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DNA, RNA, and Amino Acids
Ch. 26.1-10, 13, Ch. 21.1-4, 8, 13-17
ChemV12B, Organic Chemistry II
Molecular Biology
Genes• Gene:
• Genome:
In perspective:• E. coli, a bacteria, has 4,291 genes.• C. elegans, a roundworm, has about 20,000 genes.• Humans share 99% of their genes with mice.• Almost 99.9% of all nucleotide bases are identical from person to person.• Over 50% of human genes have no known function.
Structure of DNA
• DNA:
• Nucleotide:
O
OP
O
O– O
B
D-riboseD-ribose deoxyribose
OHH
OHH
HH
CHO
CH2OH
deoxyribose
OHH
OHH
HH
CHO
CH2OH
Nitrogenous Bases
N
N
N
N
NH H
adenine
N
N
NH2
O
cytosine
N
N
N
N
O
NH2
H
guanine
NH
N
O
O
thymine
DNA Chains
• Nucleic acid:
Base Pairs
major groove
minor groove
A T
OHN
N
N
N
N H N
N
O
H
major groove
minor groove
A T
OHN
N
N
N
N H N
N
O
H
CG
major groove
minor groove
CG
major groove
minor groove
Structures of DNA
• Primary structure:
• Secondary structure:
The Case of the Limes
• Intercalation: 5,6-dimethoxypsoralen5,6-dimethoxypsoralen
[2+2] cycloaddition[2+2] cycloaddition
Replication
• Replication:
• DNA helicase:
• DNA polymerase:
• Leading strand:
• Lagging strand:
Transcription
• Transcription:
• RNA:
RNA
• D-Ribose:
• Uracil:
D-ribose
CH2OH
CHO
HOH2C
OHH
OHH
HOH
O
OH
OH
OH
D-ribose
CH2OH
CHO
HOH2C
OHH
OHH
HOH
O
OH
OH
OH
missing methyl group!
adenine cytosine guanine uracil
N
NH
O
O
NH
NN
N
NH2
O
N
N
NH2
O
N
NN
N
NH2
missing methyl group!
adenine cytosine guanine uracil
N
NH
O
O
NH
NN
N
NH2
O
N
N
NH2
O
N
NN
N
NH2
Structures of RNA
• Primary structure:
• Secondary structure:
Types of RNA
• Messenger RNA (mRNA):
• Transfer RNA (tRNA):
• Ribosomal RNA (rRNA):
• Small nuclear RNA (snRNA):
• Micro RNA (miRNA):
• Small Interfering RNA (siRNA):
Translation
• Translation:
• Codon:
• Initiation:
• Termination:
Genetic Code
Amino Acids
• Amino acid:
• Zwitterion:
• Isoelectric point:
amine carboxylic acid
side chainredrawn
RH
NH2COOH NH2
OH
O
R
amine carboxylic acid
side chainredrawn
RH
NH2COOH NH2
OH
O
R
a-carbon
amine carboxylic acid amino acid zwitterion
NH2
OH
O
NH2 OH
O
O–
O
H3N+
+
amine carboxylic acid amino acid zwitterion
NH2
OH
O
NH2 OH
O
O–
O
H3N+
+
The List of Amino AcidsNAME 3-LETTER 1-LETTER NAME 3-LETTER 1-LETTER
Alanine Ala A Methionine Met M
Cysteine Cys C Asparagine Asn N
Aspartic Acid Asp D Proline Pro P
Glutamic Acid Glu E Glutamine Gln Q
Phenylalanine Phe F Arginine Arg R
Glycine Gly G Serine Ser S
Histidine His H Threonine Thr T
Isoleucine Ile I Valine Val V
Lysine Lys K Tryptophan Trp W
Leucine Leu L Tyrosine Tyr Y
* Non-intuitive abbreviations
Categories of Amino Acids
• Essential/Non-essential:
• Acidic:
• Basic:
• Aromatic:
• Aliphatic:
• Polar:
• Sulfur:
• Twisty:
Acidic Amino Acids
NH2
OH
OH
O
Basic Amino Acids
pKa = 12NH
NH2
NH
OH
O
H2N
pKa = 12NH
NH2
NH
OH
O
H2N
pKa = 10NH2
OH
O
H2N
pKa = 10NH2
OH
O
H2N
pKa = 7
N
NH
OH
O
H2N
pKa = 7
N
NH
OH
O
H2N
Aromatic Amino Acids
O
OHNH
2
O
OHNH
2
NH
Aliphatic Amino Acids
NH2
OH
O
CH3
NH2
OH
O
NH2
OH
O
NH2
O
OH
Polar Amino Acids
NH2
OH
O
NH2
O
NH2
OH
O
NH2
O
NH2
OH
O
OH
O
OH
OH
NH2
Sulfur Amino Acids
NH2
OH
O
S pKa = 9
NH2
OH
O
SHpKa = 9
NH2
OH
O
SH
Twisty Amino Acids
NH2
OH
O
NH2
OH
O
OH
O
NH
Proteins
• Peptide:
• Peptide bond:
O-NH3
+
O
R
+ O-NH2
+
O
R
H
Structures of Proteins
• Primary structure:
• Secondary structure:
parallel
NH
OH
O R
O
NH
NH
OH
O R
O
parallel
NH
OH
O R
O
NH
NH
OH
O R
O
antiparallel
NH
NH
OH
O R
O
NH
NH
O
R
OH
O
antiparallel
NH
NH
OH
O R
O
NH
NH
O
R
OH
O
Structures of Proteins• Tertiary structure:
• Covalent bonds:
• Hydrogen bonding:
• Salt bridges:
• Metallic ion coordination:
• Hydrophobic interactions:
• Quaternary structure:
Sickle Cell Anemia
Genetic Modification
5'-GTGTGTGT-3' 5'-GTGTGTGT...-3'
3'...CACACACA-5' 3'-CACACACA-5'DNA DNA
transcription
galacturonase gene antisense gene
5'-GUGUGUGU-3' 3'-CACACACA-5'
deactivated
transcription
3'-CACACACA-5'5'-GUGUGUGU-3'
5'-GTGTGTGT-3' 5'-GTGTGTGT...-3'
3'...CACACACA-5' 3'-CACACACA-5'DNA DNA
transcription
galacturonase gene antisense gene
5'-GUGUGUGU-3' 3'-CACACACA-5'
deactivated
transcription
3'-CACACACA-5'5'-GUGUGUGU-3'
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