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a. A cell’s genome includes __ and __
b. Genotype: __/ Phenotype: __
c. The entire genome does not consist of back-to-back genes
i. __ occur in most genomes
- chromosomes and plasmids
- collection of genes
- collection of proteins
- Noncoding regions called short tandem repeats (STRs)
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a. Replication requires enzymes
i. __: relaxes supercoiling
ii. __: unwinds and separates two strands
iii. __: newly added nucleotides are joined by this enzyme; adds only onto the 3’ end
iv. Point at which replication occurs is the __
- Topoisomerase or gyrase
- Helicase
- DNA Polymerase
- replication fork
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a. Semiconservative model: __
b. Directionality
i. Paired bases are __ relative to each
ii. The two strands fit together in the __direction of one strand, which runs counter to the __ of the other strand
c. Energy is supplied by the __
i. __ are removed to add the nucleotide
- new strand contains one parent strand and one new srand
- upside down
- five to three
- five to three direction
- nucleotides
- Two phosphate groups
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a. DNA replication in bacteria is __, meaning what?
- bidirectional
- i. Two replication forks move in opposite directions away from the origin of replication and meet when replication is finished
- 1. The two loops must be separated by a topoisomerease
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a. RNA and Protein Synthesis
i. Transcription: __
1. __ and __ play a part
2. genetic info stored in the __ is rewritten so that the same info appears in the base sequence of mRNA
3. requires __, which binds to __; synthesizes in the __ until reaching the __
- DNA--> RNA
- rRNA and tRNA
- sequence of nitrogenous bases of DNA
- RNA polymerase,
- DNA promoter site
- five-->three direcition
- terminator
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i. Translation: __
1. mRNA is in __, which determine the sequence o famino acids (__)
a. most amino acids have several __, called __
- RNAà Protein
- codons
- 64 codons
- alternative codons
- degeneracy of the code
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i. 61 are __; 3 are __
1. Sense code for __
2. Nonsence are stop condos:__, __, __
3. Start is __, which codes for __ rather than __
- sense codons
- nonsense codons
- amino acids
- UAA, UGA, UAG
- AUG
- formylmethionine rather than methionine
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1. Each tRNA has an __so that it can base pair with its associated codon
2. Process: ___
anticodon
- 1) Components come together
- 2) on ribosome, a tRNA carrying the first amino acid is paired with the start codon on mRNA at the P site
- 3) the second codon of the mRNA pairs with a tRNA carrying the second amino acid at the A site
- 4) the ribosome moves along the mRNA until the second tRNA is in the P site; the next codon to be translated is brought into the A site, while the first exits the E site
- 5) the second amino acid joins the third by a peptide bond and the first tRNA is release
- 6) the ribosome continues to move along the mRNA, and new amino acids are added
- 7) stop codon releasesthe polypeptide
- 8) the last tRNA is released and the ribosomes comes apart
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a. The common feature of all metabolic reactions is that they are __
b. __ stops enzymes that have already been synthesized
c. Many genes are not regulated but are instead __, meaning that __
i. These genes, which are turned on all the time, code for __
- catalyzed by enzymes
- Feedback inhibition
- constitutive
- their products are constantly produced at a fixed rate
- enzymes that the cell needs in large amounts for its major life processes
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a. Pre-Transcriptional control: control __ and __ in cell, not __
i. Repression: __
1. Mediated by __, which do what?
- formation and amounts of enzymes
- activities
inhibits gene expression and decreases the synthesis of enzymes; response to overabundance of end-product of metabolic pathway, causing decrease in rate of synthesis of enzymes leading to formation of product
- repressors
- block the ability or RNA pol to initiate transcription from the repressed gene
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Induction : __
1. Inducer: __
2. Enzymes that are synthesized in the presence of inducers: __
- turns on transcription of genes
- induces transcription
- inducible enzymes
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i. The Operon Model of Gene Expression
1. Genes that are regulated together are __
2. In the control region of the lac operon are two relatively short segments of DNA
a. Promoter: __
b. Operator: is a __
3. The promoter and operator sights, as well as structural genes: __
4. A regulatory gene can __ that does what?
- structural genes
- region where RNA Pol initiates transcription
- traffic light that acts as a go or stop signal for transcription of the structural genes
- operon
- encode a repressor protein that switches inducible and repressible operons on or off
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1. In inducible operons:what happens?
- a. In the absence of lactose, for example, the repressor binds to the operator site, thus preventing transcription
- b. If present, the repressor binds elsewhere
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1. In repressible operons, what happens?
- a. Structural genes are transcribed until they are turned off, or repressed
- b. When excess of something is present, the excess object acts as a corepressor binding to the repressor protein i. The repressor protein can now bind to the operator, stopping further tryptophan synthesis
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i. Positive Regulation
1. cAMP: derived from __that serves as a __
a. when glucose is not available, cAMP __, which binds to the __, initiating transcription by doing what?
b. it is an __, a chemical alarm signal that promotes a cell’s response to environmental or nutritional stress
c. inhibition of the metabolism of alternative carbon sources b glucose is __
i. when glucose is available, the level of cAMP in the cell is __, and consequently __
- ATP
- cellular alarm signal
- accumulates and binds to the allosteric site of catabolic activator protein (CAP)
- promoter
- making it easier for RNA polymerase to bind to the promoter
- alarmone
- catabolite repression
- low
- CAP is not bound
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i. epigenetic control
1. eukaryotic and bacterial cells can turn genes off by __, which are passed to offspring cells-> epigenetic inheritance
methylating certain nucleotides
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a. Posttranslational Control
i. Single-stranded RNA molecules of approximately 22 nucleotides, called __inhibit protein production in eukaryotic cells; allow different cells to produce different proteins
ii. An miRNA binds with complementary mRNA, forming a __, which is __ so that the __ is not made
- microRNAs
- double-standard RNA
- enzymatically destroyed
- mRNA-encoded protein is not made
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i. __: single base is replaced; in translation, it may cause another amino acid, which is a __--> bad (sickle cell)
ii. __: creating a stop codon in the middle of an mRNA molecule
iii. __: one or a few nucleotide pairs are deleted or inserted in the DNA, changing the codons
iv. What are spontaneous mutations?
- Base substitution
- missense mutation
- Nonsense mutation
- Frameshift mutation
Spontaneous mutations occur in absence of mutation causing agents, which are called mutagens
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I. Mutagens
a. Chemical:
1) Nitrous acid
2) Nucleoside analog
3) Other
- i. Nitrous acid: A pairs with Cà two different strands (one with AT and another with CG)
- ii. Nucleoside analog: slightly altered base-pairing properties; the analogs are randomly incorporated into cellular DNA in place of normal basesà mistakes in base pairing
- iii. Other chemical mutagens cause small deletions or insertions, which can result in frameshifts (they are often potent carcinogens)
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Mutagens: Radiaiton
X and Gamma rays
- i. can ionize atoms and molecules, causing electrons to pop out of their usual shells, which then cause more damage to other molecules
- 1. Can oxidize bases in DNA, resulting in errors in DNA replication
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Mutagens: Radiaiton
UV rays
- i. form covalent bonds between certain bases, creating dimers
- 1. Enzymes can repair UV induced damage, like photolases (separate the dimer)
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i. __: repair mutations by cutting out and filling in the gap with correct bases
1. __add a __ to selected bases soon after a DNA strand is made to allow them to be recognzed
- Nucleotide excision repair
- Methylases
- methyl group
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c. The frequency of mutation
- Mutation rate?
- How specific
- Mutations can be __ and __
- mutagen
- i. Mutation rate: probability that a gene will mutate when a cell divides
- ii. Occur randomly along a chromosome
- iii. Mutations can be adaptive and beneficial
- iv. A mutagen increases the spontaneous rate of mutation
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Identifying mutants
- positive
- negative
- i. Positive (direct) selection: detection of mutant cells by rejection of the unmutated parent cells
- ii. Negative (indirect) selection: selects a cell that cannot perform a certain function, using replica plating
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How to test via negative indirect selection
- 1. Grow all on one plat with nutrients, histidines, etc., then transfer them, via a velvet paper, to other plates that lack what is trying to be tested for.
- a. Any mutant microorganism having a nutritional requirement that is absent in the parent is an auxotroph
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Identifying Chemical Carcinogens
- i. Ames test: uses bacteria as carcinogen indicators
- 1. Based on observation that exposure of mutant bacteria to mutagenic substances may cause new mutations that reverse the effect of the original mutation: reversions
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