On several occasions, I have referred to DNA as the hereditary material -- we have discussed DNA as being one of the major components of the structures called chromosomes and that these chromosomes are transmitted from generation to generation through reproduction. Today I wish to consider the structure and function of DNA in greater detail.
DNA was first discovered in the 1860’s -- isolated by a doctor from the nuclei of pus cells taken from the bandages of wounded soldiers -- substance had the characteristics of an acid and was thus named "nucleic acid" -- was not known at this time that DNA was the hereditary material.
By the 1940’s it was known that chromosomes in the nuclei of cells carried the genetic instructions and that chromosomes were composed of DNA and proteins called histones -- biologists debated whether DNA or protein was actually the hereditary material.
DNA was shown to be the hereditary material in the early 1950’s through two sets of experiments conducted by Hershey and Chase using a virus, bacteriophage T2 and bacterial cells.
For DNA to be the hereditary material, it must be capable of 3 things:
1. replication -- must be able to make more copies of itself so that genetic information can be passed on from one generation to the next.
2. direct protein synthesis -- the phenotype of an organism is largely a function of the proteins its cells make -- proteins have very precise amino acid sequences and must be assembled according to specific instructions.
3. mutation -- genetic variation, the product of mutation, is the raw material of evolution.
Recall that DNA is a nucleic acid -- a long chain of nucleotides.
DNA nucleotides have the following characteristics:
1. always contain sugar deoxyribose.
2. nitrogenous bases are either
a. purines -- double ring structure: adenine or guanine.
b. pyrimidines -- single ring structure: thymine or cytosine.
Figure 12.6.
DNA Replication: the structure of the DNA molecule is the key to understanding how DNA replicates itself -- structure first proposed by James Watson and Francis Crick -- "the double helix model".
Watson and Crick hypothesized the structure of DNA based on information collected by other scientists.
The most important for Watson and Crick were data collected by Erwin Chargaff -- analyzed characteristics of DNA from cells of many different organisms -- found that amounts of adenine in DNA from any one species always equals the amount of thymine (A = T) and that the amount of guanine always equals the amount of cytosine (G = C).
"Chargaff’s Rule" led Watson and Crick to propose a structure for DNA based on complimentary base pairing -- more in a moment.
Watson and Crick's Double Helix Model -- the double helix can be envisioned as a ladder formed from a double chain of nucleotides that has then been twisted.
1. sides of ladder formed by sugar-phosphate backbone.
2. rungs (or steps) formed by hydrogen bonding between bases of nucleotides in different chains.
3. bases display complimentary base pairing -- purine always bonded to a pyrimidine; more specifically, A always bonds with T and G always bonds with C.
Figure 12.7:
This structure and especially complementary base pairing suggested to Watson and Crick how DNA replication occurs -- notice that each of the two nucleotide chains of the molecule is the "complement" or "mirror-image" of the other -- during replication, each chain serves as a template for the construction of its complementary chain.
Here's how replication occurs:
1. the two strands of the DNA molecule separate -- "unzipped."
2. free nucleotides stockpiled in nucleus pair up with complementary bases on the exposed "parent" strand of DNA.
3. new nucleotides joined together -- new sugar-phosphate backbone formed.
4. process is completed -- two new DNA molecules are present --identical to each other and to the original molecule.
Figure 12.9.
Miscellaneous points:
1. each step is enzymatically controlled -- DNA polymerase responsible for nucleotide assembly on parent strand.
2. energy (ATP) required for breaking and forming bonds between nucleotides.
3. since each new molecule consists of one strand from the old molecule and one strand of a new molecule, the replication process is said to be semiconservative.
4. on rare occasions, noncomplementary bases may pair -- results in a change in the nucleotide base sequence of the DNA molecule -- this is a mutation -- we will explore the importance of the DNA base sequence shortly.
Questions??
Besides the ability to replicate and mutate, DNA also must have the ability to direct protein synthesis -- directions on how to make every protein the cell produces are carried in the DNA = the genetic message -- specifies the exact sequence of amino acids for each protein -- function of a protein is determined by its amino acid sequence, so the DNA instructions must be exact.
Gene = segment of a DNA molecule (chromosome) that contains the instructions of how to construct a complete polypeptide (=protein).
Protein synthesis involves (1) transcription: copying the message from the DNA in the nucleus and sending it to the ribosomes, where amino acids are linked together to form polypeptides; and (2) translation: conversion of the message into protein at the ribosomes.
Let’s first consider the nature of the genetic message.
Question: Where in the DNA molecule is the message located?
Answer: instructions of how to synthesize a polypeptide are encoded as the sequence of nucleotide bases on one-half of the DNA molecule -- this is the genetic code.
Recall that 1) there are 20 different amino acids found in the proteins of living organisms and that 2) there are 4 different bases in DNA nucleotides (A, T, G, C).
Obviously, 1 base cannot specify 1 a.a.; 2 bases at a time also won't work (42 = 16) -- but, 3 bases will give more than enough combinations to specify each a.a. (43 = 64) with combinations to spare -- in addition, some sequences serve as "punctuation" by indicating where the instructions for a specific gene start and stop.
So, amino acids are specified by DNA base triplets found on one-half of the DNA double helix.
A gene contains all the DNA base triplets needed to specify the a.a. sequence of one polypeptide -- e.g. the gene for producing a protein 100 a.a. in length would contain 300 bases (100 base triplets).
Now, let's look at the process of protein synthesis.
I. Transciption -- takes place in the cell nucleus -- DNA triplet sequence copied (transcribed) to a messenger molecule that will carry the message to the ribosomes -- messenger molecule is called "messenger RNA" -- a nucleic acid consisting of a single chain of nucleotides -- RNA nucleotides differ slightly from those in DNA: contain sugar ribose and bases G, C, A, and Uracil (instead of T as in DNA.
A. DNA molecule (gene to be transcribed) unzips as in DNA replication.
B. 1 strand of DNA (strand carrying the message) serves as a "template" for formation of mRNA with the help of the enzyme RNA polymerase.
C. complimentary pairing of bases occurs between DNA bases and RNA nucleotides -- DNA base triplets converted to mRNA codons.
D. RNA nucleotides bonded together into chain (mRNA).
E. mRNA breaks away from DNA and goes out through nuclear envelop to ribosomes in cytoplasm.
F. DNA zippers itself back up.
Figure13.4 illustrates this process.
In the figure on the left, the yellow area represents the portion of the DNA molecule to be transcribed.
The figure on the right shows the exposed template DNA and mRNA being formed.
Here's a detailed view of mRNA transcription (Figure 13.4d and 13.4e):
II. Translation: translation of mRNA message (originally DNA message) into polypeptide (amino acid chain) -- again, energy, enzymes and raw materials required.
A. Ribsomes -- made up of ribosomal RNA (rRNA) -- physically serve as "workbench" for translation -- mRNA attaches to ribosome.
B. transfer RNAs (tRNAs) -- different kinds present in cytoplasm -- each binds a specific amino acid to one end -- other end contains a 3 nucleotide sequenc called the tRNA's anticodon -- a tRNA with a particular anticodon will only attach to a particular amino acid.
Figure 13.8
C. tRNAs bring their a.a. to the ribosome -- find a mRNA codon that is the complement of its anticodon -- a.a.'s on adjacent tRNAs are bound together by a peptide bond -- polypeptide chain begins.
D. tRNAs release their a.a., go back into cytoplasm, pick up another of "their" a.a. and bring it to ribosome.
E. process proceeds until a "stop codon" (UAA, UAG, UGA).
Figure 13.10:
Several important points about protein synthesis and the genetic code:
1. code is degenerate (see Figure 13.7, pg. 204) -- each amino acid is specified by 1-6 different codons, so there are "synonym" codons -- 61 codons specify amino acids and 3 indicate "stop."
Figure 13.7
2. mRNA codons are the complement of the DNA base triplets; tRNA anticodons are the complement of mRNA codons; therefore, tRNA anticodons are the same as DNA base triplets except that U replaces T in anticodons -- by remembering this, you should be able to convert messages from DNA to mRNA to tRNA, etc.
3. the genetic code is universal -- all organisms on earth utilize the same genetic code -- e.g. codon CUU in bacteria specifies the amino acid leucine -- same codon specifies leucine in redwoods, humans, etc. -- can be taken as evidence supporting the hypothesis that all lifeforms on this planet are descendants of a common ancestor that used this genetic code.
4. mutations are changes in the base sequence of a gene that occur in meiosis during DNA replication -- errors in replication that produce new alleles.
a. base deletions.
b. base insertions.
c. base substitutions.
Deletions and insertions are sometimes called frameshift mutations and result in gibberish polypeptides.
Base substitutions may result in amino acid substitutions in the polypetide -- e.g. human hemoglobin is a protein madeup of 4 polypetide chains and a total of about 600 amino acids -- a single base substitution has resulted in the amino acid valine being substituted for glutamate at one place in the molecule -- the resulting allele produces a form of hemoglobin that produces sickle-cell anemia.
Next time: RECOMBINANT DNA AND GENETIC ENGINEERING