MOLECULAR BIOLOGY
I.
DNA STRUCTURE AND FUNCTIONS
A. DNA Structure
1. Composed of multiple copies of 4 nucleotides
a) Each nucleotide consists of a phosphate group, pentose sugar (deoxyribose), and
one nitrogen base
b)
The 4 types of nitrogen bases are adenine (a) and guanine (G) and thymine (T)
and cytosine (C)
2. Watson and Crick model of DNA consists of 2 strands of nucleotides, twisted together
a) A pairs with T and G pairs with C held together with hydrogen bonds.
3. DNA versus RNA Structure
a) Compared to DNA, RNA is single stranded, has the sugar ribose, and has
adenine, guanine, cytosine, and uracil (U) as the 4 bases (U replaces T)
B. DNA Functions
1. DNA, as the hereditary material,:
a) Replicate with high accuracy and be transmitted from one generation to the next
generation;
2. DNA Controls the Cell
a) One gene  one protein
b) A gene is a section of a DNA molecule that determines a sequence of amino acids
in a polypeptide chain of a protein
II. TRANSCRIPTION
A. Central dogma of modern genetics
1. DNA not only serves as a template for its own replication, but it also acts in the
nucleus as a template for RNA formation (transcription), which in turn is used to
synthesize proteins (translation) in cytoplasm of the cell at the ribosome.
B. DNA Base Sequence
1. The order of bases in DNA must code for order of amino acids in a polypeptide
2. A codon is a ``triplet'' of 3 nucleotides in messenger RNA (mRNA) that codes for a
particular amino acid
C. Transcription
1. During transcription, the DNA code is passed to mRNA
a)
The mRNA sequence is complementary to DNA (uracil substituted for thymine)
and RNA nucleotides are joined together by RNA polymerase
2. Processing (splicing)
a) Exons
(1) Portion of a gene that is ultimately expressed by coding for the amino acid sequence in a
protein
b) Introns
(1) Portion of a gene that is not expressed (intervening “junk” segments)
(2) This portion is processed (enzymatically removed) before mRNA exits from nucleus
III. CHEMISTRY OF TRANSLATION
A. Amino acids added to carboxyl group of peptide chain
1. Dehydration synthesis reaction
2. Peptide bond formation
3. Catalyzed by ribosomes
IV. AMINO ACID SEQUENCE
A. General
1. The amino acid sequence of every protein is encoded for by the nucleotide sequence
of DNA
2. DNA’s nucleotide sequence is not used directly, but is transcribed into mRNA
3. There are 20 amino acids that are commonly found in proteins
B. The Genetic Code
1. Definition
a) Nucleotide sequences (codons) correspond to specific amino acid types and
translational signals
2. The codon
a) There are 20 amino acids and 4 nucleotide bases
(1) Obviously single nucleotides cannot code for amino acids
b) Codons are sequences of three nucleotides
(1) Three bases are read sequentially to code for an amino acid
c) Special codons
(1) Stop codons
(a) Three codons do not code for any amino acid
(b) UAA, UAG, UGA
(c) These are the site that ribosomes stall on mRNA molecule, resulting in termination of
translation
(2) Start codons
(a) AUG is referred to as a start codon
(b) This is where translation begins
(c) AUG codes for methionine
3. Universality of the genetic code
a) A specific codon codes for the same amino acid, regardless of the species
(1) The genetic code is the same for viruses, bacteria, protists, fungi, plants and animals
(2) The genetic code is thought of as universal
V. TRANSFER RNA AS ADAPTER MOLECULES
A. Amino acids do not have direct affinity for nucleic acids
1. Therefore, mRNA can not directly serve as a template for protein synthesis
2. There must exist an “adapter molecules” which can read the RNA sequence (codon)
and bring with it the correct amino acids
a) This is the function of tRNA molecules
B. Regions of tRNA molecules
1. Anticodon
a) One loop contains three nucleotides that interact with mRNA during translation
(1) These three nucleotides of tRNA are referred to as an anticodon
2. Amino acid attachment site
a) Specific amino acids are covalently attached here by enzymes
C. 61 different tRNAs
1. Differ in their anticodon sequence and amino acid attached
a) There are no tRNA molecules with anticodons for the stop codons (UAG, UAA,
UGA)
D. Anticodon binding to codon
1. General
a) The anticodons of tRNAs are complimentary to the codons of mRNA
b) It is this complimentarily that is essential for tRNA binding to mRNA, not the amino
acid attached to it
VI. RIBOSOMES
A. Composition
1. Two subunits that can dissociate
2. Contains many proteins and several RNA molecules
B. Enzyme
1. Form peptide bonds
C. Scaffold
1. P (peptidyl) tRNA binding site
2. A (aminoacyl) tRNA binding site
VII. PROTEIN SYNTHESIS
A. INITIATION
1. 30S subunit of ribosome binds to mRNA at AUG
a) tRNA-methionine occupies the P site
B. ELONGATION
1. Amino acid-tRNA binds to A-site
a) tRNA must have proper anticodon
b) H-bonds between codon and anticodon nucleotides
2. Peptide bond formation
a) Amino acid in P-site is attached to the amino acid in A site
(1) Covalent bond
3. Translocation
a) Ribosome moves down mRNA to next codon
(1) tRNA in P-site is released
(2) tRNA in A-site is moved to P-site
(a) A-site is now empty
4. Elongation steps repeat, adding more amino acid
C. TERMINATION
1. Ribosome stalls when it reaches a stop codon (UAA, UAG, or AGA)
a) Interactions with another protein, the releasing factor causes the ribosome to
dissociate, releasing the newly synthesized protein