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148 Cards in this Set
- Front
- Back
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Draw Ribose
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lookup
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Draw Deoxyribose
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lookup
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Draw Pyrimidine
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Draw Purine
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Draw U T and C pyrimidines
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lookup
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Draw A and G purines
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lookup
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Draw an AG strand of DNA
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lookup
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What are the forces that stabilize DNA?
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Stacking Interactions
Hydrogen Bonds Hydrophobic Effects Charge-Charge Interactions |
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Dehydrated, more tightly wound form of DNA
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A-DNA
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Form of DNA with no grooves due to G/C rich regions
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Z-DNA
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Absorbance of DNA occurs at this wavelength of light
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260nm
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Single-stranded DNA absorbs more or less light than double stranded?
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More
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Temperature at which half the DNA has separated is what?
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The melting point T(m)
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Nucleotides which separate at a lower temperature and those that separate at a higher temperature
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A/T ; G/C
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Initiation site are often rich in what types of nucleotides?
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A/T
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Differences of RNA to DNA
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Less stable
Uracil Single stranded Multiple copies in different forms Secondary Structures (stem-loops, pseudoknots, base triples) |
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Most abundant RNA (80%). An integral part of ribosomes
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rRNA (Ribosomal RNA)
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Carry activated amino acids to the ribosomes for incorporation into growing peptide chains during protein synthesis. (15%)
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tRNA (transfer RNA)
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Encode the sequences of amino acids in proteins. Carry information from DNA to the translation complex where proteins are synthesized. Least stable of its group. (3%)
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mRNA (messenger RNA)
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Present in all cells. Contribute to catalytic activity of proteins. Associated with RNA modification after RNA sythesis
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small RNA
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In prokaryotes, circular DNA forms what?
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Supercoil
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A class of proteins that bind to DNA to form chromatin only found in eukaryotic cells.
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Histones
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Name the 5 histones
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H1, H2A, H2B, H3, H4
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"beads" of DNA-Histone complexes
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Nucleosomes
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Histone molecules combine to form what?
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Histone Octamer
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Responsible for higher levels of chromatin structure, bringing nucleosomes even closer together.
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H1
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Produces fragments of DNA by binding to specific sequences
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Restriction endonucleases
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Each strand serves as a template for the synthesis of a complementary strand
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Semiconservative
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Replication begins at the origin and proceeds in both directions away from the replication fork to the termination site in what is known as?
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bidirectional
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Basic requirements of replication
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DNA Polymerase
free 3'OH (primer) template DNA strand dNTPs (dATP, dCTP, dGTP, dTTP) |
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Describe the three types of DNA polymerase in E. Coli
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I. Fills gaps
II. Repairs III. Replicates DNA 5'->3'(10 subunits) |
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Arthur Kornberg received the Nobel for what?
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Discovering DNA Polymerase
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DNA polymerase remains bound at the replication fork due to the beta subunit which forms a clamp around DNA. This is characterized as what quality?
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Processive
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DNA polymerase III contains what proofreading mechanism which catalyzes removal of mispaired nucleotides
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3' to 5' exonuclease activity in ε subunit.
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Leading strand is synthesized ______ toward the replication fork.
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continuously
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Lagging strand is synthesized _______ away from the replication fork in short fragments
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discontinuously
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____ produces a DNA dependent RNA _____ for each Okazaki fragment.
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Primase; Primer
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What extends Okazaki fragments across the nick?
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DNA polymerase I
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What removes the RNA primer from Okazaki fragments?
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5'->3' exonuclease activity
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Catalyzes formation of a phosphodiester linkage, sealing the nick, creating a continuous lagging strand in an NAD+ dependent manner
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DNA ligase
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Differences in the replication of eukaryote DNA
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Slower
Smaller replicons (replicating units Enzymes not as well characterized Multiple origins of replication Linear chromosomes Telomeres (ends of chromosomes, repeated) |
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______ recognizes and binds to thymine dimers catalyzing cleavage of the dimers in visible light, repairing UV damage. A form of DIRECT REPAIR.
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DNA photolyase
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Detects and removes damaged DNA leaving a gap filled by DNA polymerase and sealed by ligase.
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Excision repair enzymes
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DNA that is transcribed
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Gene
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Differences in prokaryote transcription
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Transcription/Translation occur simultaneously
Gene in operons - polycistronic No intervening sequences |
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Differences in eukaryote transcription
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Transcription occurs in nucleus; mRNA processed
Each gene has own regulatory element (no operons) Introns must be removed before transport to cytoplasm |
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Basic requirements of transcription
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RNA Polymerase
DNA template (one strand) NTPs (ATP, UTP, CTP, GTP) |
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Describe functions of each α2ββ'ωσ
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Scaffolding
Active site DNA Binding Unknown Initiation |
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RNA Primase is described as a ______ protein
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Oligomeric
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Three phases of transcription
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Initiation
Elongation Termination |
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In initiation of transcription there is no _________
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Primer
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Region of DNA where RNA polymerase binds during transcription initiation
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Promoter
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Common pattern of promoter regions
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Consensus sequence
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Reduces the affinity of core polymerase for nonpromoter regions, speeding up the reaction
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Sigma Factor
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What is the flow of RNA transcription
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5'->3'
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First promoter region in E. Coli
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-10 TATA box (TATAAT)
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Second promoter region in E. Coli
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-35 region (TTGACA)
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Know transcription process from diagram
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lookup
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Describe transcription elongation
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RNA Synthesis
RNA-DNA Hybrid Instability; RNA is displaced by coding strand of DNA |
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In one form of transcription termination, __________ form a hairpin structure that disrupts transcription
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termination sequences
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In another form of transcription termination, __________, triggered destabilization of complexes at pause sites.
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Rho-Dependent
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What is the location of RNA polymerase I, II, and III?
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Nucleolus
Nucleoplasm Nucleoplasm |
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What are the products of RNA polymerase I, II, and III?
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rRNA
mRNA/small RNA tRNA/rRNA/small RNA |
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What is the number of subunits in each RNA polymerase?
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2 Large and 7-12 smaller
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A protein that binds to the promoter region during assembly of the transcription initiation complex.
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Transcription factor
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Genes expressed in every cell (housekeeping) are said to be ______?
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Constitutive
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Genes in cells that are expressed at high levels in some circumstances and not at all in others are said to be _______?
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Regulated
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A regulatory protein which activates transcription of a positively regulated gene is a(n) __________?
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Activator
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Transcription of a negatively regulated gene is prevented by a regulatory protein called a(n) _________?
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Repressor
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Ligands that bind to and inactivate repressors are called ________?
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Inducers
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Ligands that bind to and activate repressors are called _______?
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Corepressors
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Repressor binding sites are known as _______?
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Operators
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Three genes contranscribed from a single promoter to produce a large mRNA molecule containing three separate protein coding reagions
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Lac Operon
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Repressor binding sites are called ______?
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Operators
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The lac repressor locates an operator and blocks transcription very effectively by binding ________ and searching in ______.
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Nonspecifically; One Dimension
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Reactions that transform a primary RNA transcript into a mature RNA molecule are referred to collectively as _______?
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RNA Processing
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Specific nucleotides from the middle of an mRNA primary transcript are removed and the resulting fragments get ligated together to produce mature mRNA. This process is known as ________?
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Splicing
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5'-5' triphosphate linkage protecting mRNA from exonucleases, converts mRNA precursors into substrates, and the site where ribosomes attach during protein synthesis.
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5' cap
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Increases the time required for exonucleases to reach the coding region of mRNA.
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3' poly A tail
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Internal sequences that are removed from the primary RNA transcript are called ______?
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Introns
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Sequences that are present in the primary RNA transcript and in the mature RNA molecule are called ______?
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Exons
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The junction of introns and exons where mRNA precursor is cut and joined is called _____?
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splice sites
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Write the reaction in the urea cycle that actually produces urea
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arginine + H2O -> urea + ornithine
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What enzyme is responsible for incorporating ammonia into metabolism at low ammonia concentrations?
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glutamine synthetase
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Write the reaction catalyzed by glutamine synthetase.
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glutamate + NH3 + ATP -> ADP + Pi + glutamine
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DNA code is degenerate meaning what?
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A particular amino acid may have several codons. (all 64 possible combinations of 3 bases code for something)
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Why is having degenerate DNA a good thing?
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Mutagenic event damage is minimized since the mutated codon will still code for something, not producing a gap in the coding sequence.
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A unique sequence of three-letter words in mRNA that is a potential translation initiation point.
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Reading frame
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The genetic code is ________ meaning that each codon corresponds to one, and only one, amino acid.
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Unambiguous
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Different codons that specify the same amino acid are known as _______?
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Synonymous Codons
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Only 61 of 64 codons specify amino acids. The remaining UGA, UAA, and UAG are known as ________ or ________?
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Termination Codons
Stop Codons |
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The methionine codon AUG specifies the initiation site for protein synthesis and is often called the _________?
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Initiation Codon
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The three base sequence that binds to a complementary codon in mRNA.
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Anticodon
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Different tRNA molecules that can attach to the same amino acid are called ______?
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Isoacceptor tRNA molecules
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Component which catalyzes peptide bond formation
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Ribosome
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Component which carries the activated amino acids
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Aminoacyl-tRNA
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The four components of protein sythesis
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ribosome
accessory protein factors mRNA aminoacyl-tRNA |
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What is the role of IF-3?
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To maintain ribosomal subunits in their dissociated state by binding to the small subunit. Prevents premature formation of the 70S complex.
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What is the role of IF-2?
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To b GTP allowng recognition of the initiator tRNA.
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What is the role of IF-1?
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To bind to 30S subunit and facilitate action of IF-2 and IF-3.
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What is the role of eIF-4?
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A cap binding protein leading to formation of the preinitiation complex
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The structure formed by the binding of many translation complexes to a large mRNA molecule, also known as a polyribosome.
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Polysome
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What is EF-Tu?
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A monomeric protein that contains a binding site for GTP. Inserts aminoacyl tRNA into the A site.
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Enzymatic actvity responsible for catalyzation (formation) of the peptide bond is referred to as _______?
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peptidly transferase
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The position on the ribosome referred to as the exit site aka ____?
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E site
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The third step in the chain elongaotin microcycle where mRNA shifts by one codon relative to the ribosome is known as _____?
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Translocation
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The third elongation factor required by translocation. Moves RNA 3 bases.
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EF-G
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Three accessory protein factors of elongation in eukaryotes
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EF-1alpha
EF-1beta EF-2 |
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Docks the aminoacyl-tRNA in the A site
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EF-1alpha
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Recycles EF-1alpha
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EF-1beta
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Protein factor that carries out translocation in eukaryotes
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EF-2
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Protein factor in prokaryotes that regenerates EF-Tu
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EF-Ts
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Recognizes a termination codon and causes hydrolysis of peptidyl-tRNA, releasing the polypeptide.
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Release Factors
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Binds to GTP enhancing the effects of RF-1 and 2
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RF-3
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Binds to the A site, releasing the polypeptide.
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RF-1 and 2
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Modifications that occur before the polypeptide chain is complete are said to be ______?
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Cotranslational
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Modifications that occur after the polypeptide chain is complete are said to be ______?
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Postranslational
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Portion of the precursor that signals the protein to cross a membrane
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Signal Peptide
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What is thought to be the origin of chloroplasts and mitochondria in eukaryotes?
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They are thought to have been prokaryotic organisms that became endosymbionts
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The properties of water dominate living organisms. There are two reasons for this. What are they?
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Ability to form up to 4 hydrogen bonds per molecule
Its high concentration (abundance) |
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Rotation about the peptide bond is restricted, explain why.
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Because of electronegativity differences, the bond has significant double bond character.
O-C=N-H s- s+ |
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Regularly repeating structure in proteins is called ______________?
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Secondary Structure
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Secondary Structure is primarily composed of _____?
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Alpha helices and Beta sheets
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Gathering of reactants at the enzyme active sites is known as ______ and can produce rate increases of up to 10^8.
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The proximity effect
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What enzyme is associated with hydride transfer only in its biochemical function?
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NAD+
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What is the most common catalytic cofactor?
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Mg2+
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What is the thermodynamic origin of the hydrophobic effect?
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Entropy
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If the delta E of a reaction is negative, are the products or reactants favored?
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Reactants
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Thioester bonds have relatively high free energies of hydrolysis, why?
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The sulfur electrons are less delocalized than on oxygen.
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Plants and cyanobacteria differ from photosynthetic bacteria in their production of _______?
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O2
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In terms of organization, plants and cyanobacteria differ from photosynthetic bacteria how?
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Plants and cyanobacteria employ two photosystems whereas photosynthetic bacteria employ only one.
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Write the reaction catalyzed by the enzyme found only in plants that fix their CO2
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Ribulose-1,5-bisphophate + CO2 -> 2(3-phosphoglycerate)
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What type of bond joins two nucleotides?
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A Phosphodiester Bond
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What is the structural difference between thiamine and uracil?
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Presence of a methyl group on thiamine at C5
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Breaks hydrogen bonds between parental strands of DNA
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DNA Helicase
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What is the main enzyme involved in transcription?
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RNA Polymerase
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The role of a _______ in regulating transcription is to block transcription
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Repressor or Inhibitor
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The role of a(n) _______ is to stimulate transcription.
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Activator
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The lac operon is negatively regulated by the ______
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lac repressor
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The lace operon is positively regulated by the _______.
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CRP-cAMP
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Describe the types of post-transciptional processing in eukaryotic mRNA
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Capping of the 5' ends
Poly A of the 3' ends Removal of introns (splicing) |
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Give 4 characteristics of genetic code.
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Unambiguous
Degenerate Nonoverlapping Universal |
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What is the Shine-Dalgamo sequence?
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Aligns mRNA (in prokaryotes) so that start codon is at the P site
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What is ubiquitin?
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A chemical label(protein) attached to a protein that is to be degraded.
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What is 23S rRNA in 50S subunit?
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Carries out actual peptide bond formation.
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How many ATP for one amino acid into a protein?
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4
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How is ATP used in protein synth?
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2 for coupling to tRNA (activation)
1 for insertion to A site 1 to move mRNA three bases |
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What enzymatic features of glutamate synthetase is the reason it is a controlling enzyme?
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It has a lower Km for ammonium than glutamate dehydrogenase
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Write the reaction used by C4 and CAM plants to reduce photorespiration
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CO2 + Phospoenolpyruvate -> Oxaloacetate + Pi
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