization of >200 adenine residues to the 3’-end of nascent mRNA molecule - catalyzed by Poly-A polymerase (PAP) |
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Translation
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blocks of three nucleotides, codons, are decoded into a linear sequence of linked amino acids.
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tRNA
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- links mRNA codon with appropriate amino acid
-Each tRNA arriving at the ribosome carries a specific amino acid at one end and has a specific nucleotide triplet, an anticodon, at the other |
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anti codon
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- nucleotide triplet
- base pairs with a complementary codon on mRNA |
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tRNA
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- a single strand of RNA (one polypeptide chain)
- regions of double strand where tRNA is folded on itself - single strand loop at the end (triplet) |
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Important sites on tRNA
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- anticodon that attaches to mRNA
- amino acid attachment site |
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how do you build a polypeptide chain in translation?
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Codon by codon, tRNAs deposit amino acids in the prescribed order and the ribosome joins them into a polypeptide chain.
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wobble
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pairing between the third base of the codon and anticodon are relaxed
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Ribosomes
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facilitate the specific coupling of the tRNA anticodons with mRNA codons
- 2 subunits one large one small - composed of rRNA and proteins |
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How does a ribosome function in protein synthesis?
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- A ribosome holds mRNA and tRNA together and connects amino acids from the tRNA to the growing polypeptide chain
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Large unit vs small unit
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tRNA binding sites vs mRNA binding site
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Initiation (translation)
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- establish where translation will begin
- mRNA binds to small unit - special initiator tRNA binds to start codon - anti codon UAC binding to AUG - large unit binds to small one creating a functional ribosome |
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Each ribosome has a binding site for mRNA and three binding sites for tRNA molecules.
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- The P site holds the tRNA carrying the growing polypeptide chain.
- The A site carries the tRNA with the next amino acid. - Discharged tRNAs leave the ribosome at the E |
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Protein Translation requires:
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1. mature mRNA
2. amino-acyl tRNA 3. large and small ribosome units 4. rRNA 5. protein factors, e.g. IFs, EFs and RFs 6. Cell energy, in form of ATP, GTP |
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Elongation (translation)
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- consists of a series of three step cycles as each amino acid is added to the proceeding one.
- Codon recognition; peptide bond formation; translocation |
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codon recognition
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an elongation factor assists hydrogen bonding between the mRNA codon under the A site with the corresonding anticodon of tRNA carrying the appropriate amino acid.
- mRNA and tRNA bonding in the ribosome |
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Peptide bond formation (transamination)
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- polypeptide separates from the tRNA to which it was bound
- polypeptide on Psite tRNA bonds to A site amino acid - ribosome catalyzes formation of the bond - one more amino acid is added |
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translocation (translation)
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- the ribosome moves the tRNA with the attached polypeptide from the A site to the P site.
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Translocation
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Because the anticodon remains bonded to the mRNA codon, the mRNA moves along with it.
The next codon is now available at the A site. The tRNA that had been in the P site is moved to the E site and then leaves the ribosome. Translocation is fueled by the hydrolysis of GTP. Effectively, translocation ensures that the mRNA is “read” 5’ -> 3’ codon by codon. |
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Stop codon
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- elongation continues until it reaches a stop codon at the site A
- this is termination - polypeptide is released from the last tRNA - ribosome splits |
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A site vs P site
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A site recieves polypeptide chain
P gives up polypeptide chain |
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61 sense codons on mRNA encode the...
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20 amino acids
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In eukaryotes, the________ _______ segregates transcription from translation
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- nuclear envelope
-In addition, extensive RNA processing is inserted between these processes. |
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Transcription, RNA processing, and translation are the processes that ...
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link DNA sequences to the synthesis of a specific polypeptide chain
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Any change in the nucleotide sequence of DNA is called a
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mutation
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