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[VERSION 2] GENERAL BIOLOGY I Study Guide for Test 3

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Department
Biological Sciences
Course
01:119:115
Professor
A L L
Semester
Fall

Description
Biology Study Guide Test 3 Nucleic Acid Structure, DNA Replication, and Chromosome Structure Genetic material Genetic Material criteria: Information, replication, transmission, variation Levine 1910: 4 nucleotides are present in about equal amts. Chargaff 1940s: revised Levine’s observations Griffith: bacterial transformation; Smooth (fatal) + Rough (nonfatal) S. pneumonia = transfer of DNA • R WITHOUT capsule = not fatal • S WITH capsule = fatal • Heat-killed S = not fatal • Live R + Heat-killed S = fatal Avery, MacLeod, McCarty: DNA = genetic material; purified DNA transformed type R into fatal; DNase, RNase, and protease don’t work Hershey+Chase: 35S=protein, 32P=DNA; which radiation in cell  DNA = genetic material Nucleic Acids Nucleotides: building blocks of DNA + RNA; made of phosphate group, pentose sugar (deoxyribose/ribose), nitrogenous base (purines [double ring] = G/A; pyrimidines [single ring] = C/T or U; C=G; A=T hydrogen bonding) Strand: linear polymer strand of DNA or RNA; nucleotides = covalent [aka phosphodiester] bonds Double helix: two strands of DNA = complementary, antiparallel, 10 bp per turn, sugar- phosphate backbone; (Chargaff: A=T, C=G); (Franklin: double helix); (Linus Pauling: ball+stick model) Chromosomes: DNA associated with an array of different proteins into a complex structure • Chromosome: discrete unit of genetic material; may be 100s of millions of bp long • Chromatin: DNA-protein complex • Compacting: (1) DNA wraps around histones to form nucleosome (2) Nucleosomes get formed into zigzag structure (3) Zigzag fibers get looped; radial loop domains anchor to nuclear matrix (each chromosome is located in discrete territory; lvl of compaction is not uniform = heterochromatin [very tightly compacted] vs. eucrhomatin) (4) Radial loops further compact to form heterochromatin • When cells divide (metaphase) = more compacted Genome: complete complement of genetic material in an organism DNA Replication Semiconservative Model: DNA replication produces DNA molecules with 1 parental strand and 1 newly made daughter strand. (proved: 15N = parental; 14N = daughter Conservative Model: DNA replication produces 1 double helix with both parental strands and the other with 2 new daughter strands. Dispersive Model: DNA replication produces DNA strands in which segments of new DNA are interspersed with the parental DNA. Origin of replication: site of start point for replication; bidirectional; many in eukaryote; one in prokaryote Bidirectional replication: replication proceeds outwards in opposite directions Primase: adds RNA primer 1. DNA helicase binds to origin of rep and unwinds DNA 5’ to 3’ using ATP. 2. DNA topoisomerase travels ahead of rep fork and relieves coiling caused by helicase. 3. Single-stranded binding proteins coat DNA strands and keep them from reforming a double helix so they can act as templates. 4. Requirements: must be nucleic acid primer; DNA pol III always adds nucleotides at the 3’ end of the primer; DNA replication begins outwards from 2 rep forks. 5. DNA pol covalently links nucleotides 6. DNA rep continues in both directions Leading Strand (begins in direction of replication fork) - DNA synthesized as one long continuous molecule - DNA primase makes 1 RNA primer - DNA pol attaches nucleotides in 5’ to 3’ direction Lagging Strand (opposite direction of replication fork) - DNA synthesized by DNA pol III 5’ to 3’ as okazaki fragments 7. RNA primer removed by DNA pol I and filled with DNA 8. DNA ligase joins adjacent DNA fragments Accuracy of DNA rep 1. hydrogen bonding b/w A/T and G/C is more stable than mismatched combos 2. active site of DNA polymerase is unlikely to form bonds if pairs mismatched 3. DNA polymerase can proofread to remove matching pairs (DNA pol backs up and digests linkages) Important: speed, fidelity, completeness More than one type of DNA polymerase (humans have 12; α: built-in primase subunit) Ex: E. coli (III [replication], I [removal of RNA primers], II, IV, V [repair and replicate damaged DNA]) Telomers: short nucleotide sequences repeated at the end of chromosomes in eukaryotes At 3’ does not have complementary strand; called 3’ overhang No place for upstream primer to be made (DNA pol can’t copy the tip Telomerase attaches to many copies of DNA repeat sequences to the end of chromosomes Shortening of telomeres = cellular senescence High telomerase leads to cancer 1. Telomerase binds to a DNA repeat sequence. 2. T synthesizes a 6 nucleotide repeat sequence. 3. T moves 6 nucleotides to the right + begins to make another repeat. 4. Primase makes an RNA primer near the end of the telomere, and DNA polymerase synthesizes a complementary strand in the 5’ to 3’ direction. RNA primer is removed. Gene Expression One gene = one functional product Transcription: produces mRNA transcript of gene - mRNA: carries message from DNA to ribosome (CODON) - rRNA: structural component of ribosome - tRNA: translates message to bring right a.a. to ribosome (ANTICODON) - regulatory sequence (influences rate of transcription), promoter, transcribed region, terminator 1. initiation: (euk needs 5 transcription factors) Promoter functions as recognition site for sigma factor. RNA polymerase is bound to sigma factor, which causes it to bind to the promoter. DNA is unwound. 2. elongation: Sigma factor is released, and RNA pol. II synthesizes RNA (flipped + U) 3. termination: RNA pol. reaches terminator. It + RNA transcript dissociate from DNA. - Sometimes, termination sequence is transcribed and folds to form hairpin structure to dislodge RNA pol from DNA and terminate transcription RNA processing (eukaryotes only): DNApre-mRNAmRNAProtein - splisosome remove introns (alternative splicing allows for mult. proteins from single gene), add 5’ cap (needed to exit nucleus), add 3’ poly-A tail (100-200 a;↑stability in cytosol) Translation: making polypeptide using mRNA transcript Requires: mRNA, tRNA, ribosomes, translation factors, large E Has: anticodon, acceptor stem for a.a. binding at 3’ end Aminoacyl-tRNA synthetase catalyzes attachment of a.a. to tRNA 1. specific a.a. and ATP bind to aminoacyl-tRNA synthetase 2. a.c. is activated by covalent binding of AMP. Pyrophosphate is released. 3. correct tRNA binds to synthetase. a.a. is covalently attached to tRNA. AMP is released. 4. charged tRNA is released Euk: distinct ribosomes in diff. cellular compartments CYTOSOLIC RIBOSOMES; large (50S) +small (30S) subunits; overall ribosome shape determined by rRNA - ribosomal binding site/guanosine cap at 5’, start codon (more variable), coding sequence, stop codon - start: AUG; stop: UAA/UAG/UGA - A site (aminoacyl), P site (peptidyl), E site (exit) 1. initiation: mRNA binds to small ribosomal subunit, initiator tRNA binds to start codon in mRNA, large ribosomal subunit binds (requires initiation factors and E); initiator tRNA is in P site 2. elongation: synthesis from start to stop codons; aminoacyl tRNA brings new a.a. to A site; catalyzes attachment of a.a. to tRNA; peptide bond formed b/w a.a. at A site and growing polypeptide chain; ribosome moves towards 3’ end of mRNA by one codon; shifts tRNAs at P and A sites to E and P sites 3. termination: complex disassembles at stop codon, releasing completed polypeptide Gene Regulation Gene regulation: ability of cells to control their level of gene expression Important to produce right amount of proteins at right time; conserves E; exception: constitutive genes Survival in prokaryotes vs. homeostasis eukaryotes Prokaryotic Gene Regulation: (transcription; can also control rate of translation; can be regulated at protein/post-translational lev
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