Chemistry 121 Winter 17 Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State) E-mail: upali@latech.edu Office: 311 Carson Taylor Hall ; Phone: 318-257-4941; Contact me trough e-mail if you have questions Online Tests on Following days December 16, 2016: Test 1 (Chapters 12-13) January 23, 2017 : Test 2 (Chapters 14-16) February 10, 2017 : Test 3 (Chapters 17-19) February 22, 2017 : Test 4 (Chapters 20-22) February 23, 2017: Make Up Exam: Chapters 12-22)

Chapter 22 and GHW#11 Questions Nucleic Acid

Chapter 22: Nucleic Acids 22.1 Types of Nucleic Acids, 798 22.2 Nucleotide Building Blocks, 799 22.3 Nucleotide Formation, 800 22.4 Primary Nucleic Acid Structure, 802 22.5 The DNA Double Helix, 806 22.6 Replication of DNA Molecules, 809 22.7 Overview of Protein Synthesis, 814 22.8 Ribonucleic Acids, 814 22.9 Transcription: RNA Synthesis, 815 22.10 The Genetic Code, 819 22.11 Anticodons and tRNA Molecules, 822 22.12 Translation: Protein Synthesis, 825 22.13 Mutations, 830 22.14 Nucleic Acids and Viruses, 833 22.15 Recombinant DNA and Genetic Engineering, 834 22.16 The Polymerase Chain Reaction, 838 CHEM 121 Winter 2013

Nucleic acids pentose Nucleotide A nucleic acid is a polymer in which the monomer units are nucleotides. There are two Types of Nucleic Acids: DNA: Deoxyribonucleic Acid: Found within cell nucleus for storing and transfering of genetic information that are passed from one cell to other during cell division RNA: Ribonucleic Acid: Occurs in all parts of cell serving the primary function is to synthesize the proteins needed for cell functions. pentose Nucleotide

Heterocyclic Bases Deoxyribose Phosphate Ribose

Nucleotide Formation guanine guanine

Nucleotides

1) Give the names of names of pentose sugars written in Fisher projections (linear form) below

2) Give the names of names of pentose sugars written in Haworth projections (cyclic hemiacetal form) below. (Label the carbon atoms)

Four types of DNA nucleotides

3) Give the names of names of bases and identify them as purines and pyrimidines (Label the atoms in the ring)

Naming DNA Nucleotides Name Base Nucleoside 5'-Nucleotide dAMP Adenine 2'-Deoxyadenosine 2'-Deoxyadenosine-5'-monophosphate dCMP Cytosine 2'-Deoxycytidine 2'-Deoxycytidine-5'-monophosphate dGMP Guanine 2'-Deoxyguanosine 2'-Deoxyguanosine-5'-monophosphate dTMP Thymine 2'-Deoxythymidine 2'-Deoxythymidine-5'-monophosphate

4) a) What is phosphate and phosphate mono/di-esters 4) a) What is phosphate and phosphate mono/di-esters? b) What is a nucleotide? c) Draw the structure of dAMP and GMP

Primary Structure

DNA Double Strands (secondary stucture)

DNA Double Strand Complimentary Base Pair Hydrogen Bonding Weak Hydrogen Bonding

5) Draw the following a) Backbone of a nucleic acid   b) DNA sequence 5'-TGA CGG TAC CC-3'

6) What are the difference between DNA and RNA?    DNA  RNA  number of strands  sugar used  bases used  base pairs  possible locations  full name

Current Interests DNA structure and types Gene Expression Gene Replication Genome Project Cancer and Aging Forensic and Archeology Epigenetic Biotechnology Recombinant-transgenic DNA Cloning and Stem Cell Research Bio-ethics

Replications Prokaryotic Human Chromosomes Eukaryotic

Gene Expression The process by which information from a gene is used in the synthesis of a functional gene product: Proteins Transcription RNA processing RNA export Translation Folding Protein transport

Five types of RNA RNA molecules found in human cells are categorized into five major types, distinguished by their function. Heterogeneous nuclear RNA (hnRNA), Small nuclear RNA (snRNA) Messenger RNA (mRNA) Ribosomal RNA (rRNA) Transfer RNA (tRNA).

RNA Functions

7) Write the type of RNA used for each of the following functions: a) Makes up parts of the ribosome b) Delivers amino acid to the ribosomes c) Codes for proteins

Triplet Nucleotides Codons Second nucleotide U C A G Third nucleotide UUU Phenylalanine (Phe) UCU Serine (Ser) UAU Tyrosine (Tyr) UGU Cysteine (Cys) UUC Phe UCC Ser UAC Tyr UGC Cys UUA Leucine (Leu) UCA Ser UAA STOP UGA STOP UUG Leu UCG Ser UAG STOP UGG Tryptophan (Trp) CUU Leucine (Leu) CCU Proline (Pro) CAU Histidine (His) CGU Arginine (Arg) CUC Leu CCC Pro CAC His CGC Arg CUA Leu CCA Pro CAA Glutamine (Gln) CGA Arg CUG Leu CCG Pro CAG Gln CGG Arg AUU Isoleucine (Ile) ACU Threonine (Thr) AAU Asparagine (Asn) AGU Serine (Ser) AUC Ile ACC Thr AAC Asn AGC Ser AUA Ile ACA Thr AAA Lysine (Lys) AGA Arginine (Arg) AUG Methionine (Met) or START ACG Thr AAG Lys AGG Arg GUU Valine Val GCU Alanine (Ala) GAU Aspartic acid (Asp) GGU Glycine (Gly) GUC (Val) GCC Ala GAC Asp GGC Gly GUA Val GCA Ala GAA Glutamic acid (Glu) GGA Gly GUG Val GCG Ala GAG Glu GGG Gly

8) What is the name given to the short (6­ &10 bp) sequence of bases in the RNA prior to the start of transcription to which the RNA polymerase binds? Promoter (3) : 6­ &10 base pairs

Protein Synthesis 3-base code (triplet) is an “anticodon” Protein molecule Attached amino acid that is carried from cytoplasm to ribosomes

t-RNA

9) How many nucleotides make up a codon? (b) How many different codons are there? (c) How many different amino acids are there?

Thr-Lys-Ala-Start-Leu-Ile-Val-Gly-Ala-Stop 10) Write the RNA sequence transcribed from the following DNA sequence. Then write the amino acid sequence of the protein translated from that RNA. 5'-TGA TTT CGG TAC GAT TAA CAA CCT CGA ATT CC-3‘ 5'-ACU AAA GCC AUG CUA AUU GUU GGA GCU UAA GG-3‘ Thr-Lys-Ala-Start-Leu-Ile-Val-Gly-Ala-Stop

11) What causes the variation in traits that is the basis for evolution?

13) (a) What is gene expression? (b) Why is gene expression regulated?

14) For each of the following mutations in the DNA sequence below, show and explain the effect that the mutation will have on the RNA and protein sequence and, if applicable, on the protein in general. (The numbers for each correspond to the arrows above the sequence.) 5'-TGA TTT CGG TAC GAT TAA CAA CCT CGA ATT CC-3' T in GAT is replaced by C b) T in TAA is replaced by C c) first A in TAA is replaced by G d. C in CAA is replaced by Ae) delete CAA f) delete T in GAT

Epigenetics the term refers to gene expression caused by mechanisms other than changes in the underlying DNA sequence, hence the name epi- (Greek: επί- over, above). neo-Lamarckism: genetic materials in the cytoplasm: environment led to adaptive changes that were passed on.  Genogrphics: Mitochondrial Eve

Genogrphics