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179 Cards in this Set
- Front
- Back
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Messenger RNA (mRNA)
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Intermediary that passes information from DNA to protein.
-fully processed transcript that can be exported out of the nucleus -5' half of the RNA undergoes processing while 3' half is being synthesized |
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Functional RNA
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RNA does not encode information to make protein. RNA itself is the final product.
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Transfer RNA (tRNA)
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molecules are responsible for bringing the correct amino acid to the mRNA in the process of translation
-found in both eukaryotes & prokaryotes |
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Ribosomal RNA (rRNA)
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molecules are the major components of ribosomes, which are large macromolecular machines that guide the assembly of the amino acid chain by the mRNAs & tRNAs
-found in both eukaryotes & prokaryotes |
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Small nuclear RNAs (snRNAs)
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part of a system that further processes RNA transcripts in eukaryotic cells.
Some snRNAs unite with several protein subunits to form the SPLICEOSOME that removes introns from eukaryotic mRNAs. |
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MicroRNAs (miRNAs)
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role in regulating the amount of protein produced by many eukaryotic genes
(GENE REGULATION) |
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Small interfering RNAs (siRNAs)
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help protect the integrity of plant & animal genomes.
-inhibit the production of viruses & prevent the spread of transposable elements to other chromosomal loci (GENOME DEFENSE) |
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Transcription
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-Synthesis of RNA
-Asymmetrical: only one strand of the DNA of a gene is used as a template for transcription. This strand is in 3' to 5' orientation, and RNA is synthesized in the 5' to 3' direction. |
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Coding strand
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non-template strand of the DNA
***TEMPLATE strand is the one that is complementary to the RNA strand (mRNA) |
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Consensus sequence
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the nucleotide sequence of a segment of DNA that is in agreement with most sequence reads of the same segment from different individuals
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5' untranslated region (5' UTR)
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intervening part between the initiation site (where the transcription starts) & where the gene starts actually encoding.
Prokaryotes: ATG sequence is where it starts encoding Eukaryotes: TATA box, CAAT box, G-C rich region are in the 5' UTR |
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RNA Polymerase Holoenzyme
**PROKARYOTE |
bacterial RNA polymerase that scans the DNA for a promoter sequence
-Sigma factor: binds to the -10 & -35 regions, positioning the holoenzyme to initiate transcription correctly at the start site; -Sigma factor subunit dissociates from the rest of the complex after core enzyme is bound to DNA & transcription begins. |
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Ribozyme
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RNA that functions like an enzyme; has enzyme-like behavior
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RNA Polymerase I
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rRNA (ribosomal RNA)
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RNA Polymerase II
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mRNA
**in eukaryotes -- some snRNAs |
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RNA Polymerase III
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some snRNAs, 5S RNA, tRNA
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Termination in Prokaryotes during Transcription
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A hairpin structure forms by complementary base pairing within a GC-rich RNA strand. Most of the RNA base pairing is between G & C but there is 1 A-U pair.
-Rho factor: protein recognizes the termination signals for RNA polymerase. |
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3' untranslated region (3' UTR)
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when transcription of the original gene continues beyond the protein-encoding segment;
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General Transcription Factors (GTF's)
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-the proteins that bind to a promoter before RNA polymerase II binds to it.
-TFIIA, TFIIB, ... |
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pre-mRNA
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newly synthesized RNA right after transcription
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Pre-initiation complex
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General transcription factors & RNA polymerase II
-6 GTFs, each of which is a multiprotein complex & RNA polymerase II core is made up of dozen or more protein subunits. |
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TATA-binding protein (TBP)
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-binds to the TATA box and attracts other GTFs and the RNA polymerase II core to the promoter, thus forming the pre-initiation complex.
-part of the TFIID complex |
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Carboxyl tail domain (CTD)
-Eukaryotic RNA polymerase** |
-protein tail
-Helps recruit other proteins important for transcription (ex. Mediator complex) -CTD = YSPTSPS (amino acids that can be phosphorylated); repeats of 7 amino acids - binding sites for some of the enzymes and other proteins that are required for RNA capping, splicing, cleavage after polyadenylation. -Initiation phase ends & the elongation phase begins after the CTD has been phosphorylated by one of the GTFs. -TFIIH phosphorylates CTD when transcription begins |
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Transcript
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RNA
**DNA is said to be transcribed into RNA |
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Co-transcriptional
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partly synthesized (nascent) RNA is undergoing processing reactions as it emerges from RNA poly II complex.
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Polyadenylation signal
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AAUAAA or AUUAAA conserved sequence near the 3' end of mRNA
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5' Cap
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Methylated guanine cap, added to the 5' end by several proteins that interact with CTD as the newly synthesized RNA first emerges from RNA polymerase II
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RNA Splicing
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removal of introns & joining of exons
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Alternative Splicing
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different mRNAs and subsequently, different proteins are produced from the same primary transcript by splicing together different combinations of exons.
-proportion of alternatively spliced genes varies from species to species. -more than 70% of human genes are alternatively spliced. |
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Why does the # of proteins in humans outnumber the # of human genes?
~25,000 genes ~100,000 proteins |
Genes can encode multiple proteins through alternative splicing**
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What did Griffith demonstrate in 1928?
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Transformation of
R (rough-nonvirulent) cells into S (smooth-virulent) cells Presence of heat-killed S cells transforms live R cells into live S cells Transformed R strain = has properties like S strain Illustrated that you can pass along some substance between organisms |
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What did Avery, MacCleod, McCarty demonstrate in 1944?
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That DNA was the transforming agent
All the mice were treated with S extract (smooth, virulent) They all died except for when the DNA was removed by DNAse 1st demonstration that genes (the hereditary material) are composed of DNA *If the DNA in an extract of heat-killed S-strain cells is destroyed, then mice injected with a mixture of the heat-killed cells and the live nonvirulent R-strain cells are no longer killed. |
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Hershey and Chase 1952
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Viral DNA can transform cells
-Demonstrated that the genetic material of phages is DNA, not protein. -Experiment uses 2 sets of T2 bacteriophage. -In one set, protein coat is labeled with radioactive sulfur 35S, not found in DNA -In the other, DNA is labeled with phosphorous 32P, not found in protein =RESULT: only the 32P injected into e.coli --> DNA is the agent necessary for the production of new phages |
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Watson, Crick, Franklin 1953
**Watson, Crick, Wilkinson - got the nobel prize |
DNA structure - double helix
-Franklin: x-ray crystallography -Watson & Crick - 2 strands; franklin's data showed them the results |
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Meselson & Stahl experiment
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Semi-conservative replication
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3 key properties of DNA - the hereditary material
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1) faithful replication
2) must have informational content 3) must be allowed to change (mutability) |
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Chargaff's rules of base composition
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1) total amount of pyrimidine nucleotides (T & C) always equals the total amount of purines (A & G)
2) T=A; C=G |
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Semi-conservative replication
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The 2 strands of the parental double helix unwind, and each specifies a new daughter strand by base-pairing rules.
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Conservative replication
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parent DNA molecule is conserved, and a single daughter double helix is produced consisting of 2 newly synthesized strands
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Dispersive replication
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daughter molecules consists of strands each containing segments** of both parental DNA and newly synthesized DNA.
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Epistasis
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When a mutant allele of 1 gene masks expression of a mutant allele of another gene & expresses its own phenotype instead.
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Linkage hypothesis
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how allele combinations from the parental generations remain together
-genes are physically attached by the segment of chromosome between them -linked alleles tend to be inherited together |
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Recombinant frequency of less than 50% indicates that the genes are...
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LINKED
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Chiasmata forms between ...
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2 nonhomologous sister chromatids
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Cis conformation
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2 dominant, wild type, alleles are present on the same homolog
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Trans conformation
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on different homologs
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Double crossover between 2 chromatids
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produces double recombinant chromatids that have the parental allele combinations at outer loci
-2 crossovers |
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Interference
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when crossovers inhibit each other somewhat in an interaction
I = 1- c.o.c -greater at shorter distances I = 1 at very small distance I = 0 at long distances |
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Coefficient of coincidence
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ratio of observed to expected double recombinants
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Haplosufficiency
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one functioning wild-type copy is enough -- gene product does the job/gives the trait
associated with recessive disorders such as PKU, albinism |
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Haploinsufficiency
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one copy is not enough - gene product is non-functional and 1/2 of wild type is not enough to elicit the trait
*dominant disorders |
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Dominant negative
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mutant gene product inhibits function of WT
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Incomplete dominance
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heterozygote displays an in-between phenotype
ex. red x white = pink |
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Co-dominance
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heterozygote expresses both traits
ex. white & red alleles both show up ex2. A & B blood types are codominant |
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Multiple alleles
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more than 2 versions of a gene
--different interactions --ex. ABO blood types |
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What blood type is the universal donor?
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O because it has no surface detector - will not trigger an immune response
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What blood type is the universal acceptor?
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AB - has both antibodies for A & B, doesn't need one for O
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Pleiotropy
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One gene can affect many different traits
ex. sickle cell -- a change in its shape can affect many different functions in the body |
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Polygenic effect
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more than 1 gene can affect a trait
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Complementation test
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tests # genes that result in same mutation
-complementation occurs when 2 mutants (with the same mutant phenotype) create Wild type offspring ex. aaBB x AAbb = AaBb red x red = white |
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Sum rule
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prob of either of 2 mutually exclusive events occurring is the sum of their individual probabilities
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Genetics
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study of heritable traits
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What, molecularly, are responsible for traits?
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Proteins
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Proteins
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Molecular machines, action molecules; primarily proteins that determine traits
sequence of amino acids folded into some unique structure (3-d) |
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Protein functions
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Enzymes (biological catalysts)
Structure (collegen, myosin/actin) Transport (hemoglobin) Signaling (sending information to other cells) |
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Heredity
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passing of material from parents to offspring
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Do we inherit our proteins?
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No. Every cell has different proteins, might get some from egg & sperm
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DNA
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heritable material;
molecule that contains the information (genes) to create proteins Double stranded molecule |
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Genome
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entire DNA sequence in an organism
-only a small percentage of DNA is genes (2-3% of DNA are genes) |
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Wild type
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normal condition in a population
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Sickle cell mutation
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-normal hemoglobin protein (transports oxygen)
-Sickle cell mutation: change in 1 base pair (nucleotide pair) of the gene -alters the 3-D structure of protein debilitating disorder |
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Transmission genetics
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pattern of inheritance of traits over time
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Law/Principle of Equal segregation
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parent only passes 1 allele to offspring
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Human karyotype
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chromosomes in a human cell
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Interphase
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Prepping phase
G1: prep for DNA replication S: DNA replication G2: prep for DNA division **euchromatin |
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Mitosis
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DNA replicates once, all divide once
-PMAT Prophase, Metaphase, Anaphase, Telophase |
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Prophase of mitosis
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chromosomes condense into more of a structure that you can see under a microscope rather than a large string
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Metaphase of mitosis
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chromosomes line up at the cell equator
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Anaphase of mitosis
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separation of sister chromatids
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Telophase
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cells divide
= 46 dyads = 92 chromatids |
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Meiosis
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production of haploid; DNA replicates 1x, cell divides 2x
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Meiosis I
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separation of the homologous dyads; stages are same but how the chromosomes line up is different from mitosis
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Prophase I
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condensation, homologous dyads pair up, crossing over occurs between homologous chromatids, genetic information traded between the 2 dyads that are crossing over
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Metaphase I
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homologous dyads randomly line up at the equator
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Anaphase I
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dyads are pulled to opposite poles, splitting up dyads
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Telophase I
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division occurs
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Meiocyte
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progenitor, what comes before egg & sperm
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Autosomal recessive
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2 copies of affected gene cause trait; skips generation
-parents are generally unaffected -both parents with affected children/offspring are carriers (heterozygous) -25% chance of having affected offspring -greater incidence when parents are related (inbreeding, consanguineous matings) |
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Autosomal dominant
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ONE copy of affected gene cause trait (you only need one to get the phenotype)
-dwarfism -one parent must be affected; 50% offspring affected |
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X chromosome
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contains many hundreds of genes. Physically, larger than Y; genes are mostly not sex related
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SRY gene
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sex-determining gene on the Y chromosome
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Homogametic sex
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females in humans
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Heterogametic sex
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1/2 sperm get X & 1/2 get Y
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X-linked dominant
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-both female & male
-must be in parent -affected father always affects daughter -never affects sun -if mom is affected, 50% sons & daughters |
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Principle of independent assortment
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different genes don't travel together; during meiosis, the genes don't go together; they sort independently and randomly = unlinked
**mendel was looking at genes on different chromosomes |
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Syntenic genes
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genes on same chromosome, regardless of linkage status (linked or independently assorted)
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Heterochromatine
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densely coiled regions of chromosomes, lower frequency of crossing over
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P arm
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petite/short arm of the chromosome
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Q arm
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long arm of chromosome
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Metacentric
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centromere is about middle
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Submetacentric
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centromere is shifted from center, somewhat off center
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Acrocentric
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centromere is near end
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Gene dosage
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amount of gene product (in most part, proteins) created; most often proportional to the # of genes
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Robertsonian translocation
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fusing 2 different chromosomes (often at centromere)
3% of Down syndrome are due to a Robertsonian 14,21 translocation |
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Telomeres
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ends of chromosomes, looped regions, replicated by telomerase (enzyme)
-postpone the erosion of genes NP*** Blackburn, Greider, Szozak |
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PHOSPHODIESTER BOND
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-The bonds that make the sugar-phosphate bonds
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RNA polymerase I
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rRNA
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RNA polymerase II
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mRNA
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RNA polymerase III
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some snRNA, 5S RNA, tRNA
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Ribozyme
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RNA that functions like an enzyme; enzyme-like behavior
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RNA interference
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blocks mRNA expression -- degrade mRNA and degrades protein expression too
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SR proteins
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stick onto RNA, recruit proteins, enhance proteins
-goes awry, will cause cancer cells |
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hnRNP proteins
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repress/silence proteins
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Beta-Thalassemia
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Deficiency in beta-globin, subunit of hemoglobin
-solution: life-long blood transfusions -associated with decreased oxygen-carrying capacity of red blood cells -Mutations in beta-globin disrupt normal splicing - leading to B-thalassemia phenotype -Inclusion of intron fragment disrupts reading frame resulting in loss of b-globin expression |
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Anti-sense oligonucleotides
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-short single strands of DNA that are designed to be complimentary to a specific sequence
chemically modified to make them stable & nuclease resistant (their structure resembles that of DNA but slightly modified) |
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What distinguishes amino acid from each other?
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R (reactive) groups
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Gel electrophoresis
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-separate the molecules in the mixture
-because the DNA molecules contain charges, fragments will migrate through the gel to the anode at speeds inversely dependent on their size. -technique for separating DNA, RNA, or protein molecules using an electric field applied to a gel matrix -sorting of molecules based on size & charge -larger molecules move more slowly through the gel & smaller molecules move faster through it. -Different sized molecules form distinct bands in the gel |
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Agarose gel
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what a mixture of linear DNA molecules are placed in a well cut
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Ethidium bromide
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-intercalating agent
-used in agarose gel electrophoresis -The bands can be visualized by staining the DNA with ethidium bromide, which causes the DNA to fluoresce in ultraviolet (UV) light |
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Southern blotting
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a technique where a probe can identify one fragment in the mixture of the continuous smear of DNA & no discrete bands produced during electrophoresis.
-get an imprint of DNA molecules on a membrane by using the membrane to blot the gel after electrophoresis is complete (DNA must be denatured first) which allows it to stick to the membrane -Then, membrane is hybridized with labeled probe -An auto-radiogram or photograph of fluorescent bands will reveal presence of any bands on the gel complementary to the probe |
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Northern blotting
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to detect a specific RNA molecule from a mixture of RNAs fractionated on a gel
-RNA separated by electrophoresis is blotted onto a membrane & probed in the same way as DNA is blotted & probed for southern blotting. |
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Western blotting
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used to detect specific proteins in a given extract
-uses gel electrophoresis to separate out denatured proteins -proteins are then transferred onto a membrane, where they are probed (detected) using antibodies specific to the target protein |
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Probe
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complementary DNA + a tag (radioactive or fluorescent)
-this is something that they can identify ex. P32 to track DNA (tagging with radioactivity) |
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plasmid vector, pUC18
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designed for use as a vector for DNA cloning
-insertion into pUC18 is detected by inactivation of the B-galactosidase function of LacZ' ampR: amp resistance -Grow your bacteria -Put your bacteria onto a medium with ampicillin; bacteria will grow (because they have a resistance gene that allows them to grow) -Measure with reporter gene (lacZ) |
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Acrylamide gel
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most often associated with gel electrophoresis -- separation matrix of PROTEIN
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Restriction enzymes
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cut DNA into fragments of manageable size, and many of them generate single-stranded sticky ends suitable for making recombinant DNA
-ex. EcoRI in e.coli: The restriction enzyme EcoRI cuts a circular DNA molecule bearing 1 target sequence, resulting in a linear molecule with single stranded sticky ends. Because of complementarity, other linear molecules with Eco RI-cut sticky ends can hybridize with the linearized circular DNA, forming a recombinant DNA molecule. |
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Taq polymerase
in PCR (amplification of DNA) -NP Winner: Kary Mullis |
-synthesizes the newly separated single strands
-a DNA polymerase that is able to withstand high temperatures required to denature the DNA duplex -result: complementary new strands are synthesized as in normal DNA replication in cells, forming 2 double-stranded DNA molecules identical with the parental double stranded molecule. |
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Duchenne's Muscle Dystrophy (DMD)
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the absence of the dystrophin protein leads to the development of DMD
-dystrophin protein attaches to actin and anchors the plasma membrane (and attaches to the dystrophin associating binding complex - DABC) **important for this protein to be able to hold onto these structures (Connects cytoskeleton of a muscle fiber to the surrounding extracellular matrix through the cell membrane) |
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Reverse transcriptase PCR
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allows you to amplify RNA
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3' to 5' exonuclease activity
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remove incorrect bases "proof read"
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5' to 3' exonuclease activity
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to check double strand DNA
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fidelity of replication
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you don't want to pass on a mutation
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Arthur Kornberg
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Discovered pathway for synthesis of pyrimidines & purines
-isolated DNA polymerases & how they worked |
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Roger Kornberg
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discovered the structure of RNA polymerase II
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Single stranded DNA binding proteins
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keep the 2 strands from getting back together during replication after helicase unzips the strands
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Beta clamp
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help DNA pol III with DNA replication; binds with it and keeps it from dissociating with the template strand
-DNA pol III subunit beta |
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G bands
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darkly stained regions & relatively gene poor on chromosome
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Trisomy 13
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Patau
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Trisomy 18
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Edwards
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Ectopic recombination
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direct repeats within a chromosome align & crossover (same sequence - crossovers within same chromosome)
-causes deletions |
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Inverted breaks
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homologous sequences oriented in opposite directions
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Translocations
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transfer of DNA between non-homologous chromosomes
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Robertsonian translocation
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when 2 different chromosomes fuse often at centromere
problems with sex cells - trisomy, monosomy, normal, translocation 14-21 robertsonian translocation --> down syndrome (3% of the DS cases) |
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Genes
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distinct units/factors that determine heritability
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Transmission genetics
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pattern of inheritance of traits over time
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Allele
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a single gene of the pair of a gene
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Autosomes
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non-sex chromosomes
22 homologous pairs of autosomes *no variety in autosomes between men and women |
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Linked genes
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genes close on same chromosome; do not independently assort
-travel together to gamete |
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100% linkage produces what % of Recombinants?
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0 % RECOMBINATION FREQUENCY and crossing over does not occur
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Promoter
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base sequence that signals start site for gene transcription
-where RNA polymerase binds to promoter DNA to initiate transcription |
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Activators and Repressors are...
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sequence-specific regulatory proteins
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Operator
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short sequence near the promoter that assists in transcription by interacting with regulatory proteins (transcription factors)
-most binding sites for repressors in bacteria |
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Genetic switches
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comprise of the regulatory proteins & their binding sites - control the efficient changes in gene expression that occur in response to environmental conditions
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Allosteric effectors
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control ability of activator/repressor proteins to bind to their DNA target sites
-influence the DNA binding activities of activators & repressors |
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Allosteric site
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acts as a sensor that sets the DNA binding domain in 1 or 2 modes - functional or non-functional
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Structural genes
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segments that encode proteins
lac operon (Z, Y, A) -all 3 genes are transcribed into a single mRNA molecule (either ALL or NONE are synthesized) |
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Operon
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consists of PROMOTER, OPERATOR, STRUCTURAL GENES (Z, Y, A)
segment of DNA that encodes a multigenic mRNA as well as an adjacent common promoter & regulatory protein |
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allosteric transition
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when there is a change in shape
-occurs when the inducer (lactose or any of its analogs) binds to the repressor --> repressor then undergoes an allosteric transition |
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Induction
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relief of repressors
inducers -- in the lac system, lactose or any of its analogs |
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IPTG
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analog of lactose - synthetic inducer to bind to repressor
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Constitutive mutations
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Oc, I-
they caused lac operon structural genes to be expressed regardless of whether inducer was present or not damage the switch that the operon is always ON |
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Oc mutations
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restricted solely to those lac structural genes on the SAME chromosome (cis-acting)
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I- mutations
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trans-acting; gene product can regulate all structural lac operon genes whether residing on the same DNA molecule o on different ones (cis or trans)
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Partial diploids were used to....
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distinguish mutations in the regulatory DNA site (operator) from mutations in the regulatory protein (repressor encoded by I gene)
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Super repressor (Is)
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always causes repression even in the presence of an inducer (exp. constitutive operator Oc)
-dominant to I+ |
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Catabolite repression
**positive control |
when mechanisms prevent the cell from synthesizing enzymes for lactose metabolism when both glucose & lactose are present.
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Catabolite Activator Protein (CAP)
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binds to a specific DNA sequence of the lac operon
-facilitates RNA polymerase's affinity towards the promoter |
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cAMP
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production of cAMP occurs when there is a low level of glucose
-allosteric effector that binds to CAP which then allows it to bind to the CAP binding site -- initiating transcription |
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Promoter-proximal elements
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within 100 base pairs upstream of +1
-more general & cater to many different types of genes -GTF's bind to the promoter-proximal elements - expressed in most cells - available to initiate transcription at any time |
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Enhancers/Upstream Activation Sequences (UAS)
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cis-acting regulatory sequences in DNA where specific transcription factors bind to.
-targets of more specific trans.factors that control the regulation of a smaller subset of genes (cell type specific) |
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Enhancer-blocking insulators
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prevent gene activation when placed between enhancer & promoter
-avoid interfering with regulation of nearby genes |
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SWI-SNF complex
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large multisubunit complex that can reposition nucleosomes in a test tube.
-co-activator -can activate transcription by moving nucleosomes that are covering the TATA box and facilitate the binding of RNA Pol II |
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Mediator
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co-activator
-directly interacts with RNA pol II to recruit it to gene promoters |
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Carboxyl tail domains (CTD) of RNA pol II
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helps recruit other important proteins for transcription ( ex. mediator complex)
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TFIIH
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phosphorylates the carboxyl tail domain when transcription begins
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What does it mean for the genetic code to be degenerate?
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Having more than one codon to code for an amino acid
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Ribosomes are composed of...
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rRNA & proteins
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Where is the amino acid attached to on the tRNA?
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the 3' end
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active site
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where the action takes place in an enzyme; very specific to each enzyme
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