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BIOL 302: Exam 1
Nucleoside
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Base + sugar without a phosphate
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Biosynthesis
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Enzyme-catalyzed process in cells of living organisms by which substrates are converted into more complex products
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1st Law of Thermodynamics
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Energy can be transferred or transformed from one form to another, but it can't be created or destroyed
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2nd Law of Thermodynamics
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Universal tendency of things to become disordered
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Induced fit
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Configurations of both the enzyme and substrate are modified by substrate binding
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Competitive/noncompetitive inhibitors
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Competitive binds to same site, noncompetitive to different one to alter shape
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Nucleotide structure
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Nitrogen-containing ring, five carbon sugar, phosphate group
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Pyrimidine ring
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Single ring
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Purine ring
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Double ring
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Prion diseases
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Caused by rare proteins whose misfolding is infectious
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Protein motifs
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α-helix and β-sheet
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Protein level of organization
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Primary - Linear amino acid sequence
Secondary - Motifs
Tertiary - Fully-folded proteins
Quaternary - Multiple folder proteins interacting with each other
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Ligand
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Molecule that proteins bind to
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Enzyme responsible for phosphorylation
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Kinase
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Enzyme responsible for dephosphorylation
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Phosphatase
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Telomeres
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Contain repeated nucleotide sequences that enable the ends of the chromosomes to be replicated and also cap the end of the chromosome, preventing it from being mistaken by the cell as a broken DNA;
Template DNA extending beyond the DNA that is to be copied, so the end of the strand can be synthesized (was originally occupied by RNA primer)--done by telomerase
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Heterochromatin
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Gene-poor and located around the periphery of the nuclear envelope. More condensed than euchromatin
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Euchromatin
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Normal compaction state, less condense than heterochromatin
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Nucleolus
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Large dark region inside the nucleus, contains genes for ribosomal RNA
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Nucleosome
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Nucleosome core particle and one adjacent DNA linker (DNA between the histones)
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Nucleosome core particles
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8 histone proteins: 2 molecules each of histone H2A, H2B, H3 and H4; ~200 base pairs double-stranded DNA
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Linker histone (H1)
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Pulls nucleosomes together into the 30-nm fiber
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Chromatin-remodeling complexes
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Reposition the DNA wrapped around a nucleosome so it can be accessed by other proteins
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Position effect
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Activity of a gene depends on its position along a chromosome
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Coding/template strands
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Template strand is used to transcribe mRNA, coding strand matches the mRNA sequence (aka what is coded into proteins)
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DNA synthesis direction
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Added to the 3' hydroxyl end of a polynucleotide chain, so the 5'--3' direction
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DNA polymerase
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Catalyzes the addition of nucleotides to the free 3' hydroxyl on the growing DNA strand; proofreads its own work; CAN'T start a completely new chain on its own
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Okazaki fragments
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Short DNA strands on the lagging strand that are later joined together
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Lagging strand DNA synthesis
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RNA primers are made at intervals by primase, DNA polymerase binds to them to synthesize DNA up to previous primer, nucleases remove primers, DNA repair polymerase adds nucleotides left by primer gaps, DNA fragments joined together by DNA ligase
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Primase
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Makes RNA primers on the lagging strand in intervals
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Nuclease
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Removes RNA primers; excises out incorrect nucleotides and replaces them with correct ones
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What adds nucleotides left by RNA primer gaps?
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DNA repair polymerase
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DNA ligase
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Joins DNA fragments after DNA repair polymerase replaces nucleotides left by primer gaps
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Sliding clamp
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Holds DNA polymerase onto the strands and allows it to slide
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DNA helicase
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Separates the strands of parental DNA double helix by breaking down the hydrogen bonds
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Single-strand binding proteins
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Maintain separated strands as single-stranded
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Telomerase
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Adds a series of repeats of a DNA sequence to the 3' end of the template strand, which allows the lagging strand to be completed by DNA polymerase
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Depurination
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Loss of a purine; if uncorrected can lead to loss of a nucleotide pair
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Deamination
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Loss of an amino group from cytosine to be converted to the base uracil; if uncorrected results in the substitution of one base for another when the DNA is replicated
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Basic mechanism of DNA repair
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1) Excision - damage is cut out by one of a series of nucleases, each specialized for a type of DNA damage
2) Resynthesis - original DNA sequence is restored by a repair DNA polymerase, which fills in the gap created by the excision events
3) Ligation - DNA ligase seals the nick left in the sugar-phosphate backbone of hte repaired strand
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Nonhomologous end-joining (NHEJ)
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"Quick and dirty," repairs double-strand breaks by simply bringing the two broken ends together by a specialized group of enzymes and rejoined by DNA ligation
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Homologous recombination
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Flawless repair of DNA double-strand breaks; nuclease generates single-stranded ends at the break by chewing back one of the complementary DNA strands
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Transcript
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RNA strand produced by transcription; has a nucleotide sequence exactly complementary to the template strand
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RNA polymerase
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Transcribes DNA;
Unwinds DNA helix in front of it, adds nucleotides to the RNA chain (in RNA 5'--3' direction), then allows the two strands of DNA behind the polymerase to rewind
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Types of RNA produced in cells
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mRNA - code for proteins
rRNA - forms the core of the ribosome's structure and catalyzes protein synthesis
tRNA - serves as adaptors between mRNA and amino acids during protein synthesis
miRNA - regulates gene expression
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Sigma factor
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On the BACTERIAL RNA polymerase, recognizes promoter on the DNA; after transcription begins, sigma factor is released and polymerase continues synthesizing RNA without it
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Terminator
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Signals polymerase to stop chain elongation; enzyme halts and releases DNA template and newly made mRNA
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First nucleotide transcribed is designated as ___; upstream is _____, downstream is _____
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+1; upstream is negative, downstream is positive
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RNA polymerases in eukaryotic cells; require assistance of:
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RNA polymerase I
RNA polymerase II - mRNA
RNA polymerase III - tRNA;
Require the assistance of a large set of accessory proteins (general transcription factors) to initiate transcription
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General transcription factors (GTFs)
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Assemble at each promoter along with the polymerase before the polymerase can begin transcription
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TATA Box
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Do the TATA box quizlet
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Amino acids
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Do the amino acid quizlet
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Three modifications made to RNA during processing
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Capping at 5' ends with a guanine, polyadenylation at the 3' ends with poly-A tail, splicing
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snRNP
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Small nuclear ribonucleoproteins which contain small nuclear RNAs (snRNAs) and proteins; form core of the spliceosome
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Spliceosome
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Carries out RNA splicing at the intron-exon borders; cleaves out the non-coding portion
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Signal that mature mRNA is ready for export to the cytoplasm
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Cap and poly-A tail of mature mRNA are 'marked' by proteins that recognize the modifications; exon junction complex (EJC) is deposited on the mRNA after successful RNA splicing occurs; nuclear transport receptor associates with it and guides it through the nuclear pore
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Wobble effect
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Codons for same amino acid tend to contain same nucleotides at 1st/2nd positions and vary at the 3rd position
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Stop codons
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UAA, UAG, UGA
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Initiation codon
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AUG, also methionine
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The genetic code is translated by these two adapters:
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1st) Aminoacyl-tRNA synthetase - couples a particular amino acid to its corresponding DNA (called CHARGING)
2nd) tRNA molecule itself, anticodon forms base pairs with the appropriate codon on the mRNA
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Ribosome binding sites
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One for mRNA;
Three for tRNA:
A (aminoacyl-tRNA)
P (peptidyl-tRNA)
E (exit)
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Operons
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Prokaryotes; genes directing different steps in a process are organized into clusters; allows a single prokaryotic mRNA molecule to encode several different proteins
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What mediates protein degradation in eukaryotes?
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Ubiquitin-proteasome pathway (UPP)
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