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Bio 97 Midterm Review

Bio 97 Midterm Review. Talar Tfnakjian OH: T, TH 8-9 am Natural Sci I room 2108 ttfnakji@uci.edu Emily Ling OH: Mon 9-10 AM SH 149 Wed 3-4 PM SH 149 linge@uci.edu. About this Review. We are happy that you could make it and glad to see that your are utilizing your resources.

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Bio 97 Midterm Review

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  1. Bio 97 Midterm Review Talar Tfnakjian OH: T, TH 8-9 am Natural Sci I room 2108 ttfnakji@uci.edu Emily Ling OH: Mon 9-10 AM SH 149 Wed 3-4 PM SH 149 linge@uci.edu

  2. About this Review • We are happy that you could make it and glad to see that your are utilizing your resources. • This review is not meant to be a substitute to studying, but a guide to assess your knowledge for your midterm. • We will do our best to cover the important aspects, but we cannot cover every single topic. • Please feel free to stop us and ask questions, that way we can tailor the information to meet your needs. • Complete the evaluation at the end of your packet and turn it in to us and help yourselves with candy on your way out :D

  3. Lecture 1

  4. The Words to Know • Genetics is the study of inherited traits • Genes are the basic units of heredity • The Genome is the entire set of hereditary instructions • (genes + instructions for gene regulation, etc.) • Genotype the genes that comprise an individual. • Alleles (the different “flavors” of a gene) • Phenotype the physical manifestation of the genes; observed traits

  5. The Relationships Between Genotype, Phenotype, and Environment Genotype Phenotype Environment Ex of genotype as a factor: eye color Ex of environment + genotype as a factor: Height Ex of environment as a factor: HIV+ (IF your have CCR5+ wt)

  6. Griffith ExperimentDiscovered: Bacterial Transformation Point: There is SOMETHING, we don’t know what yet, that is being passed for the dead S strain cells to the R strain cells This something is making the R strain turn into S strain cells

  7. Avery (+2 other peoples’) ExperimentImplicated DNA as genetic material

  8. Hershey & Chase ExperimentDetermined that it really is DNA! Image from wikipedia

  9. Summary of Lecture 1 Slide from Professor Yi • Definitions • Gene, genome, genotype, phenotype, environment, wild-type, mutant • Classical versus molecular genetics • Experimental demonstrations that DNA is the genetic material • Make sure you understand the Griffiths, Avery, and Hershey-Chase experiments

  10. Lecture 2

  11. What is DNA composed of? • The basic building block of DNA is deoxyribonucleotide ( deoxyribose sugar, phosphate group, and a Nitrogenous base) • Note that the difference between DNA and RNA is the sugar content ( Ribose in RNA).

  12. 2 H-bonds A T 3 H-bonds G C The bases are categorized by number of rings into: 1-Purines (Adenine , Guanine) • Have two rings 2- Pyrimidines ( Cytosin, Thymidine) • Have one ring The bases are complimentary: Purines pair up with pyrimidines -Adenine pairs with Thymidine Guanine always pairs with Cytosine as a consequence the amount of A is equal to T, likewise amount of G is equal to C (Chargff’s rule)

  13. Putting the Pieces Together The building blocks of DNA polymer (WHAT ARE THEY CALLED AGAIN?) are linked together through phosphodiester bonds between the 5’ Phosphate and 3’ hydroxyl on the ribose sugar.

  14. The Double Helix • Two anti-parallel linear polymers of nucleotides form a right handed helix. • The two chains are connected by hydrogen bonds between the complimentary base pairs and stabilized by base stacking.

  15. DNA Replication • Replication happens in a semi-conservative manner; meaning each parental strand serves as a template for new strands to be synthesized.

  16. How exactly is DNA replicated? • It all begins with the origin of replication

  17. Many enzymes are required for replication to happen • Here’s what happens DNA is always synthesized 5’ to 3’ Everything sounds great, polymerase continuously adds the nucleotides 5’ to 3’ , but wait… This works for one strand only 

  18. Lagging Strand is Synthesized discontinuously • The same enzymes are still in action Tip: a great way to get used to replication and familiarize yourself with the directions is to practice… Problem solved  I will illustrate on the board..

  19. Nothing is perfect…even Replication • Every now and then, polymerase incorporates the wrong nucleotide But luckily, it possesses a proof reading function, where faulty nucleotides are recognized and are replaced by the correct one.

  20. Replication coming to an end... • Finally the RNA Primer is removed by DNA polymerase and Ligase seals the nick by forming a phosphodiester bond.

  21. Lecture 3

  22. Central Dogma Part I DNA • DNA must first be transcribed into a single stranded (ss) messenger RNA Transcription (Lecture 3) RNA

  23. DNA vs. RNA

  24. RNA • RNA uses Uracil instead of Thymine to pair with Adenine: A = U • 2’C has an -OH group (DNA doesn’t) • In our case; RNA is ss • Chargaff’s rules don’t apply

  25. Transcription • Occurs 5’->’3 • Template is READ 3’->5’ • RNA Initiation uses: • TATA box • Promoter-proximal elements • Enhancers and silencers • RNA Polymerase II • Bacteria only have 1 type of RNA polymerase • Eukaryotes have 3; I (rRNA), II (mRNA, snRNA), III (tRNA, 50S of ribosome)

  26. Sense vs. Antisense • Sense/ coding strand has the exact same 5’->3’ sequence of nt’s as the pre-mRNA • Antisense is the TEMPLATE strand.

  27. Initiation is pretty complicated in Eukaryotes • Prokaryotes have the Pribnow Box and a promoter region upstream from start site • Eukaryotes can use enhancers or silencers to regulate rate of transcription

  28. Initiation cont… Enhancers and silencers upstream from the promoter-proximal region Transcription factors (TFs) bind the promoter-proximal elements the can also bind to the enhancers and silencers

  29. Elongation and Termination • Prokaryotes: Hairpin • Eukaryotes: Region of AAUAA or AUUAAA

  30. Splicing Spliceosome recognizes 5’ GU, 3’ AG, and branch point A EXONS: Desired portion of RNA Is part of the final mRNA INTRONS: “In the way”

  31. Alternative Splicing • 1 Gene can encode many different proteins (depending on cell type as well)

  32. Summary Slide from Lecture 3 • Central Dogma • RNA and types of RNA • Transcription • Splicing • Gene expression

  33. Lecture 4

  34. Central Dogma: We’re almost at phenotypic level! • Basic idea of Central dogma is to illustrate how genotype is observable at the phenotype level We went over how DNA is transcribed into RNA, now we will go over how RNA is translated into proteins.

  35. AMIO ACID The Key players of Translation • Ribosomes • Transfer RNA • Aminoacyl-tRNA synthetase

  36. Translation Steps 1- Initiation -Prokaryotes Recognitions of Shine Dalgarno sequence on mRNA -Eukaryotes The small ribosomal subunit binds to 5’ cap and starts scanning until it reaches the start codon. Initiator tRNA binds start codon, initiation factors (IFs), and small ribosomal subunit (30S or 40S) this is called the initiation complex The IFs leave and the large ribosomal subunit Is recruited.

  37. 2- Elongation • Ribosome moves one codon down on mRNA • New tRNA enters the A (acceptor) site • Peptide bond is formed • Ribosome shift ( The new tRNA which was in A site is now in P, and the one is P site is in E site .

  38. 3-Termineation • The ribosome encounter a stop codon • Release factors are bound to the A site • The polypeptide bond is cleaved and the complex is dissociated.

  39. During elongation the polypeptide chain grows in N to C direction

  40. Degeneracy of The Genetic Code • All amino acids except Trp and Met are specified by multiple codons • Synonomous codons (specifying same amino acid) generally differ only in the third base • Much of the redundancy comes from the “wobble” in the codon-anticodon pairing at this third position in the codon • The same anticodon can bind more than one codon • A single tRNA can translate more than one codon The anticodon G can bind C OR U

  41. Crick-Brenner Experiment showed that the codon was a triplet

  42. Lecture 5

  43. Does Everyone Understand Crick-Brenner Experiment? • Two types of mutations: (+) and (-) • Single mutants do not grow, but double (+)(-) mutant can grow • Assumed that each mutation was a single base pair frameshift: (+) is a single bp insertion and (-) is a single bp deletion • The fact that the triple mutant (+)(+)(+) or (-)(-)(-) could grow (phenotype is normal) argues for a triplet code Phenotype + - + + + - - - - + (phage growth)

  44. PCR as in vitro DNA Replication -DNA primers -DNA Template of interest -Heat stable polymerase (Taq) -dNTPs -PCR buffer • Denature the template 95C • Anneal the primers 50-65C • Proceed with elongation 72C

  45. Phenylketonuria (PKU) • Another example of how genotype and environment can play a big role in phenotype

  46. Summary Slice from Lecture 5 • PCR • How does it work? • Compare to in vivo DNA replication in Lecture 2 • Human genome • Most of genome does not encode for protein • Molecular Genotype • The genotype is completely specified by the DNA sequence • Connection between genotype and phenotype

  47. Mitosis

  48. Meiosis

  49. Thank you for your time • We hope this information helped you • Good luck on your midterm…. remember to walk in with confidence 

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