1. Chemistry 121 Winter 17
Introduction to Organic Chemistry and Biochemistry
Instructor Dr. Upali Siriwardane (Ph.D. Ohio State)
Office: 311 Carson Taylor Hall ; Phone: ;
Contact me trough 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)

2. Chapter 22 and GHW#11 Questions
Nucleic Acid

3. 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

4. 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

5. Heterocyclic Bases
Deoxyribose
Phosphate
Ribose

6. Nucleotide Formation
guanine
guanine

7. Nucleotides

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

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

10. Four types of DNA nucleotides

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

12. 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

13. 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

14. Primary Structure

15. DNA Double Strands (secondary stucture)

16. DNA Double Strand Complimentary Base Pair Hydrogen Bonding
Weak Hydrogen Bonding

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

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

19. 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

20. Replications
Prokaryotic
Human Chromosomes
Eukaryotic

21. 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

22. 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).

23. RNA Functions

25. 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

26. 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

27. 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

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

30. t-RNA

31. 9)
How many nucleotides make up a codon?
(b) How many different codons are there?
(c) How many different amino acids are there?

32. 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

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

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

35. 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

36. 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

37. Genogrphics