Biochem 275: Exam 1
62 Cards in this Set
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Griffith, 1928
Rough & Smooth Bacteria
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Rough wasn't harmful while smooth killed mice
both heated -> mice survived
heat R, not S -> mouse died
heat S, not R -> mouse still died and S was present
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Avery, 1944
DNA vs Protein
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broke up the smooth bacteria into protein and DNA
DNA was the genetic material because when put into the R bacteria it killed the mouse
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Hershey, 1952
Bacteriophage
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Bacteriohage head contains the DNA
Radioactive phosphorus and sulfur to determine that DNA was the genetic material
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Nucleotide
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Deoxyribose + base + phosphoric acid
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Nucleoside
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Deoxyribose + base
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Linus Pauling, 1951
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First helical structure
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Franklin and Gosling, 1951
XRay Diffraction
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concluded there are about 10 base pairs per 360 degrees
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Chargaff's Rule
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1:1 Ratio of purines:pyramidines
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Forces within DNA in increasing order
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Dispersion, Hydrogen, Ionic, Covalent
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G-C bonds vs A-T bonds
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The G-C bonds are about 3 kcals stronger than the A-T bond
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Restriction Enzymes
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Like ecoRI, cut DNA after recognizing specific sequences
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Base + deoxyribose
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-osin
EX: adenosine
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Base + deoxyribose + 1 phosphate
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base-osine monophosphate
Ex: adenosine monophosphate
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Base + deoxyribose + 2 phosphates
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adenosine diphosphate (ADP)
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Base + deoxyribose + 3 phosphates
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Adenosine Triphosphate (ATP)
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ATP, TTP, GTP, CTP
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Building blocks because they link together for the backbone.
Forms 2 phosphate groups
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Type I Restriction Enzymes
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cut at random positions far fro the recognition sequences so they're not used in labs
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Type II Restriction Enzymes
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cut at defined points close to or within the recognition sequences (often used in labs)
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How do bacteria protect their DNA?
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Methylated DNA cannot be recognized or cleaved by the restriction enzymes like ecoRI
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Where does cleavage occur in DNA?
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Phosphate backbone and it regenerated a hydroxyl group
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Sticky Ends: Blunt Ends
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cut in the same spot on both sides and can be ligased back with many other sequences
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Sticky Ends: Cliffs
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strands are uneven and cut at same base resulting in pre-determined binding to specific strands
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Features of Bacterial Plasmid (2)
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origin of replication that is <100 bps
Promote genes of antibiotic resistance
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β-lactam
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Antibiotic resistant gene
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Cloning
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Cleaving DNA and using DNA ligase to add in an antibiotic gene, now some DNA has the resistance
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Gel Electrophoresis
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Agarose gel where smaller strands go farther towards positive charge. Mix DNA with ethidium bromide to make it visible
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mRNA
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Messenger
intermediate between DNA and protein
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tRNA
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Transfer
bind to amino acids and mRNA to link protein
anticodon on one end and a protein on the other to bind together to make polypeptide chains of amino acids
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rRNA
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Ribosomal
Interacts with proteins
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miRNA
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Micro (20 bps)
Tandemly repeated DNA
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snoRNA
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Small Nucleolar (Guide)
Modifies mRNA
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snRNA
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Small Nuclear
Helps proteins cut RNA and put it together
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RNA vs DNA (3 differences)
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RNA uses ribose not (deoxy)
uracil not thymine
RNA is single stranded and can fold on itself
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AU Bond
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Doesn't form a major/minor groove
2 Hydrogen bonds are formed
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UAU Triplet
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now possible because RNA strand can twist
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Genome
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All DNA (bases)
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Isoforms
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Genes encoding for multiple, similar proteins
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Gene
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DNA sequences coding for 1 protein that influences a trait
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Chromatin
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DNA an its associated proteins
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Compactors of DNA
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Histones
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Find binding sites and bring in assembly team
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transcription factors
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Protect DNA from degredation
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DNAse
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Other proteins in Chromatin
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allow DNA to be separated and proteins that keep pairs together
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Nucleosome
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DNA bound to histones
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Gene Density
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Decreases as the complexity increases a lot
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Noncoding DNA in bacteria
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Regulatory sequence that determines expression
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Noncoding sequences in prokaryotes
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introns
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What do we achieve by coding from both 5' to 3' and 3' to 5'?
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There can be many genes overlapping coding for different things
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Base and Ribose modifications result in...
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New functionality
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Pseudouridylation
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uracil mirrors and spins to create a new base pair bond
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2'-O-Methylation
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adds a CH3 to where the H was on the 2' position
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Secondary Structure of RNA
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The folding allows for important purposes
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10 nm fibers
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DNA is wrapped around histones
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30 nm fibers
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DNA is wrapped around histones and then this refolds onto more histones
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Core DNA
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is wrapped around core histones and is 147 base pairs long
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Linker DNA
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is between histones, is 20-60 base pairs long and allows DNA to fold into 30 nm fibers
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The Positive Amino Acids
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lysine and argenine
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Dimers
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H2A and H2B
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Tetramers
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H3 and H4 that are attracted to DNA's negative charge
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Intermediate Stage
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DNA wrapped around tetramer
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Final Stage of DNA Packing
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Two dimers add onto the tetramer and DNA for 8 protein
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N-Tails
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N-Tails are hanging off (as proved by use of protease)
Tails can be methylated or acetylated through these tails, modifying the hisotnes
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Biochem 275: Exam 2