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Week 8 Notes- Bio

by: Raquel Notetaker

Week 8 Notes- Bio BIOL 1010

Raquel Notetaker
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Molecular Bio 1 & 2
Introduction to Biology
Class Notes
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This 55 page Class Notes was uploaded by Raquel Notetaker on Thursday March 24, 2016. The Class Notes belongs to BIOL 1010 at Rensselaer Polytechnic Institute taught by in Spring 2016. Since its upload, it has received 12 views. For similar materials see Introduction to Biology in Biology at Rensselaer Polytechnic Institute.


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Date Created: 03/24/16
DNA, Genes, and Genomes What are the structures, how do we copy them, and how are they arranged? What can we learn from comparison of genomes? What’s the difference between DNA and RNA? Same basic components: base, sugar, phosphate. DNA is double stranded, RNA single stranded. Purines: adenine & guanine Pyrimidines: cytosine, thymine, and uracil. [Purines] in DNA is equal to [Pyrimidines] Although linear sequence of nucleotides appears quite similar, 3-D conformations quite different. RNA DNA Native DNA is a double helix with complementary antiparallel strands. Movie Jim Watson youtube copy Structural representation of DNA molecule Nucleic acid strands are polar, i.e, they have directionality. Animation of DNA replication • Code- Copying the code- Putting it together- DNA synthesis animation Attendance exercise • Based upon what you have learned about the structure of DNA, can you suggest a general mechanism for converting one double-stranded copy of DNA into two identical double-stranded copies of the DNA? • 4-6 sentences posted to Bulleting Board. DNA is flexible about its long axis. It can be bent. DNA packing is essential. Job of histones. TATA-box Binding Protein. Chromatin: compaction. Transcription factor. The Challenge of Packing Movie DNA Packaging Fig. 11-3 What Are Genes? Unit of heredity, either RNA (for some viruses) or DNA Controlling elements sometimes included in definition May be surrounded by sequences of unknown function Found in all cells, in the nuclei of eukaryotic cells, and in mitochondria and chloroplasts of eukaryotes. Protein-coding genes may be solitary or belong to a gene family. Gene for rubisco, the most abundant protein on earth. Other examples are protein kinases, immunoglobulins, olfactory receptors (hundreds of family members) cytoskeletal proteins (actin, tubulin), molecular motors (Kinesin, myosin, dynein Heavily used gene products are encoded by multiple copies of the gene. Ribosomal Gene Clusters From Developmental Biology by Scott Gilbert, Chap 19 How are genes organized on a chromosome? • Choose “flyover” and look at all 4 animations (1, 2, 3, 4) of a portion of chromosome 11 Exon and introns WORD VERSION OF EXONS AND INTRONS THEFOXVGLOHDSRANTOOIWSCHGTELLFAR Surprises Watson Venter, Collins Gilbert The Rise of Genomics: Genome-wide Analysis of Gene Structure & Expression. 2 NOVA Movies - Human Genome Project (on the bottom part of the video pop-up, mouse over the slider and select episodes 4 and episode 5) Robert Krulwich – narrator Movie 1 Movie 2 Eric Lander J Craig Venter Francis Collins Automated DNA sequencer Backup Links: 1, 2 Youtube Links: Movie 1 Movie 2 Automated DNA sequencing- the details From the web site follow the boxes: Techniques, Manipulation, sorting and sequencing, cycle sequencing animation. Run the animation. Complexity The number of base pairs in the human genome is 3.2 x 10 There are about 3 million words in the Bible. It would take a stack of 1000 Bibles to make as many words as there are base pairs in the human genome. Templates II – Transcription and Translation  Molecular Flow of Genetic Information: The process by which information contained in the DNA (gene nucleotide sequence) is templated to an RNA molecule which delivers the instructions for building a protein to the ribosome (site of protein synthesis). Simply stated: How the genotype is converted to the phenotype. Overview of the process in eukaryotic cells DNA Transcription RNA NUCLEUS CYTOPLASM Translation Protein How does transcription work?   Code, copying the code, putting it together, transcription video Attendance exercise  Look at the following diagram and explain what the result would be if RNA polymerase copied both strands of the DNA molecule? Remember you are transcribing a gene in this example. Post your answer to the Bulletin Board. Clicker Question A sequence in a certain stretch of DNA is 5’P-AGTCCGG-3’OH. The RNA transcribed from this template would therefore have the sequence  A 5’-CCGGACU-3’OH  B. 5’-TCAGGCC-3’OH  C. 5’-AGUGGCC-3’OH Figure 10.7_1 DNA A A A C C G G C A A A A Transcription U U U G G C C G U U U U RNA Codon Translation Polypeptide Amino acid Second base First base Third base 10.8 The genetic code is the Rosetta stone of life  Characteristics of the genetic code – Triplet: Three nucleotides specify one amino acid – 61 codons correspond to amino acids – AUG codes for methionine and signals the start of transcription – 3 “stop” codons signal the end of translation 10.8 The genetic code is the Rosetta stone of life – Redundant: More than one codon for some amino acids – Unambiguous: Any codon for one amino acid does not code for any other amino acid – Does not contain spacers or punctuation: Codons are adjacent to each other with no gaps in between – Nearly universal 10.11 Transfer RNA molecules serve as interpreters during translation  Transfer RNA (tRNA) molecules match an amino acid to its corresponding mRNA codon – tRNA structure allows it to convert one language to the other – a specific amino acident site allows each tRNA to carry – An anticodon allows the tRNA to bind to a specific mRNA codon, complementary in sequence – A pairs with U, G pairs with C Amino acid attachment site Hydrogen bond RNA polynucleotide chain Anticodon 10.12 Ribosomes build polypeptides  Translation occurs on the surface of the ribosome – Ribosomes have two subunits: small and large – Each subunit is composed of ribosomal RNAs and proteins – Ribosomal subunits come together during translation – Ribosomes have binding sites for mRNA and tRNAs Growing tRNA polypeptide molecules Large subunit mRNA Small subunit tRNA-binding sites Large subunit mRNA binding site Small subunit Next amino acid to be added to polypeptide Growing polypeptide tRNA mRNA Codons 10.13 An initiation codon marks the start of an mRNA message  Initiation brings together the components needed to begin RNA synthesis  Initiation occurs in two steps 1. mRNA binds to a small ribosomal subunit, and the first tRNA binds to mRNA at the start codon – The start codon reads AUG and codes for methionine – The first tRNA has the anticodon UAC 2. A large ribosomal subunit joins the small subunit, allowing the ribosome to function – The first tRNA occupies the P site, which will hold the growing peptide chain – The A site is available to receive the next tRNA Start of genetic message End Initiation of protein synthesis Large ribosomal subunit Initiator tRNA P site A site Start mRNA codon Small ribosomal 1 subunit 2 10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation  Elongation is the addition of amino acids to the polypeptide chain  Each cycle of elongation has three steps 1. Codon recognition: next tRNA binds to the mRNA at the A site 2. Peptide bond formation: joining of the new amino acid to the chain – Amino acids on the tRNA at the P site are attached by a covalent bond to the amino acid on the tRNA at the A site 10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation 3. Translocation: tRNA is released from the P site and the ribosome moves tRNA from the A site into the P site Peptide Bond Structure 10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation  Elongation continues until the ribosome reaches a stop codon  Applying Your Knowledge How many cycles of elongation are required to produce a protein with 100 amino acids?  Termination – The completed polypeptide is released – The ribosomal subunits separate – mRNA is released and can be translated again Animation: Translation Amino Polypeptide acid P site A site Anticodon mRNA Codons 1 Codon recognition Amino Polypeptide acid P site A site Anticodon mRNA Codons 1 Codon recognition 2 Peptide bond formation Amino Polypeptide acid P site A site Anticodon mRNA Codons 1 Codon recognition 2 Peptide bond formation New peptide bond 3 Translocation Amino Polypeptide acid P site A site Anticodon mRNA Codons 1 Codon recognition mRNA movement Stop codon 2 Peptide bond formation New peptide bond 3 Translocation DNAi  Go to the DNAi website and select Code…Reading the Code…Pieces of the Puzzle. Play the animation in puzzle piece “Breaking the Code”.  Then select Code..Reading the Code…Putting It Together…Translation. Watch Andrew Berry’s wonderful depiction of protein synthesis in real time. 10.15 Review: The flow of genetic information in the cell is DNA RNA  protein  Does translation represent: – DNA RNA or RN protein?  Where does the information for producing a protein originate: – DNA or RNA?  Which one has a linear sequence of codons: – rRNA, mRNA, or tRNA?  Which one directly influences the phenotype: – DNA, RNA, or protein? Transcription DNA 1 mRNA is transcribed mRNA from a DNA template. RNA polymerase Translation Amino acid 2 Each amino acid attaches to its proper Enzyme tRNA with the help of a specific enzyme and ATP. ATP tRNA Anticodon Large Initiator 3 tRNA ribosomal Initiation of subunit polypeptide synthesis The mRNA, the first tRNA, and the ribo- somal sub-units come together. Start Codon Small ribosomal mRNA subunit New peptide Growing bond forming polypeptide 4 Elongation A succession of tRNAs add their amino acids to the polypeptide chain as the mRNA is moved through the Codons ribosome, one codon at a time. mRNA Polypeptide 5 Termination The ribosome recognizes a stop codon. The poly- peptide is terminated Stop codon and released. DNA Transcription 1 mRNA is transcribed mRNA from a DNA template. RNA polymerase Amino acid Translation 2 Each amino acid attaches to its proper Enzyme tRNA with the help of a specific enzyme and ATP. ATP tRNA Anticodon Initiator Large ribosomal 3 tRNA subunit Initiation of polypeptide synthesis The mRNA, the first tRNA, and the ribosomal sub-units come together. Start Codon Small mRNA ribosomal subunit Protein Folding Gone Wrong: Prions So what would happen if there were an outbreak of such a disease in humans, as opposed to a single occurrence? Video: Mad Cow Disease video backup link Prions induce abnormal conformational changes. PrP* Induced Aggregation & Infection. Protein folding is dictated by the chemical properties of the amino acids of which the protein is composed. Some proteins, if deliberately unfolded by treatment with acid or with an agent such as 6M Guanidine – HCl, will re-fold spontaneously. But some fail to do this. How do they fold in vivo? The first known case was ribulose bisphosphate carboxylase in higher plants. It requires special assistance to fold correctly, which is supplied in part by another protein called a chaperonin. A lot of work on this and related proteins has been done at Rensselaer. There are many different kinds of chaperones in nature.


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