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Protein
- result of the code
- the translation
- DNA is transcribed into RNA and translated as protein
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Translation
interpretation; DNA transcribed into RNA and translated as protein
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Replication
mode by which copies of DNA are made
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Reverse Transcriptase
- transcribing RNA into DNA
- done by viruses
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Chromosome
Independently replicating peice of DNA that is passed on to all daughter cells and encodes some genes that are essential for the survival of the cell
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Genome
- Complete set of genes in a cell
- Encodes all the genes necessary for a cell to survive
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Plasmid
independently replicating piece of DNA passed on to all daughter cells but does not encode any genes essential for cell.
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Nucleotide
- -basic unit of of DNA/RNA
- -consists of a nitrogenous base, a phosphate, and a sugar
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Anti-parallel double helix
One strand points in a 5' direction and the other in a 3' direction
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DNA Replication complex
- -Helicase to unwind DNA
- -Two DNA polymerases that replicate DNA in a 5' to 3' fashion
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Leading strand
synthesized continuously 5' to 3'
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Lagging strand
synthesized in short 5' to 3' fragments that are later ligated (glued together)
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Genetic
-All the genes in the cell
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Gene
- -DNA code that results in the making of a functional unit of RNA
- -one specific unit of information
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RNA polymerase
- -enzyme
- -responsible for copying DNA into RNA
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mRNA
- -Messenger RNA
- -contains message translated into a protein
- -in prokaryotes it is immediately translated into a protein
- -in eukaryotes it must first be processed
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tRNA
- Transfer RNA
- transfers a specific amino acid to the ribosome where the protein is made; it recognizes the message in the mRNA by using a code
- there is a tRNA for each amino acid and each tRNA recognized a spec code that represents that amino acid
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rRNA
- ribosomal DNA
- this DNA with ribosomal proteins froms the ribosome
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Ribosome
Organelle that facilitates translation
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Genetic code
code of DNA bases and amino acids
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Codon
- 3 base code
- 64 codons which code for 20 amino acids
- 3 stop codons
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E site
- ejection site
- where tRNA no longer has an amino acid and is released back into cytoplasm
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P-site
- peptide site
- where tRNA is located that has peptide chain attached
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A site
- active site
- where the next tRNA comes in a decodes the mRNA
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Transpeptidation
- second step in protein synthesis
- the joining of one amino acid to another amino acid occurs via formation of a peptide bond
- occurs when P site and A site are full
- ribosome transfers the amino acid from the tRNA in the P site onto the amino acid that is on the tRNA in the A site
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Translocation
- movement of the ribosome three bases (once codon) along mRNA
- the tRNA that was in the Psite is now in the Esite
- the tRNA that has the peptide attached that was in the Asite is now in the Psite
- the A site is empty again
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Mutation
- change in the nucleotide sequence of the genome of an organsim/virus
- result in from the incorrect incorporation of a nucleotide into the genetic sequence
- some will allow an organism to become resistant to antibiotics
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Induced Mutation
result from exposure to known mutagens which are primarily physical or chemical agents thta interact with DNA/RNA in a disruptive manner
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Spontaneous Mutation
random changes in DNA arising from mistakes in replication or the detrimental effects of a natural background radiation on DNA
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Recombination
- process involving several dozen proteins
- part of one sequence is inserted into another site with high sequence similarity
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Integration
- site specific recombination with organisms genome
- results in a double stranded DNA being inserted into the genome
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What does integration require?
- 1) Integrase - enzyme which catalyzes double breaks
- 2) Recognition sequence - must be present in both organsims DNA and invading DNA
- 3) The invading DNA must encode the intergrase
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Transposon
- mobile genetic elements
- able to integrate into an organisms genome and then later move to a new location in that genome
- many are lysogenic phage
- most move from one organism to another by piggybacking during txfer of DNA from one cell to another
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Transformation
process by which cells can take up naked DNA from the environment
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Competent cells
- cells that can be transformed
- naturally competent: streptococcus, heliobacter, haemophilus, neissira
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Naturally competent
take up DNA in their normal environment
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Conjugation
self transmissable plasmids that direct the formation of a special pilus onthe surface of the bacterium
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Hfr strains
High frequency of recombination
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Transduction
transfer of genes from the donor cell to the recipient cell via a bacteriophage
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Restriction enzymes
- counteract the ease of gene transfer resulting in the rejection of most foreign DNA
- work by recognizing short sequences
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What does it mean that DNA is "semi conservative"
each daughter cell receives a chromosome with one strand from the original parental chromosome, the opposite strand being a new copy of the original chromosome.
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DNA helicase
a protein that unwinds helical DNA
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primase
- binds to open DNA and makes a short RNA copy of the DNA that is called an RNA primer
- essential b/c DNA polymerase can not start a DNA strand, it can only EXTEND a DNA strand
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DNA ligase
enzyme which "glues" together fragments of information
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Topoisomerase
enzyme which breaks open a circular chromosome to be re-linked
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Telomerase
enzyme in eukaryotes which copies last bit of DNA such that the new chromosome are the same length as old chromosomes
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operons
- transcriptional unit
- may contain one or more different genes
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Activator
- bind to DNA and help RNA polymerase to bind to DNA
- often allow RNA polymerase to bind at sites where they normally wouldnt
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Regulon
region containing the sequences that control gene expression
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Repressor
bind to DNA and prevent RNA polymerase from binding to the DNA or from copying the DNA into RNA
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Missense mutation
change that results in a different amino acid
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nonsense mutation
mutation that results in the inserting of a stop codon
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frameshift
- results in the insertion of deletion of nucleotides that change the reading frame of the mRNA
- changes all amino acids from that point forward
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supressor mutation
- mutations that result in a correction of the original mutation
- may also result in a second mutation that compensates for the orig mutation without correcting it
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What is the central dogma of genetics?
- DNA --------> RNA -------------> protein
- transcripton translation
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What are the four levels of structure of chromosomal DNA?
- 1) The strand itself
- 2) the strand wrapped around thousands of histones
- 3) The histones (ball like); form regions to make the DNA more compact
- 4) All regions can be linked together to make DNA tiny
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What is the purpose of DNA initiation
The get DNA polymerase attached to the DNA thta is to be copied
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What are the three steps of initiation of DNA replication?
- 1) Unwinding the DNA - must be opened by DNA helicase so that the initiation complex can bind to the DNA
- 2) Synthesis of an RNA primer - primase binds to DNA and makes a short copy of the DNA which is called an RNA primer
- 3) Binding of the DNA rep complex - DNA rep complex binds to RNA primer on DNA
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What are the parts of DNA replication complex?
- 1) Helicase to unwind DNA
- 2) Two DNA polymerases that replicate DNA in a 5 to 3 direction
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What is Elongation (copying of DNA)
- copying of the DNA
- involves leading strand and lagging strand
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Describe the Termination of circular DNA replication
- they are linked like a chain
- there are enzymes that break one of the chromosomes and relink it so that they are separated
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Describe termination of linear chromosome replication
in eukaryotes telomerase copies the last bit of DNA such that the new chromosomes are the same length as the old chromosomes
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Describe eukaryotic mRNA processing
- 1) 5' end is capped
- 2) Addtition of a poly-A tail
- 3) Removal of introns through splicing
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What are the three functions of a ribosome?
- 1) docking site from mRNA and inititator tRNA
- 2) docking site for additional tRNA that recognizes the mRNA
- 3) Traspeptidation enzyme which allows two amino acids to be joined together to form a peptide chain or protein
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Describe the initiation process of translation
- the ribosome binds to the mRNA molecule and rapidly scans until it finds an intitiator site
- the ribosome positions itself such that the P site is over the initiator site where the initiator or first tRNA can bind
- upon binding of initiator tRNA the ribosome now assumes an active state with the Asite open
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Elongation during protein synthesis
- 1) filling of A site
- 2) Transpeptidation
- 3) translocation
- 4) Ejection of the rRNA*
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what is generalized transduction
- virus penetrates bacterial cell and enter the lytic cycle
- viral DNA begins to replicate immediately in the bacterial cytoplasm
- during replication enzymes accidentally use some bacterial DNA to make new viruses
- bacterial genes are randomly packaged into new viruses
- some new viruses have bacterial DNA and no viral DNA
- transducing viruses enter recipient bacterium
- donor bacterial genes are incorporated into the chromosome of recipient bacterium
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How is specialized transduction different from generalized?
- viruses penetrate and enter the lysogenic cycle
- replication begins at a later time
- during release from chromosome in replication, viral DNA accidentally excises bacterial DNA to make new viruses
- bacterial genes adjacent to previously incorporated virus are packaged into new virus
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What are the steps of recombination?
- 1) Enzyme causes a double stranded break
- 2) single stranded protruding 3 ends are created by degrading the 5 strand
- 3) strand invasion occurs - strand adheres to the other DNA homolog
- 4) (eukaryotes only) DNA synthesis copies the DNA - usually for 1000 more bases
- 5) A holliday junction forms and is resolved into to separate DNA molecules
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What are the three steps of transformation?
- 1) external DNA is bound by proteins on the cell surface
- 2) DNA is taken up into the cell as either a single strand or a double strand
- 3) foreign DNA is incorporated into the cell's genetic material through recombination
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