II. Transcription.

III. Translation.

Terms.

A. Mutations in a specific gene were shown to affect the function of one specific protein and no other.
1. In 1902, a British physician, A. E. Garrod, established that in alkaptonuria, there is a block in the breakdown of homogentisic acid, which is then excreted in the urine. No other physiological process appeared to be affected. Garrod proposed that this metabolic error resulted from homozygosity for a recessive gene.

2. Beadle and Tatum, primarily studying Neurospora, showed that a mutation interferes with the function of one specific enzyme. They proposed that there is a one-to-one relationship between genes and proteins.

3. Ingram showed in 1956 that mutation changes the amino acid sequence in the corresponding protein.

B. Proteins consist of chains of amino acids joined together in a linear structure that are folded into a three-dimensional structure in their functional form.
1. Amino acids have a common structure: H₂N–CHR–COOH. The carboxyl group (–COOH) is at one end, usually written on the right. The amino group (H₂N–) is at the other end, usually written on the left.

2. The R side chain differs from one amino acid to another and is what makes them different from each other. Some are positively charged, some are negatively charged, and some are neutral. Some have hydrocarbon-like side chains and are hydrophobic. Amino acids with charged side chains are hydrophilic.

3. Twenty amino acids are found in newly synthesized polypeptide chains. Some may be modified after formation of the protein, but genes code only for 20.

C. Amino acids are joined together by covalent bonds to form a polypeptide chain. The covalent bond that joins amino acids is like any other covalent bond, but it is given a special name, peptide bond. A polypeptide chain may consist of many hundreds of amino acids. However long the chain, at one end there will be an amino group (the N-terminus), and at the other end a carboxyl group (the C-terminus).

D. The sequence of amino acids in a polypeptide chain is called the primary structure. The polypeptide folds to form secondary structures held together by hydrogen bonds and tertiary structures held together by ionic bonds and hydrophobic and other interactions. However, only the primary structure is coded directly by DNA. The folding is a consequence of the primary structure.

A. Only one of the two DNA strands is copied. The copying is catalyzed by an enzyme, RNA polymerase. Transcription begins at a specific point on the DNA and terminates at a specific point. The initial product of transcription is called the primary transcript. Some of the primary transcript codes for proteins and is also called pre-messenger RNA. It is further processed in the nucleus in eukaryotes and then moves to the cytoplasm to serve as messenger RNA.

B. The remainder of the primary transcript functions in protein synthesis but does not code for amino acid sequences.

C. A gene locus contains the information both for the amino acid sequence of a polypeptide chain and the instructions that regulate the amount of transcription. The 5' flanking region is the site at which RNA polymerase binds (also called the promoter region) and is the primary region that regulates the extent of transcription. Many other proteins, called transcription factors, also bind in the promoter region and regulate the amount of transcription.

D. In most eukaryotic genes, pre-mRNA has introns that are spliced out. The remaining exons are joined together to form mRNA. In order to function properly, a cap and a poly-A tail must also be added.

E. When mRNA is read by ribosomes, the direction is 5' to 3'. The DNA strand with the same nucleotide sequence as the mRNA is often called the sense strand. In transcription, the complementary 3' to 5' strand is used for the template and is sometimes called the antisense strand. The sense strand is also called the coding strand, since it has the same nucleotide sequence as mRNA (considering T and U to be equivalent).

A. Three types of RNA are involved.
1. Messenger RNA (mRNA) carries information for amino acid sequences from nucleus to cytoplasm.

2. Ribosomal RNA (rRNA), along with various proteins, forms ribosomes. There are two rRNA components of ribosomes: a large one and a small one. There are hundreds of copies of the genes that code for rRNA.

3. Transfer RNA (tRNA) are small molecules that provide the key for translating the nucleic acid code into the protein code.

1. Each tRNA molecule can bind only to one of the 20 amino acids. That binding is catalyzed by a series of enzymes, each of which recognizes one tRNA and one amino acid.

2. In protein synthesis, each tRNA is "charged" with its specific amino acid by means of a covalent bond involving the carboxyl group of the amino acid.

3. Every cell must be able to make amino acyl-tRNAs for each of the 20 amino acids used to make proteins. Most cells make many more than 20.

B. The genetic code refers to the nucleotide sequences that cause a particular amino acid to be added to the growing polypeptide chain.
1. Such nucleotide sequences are called codons. A codon consists of a sequence of three nucleotides. Since mRNA is read 5' —> 3', codons are also always written in the 5' —> 3' direction.

2. There are 64 possible nucleotide triplets.

a. Sixty-one code for amino acids.
b. Three code for termination of synthesis. No amino acid is added.
c. One codon, AUG, codes for the initiation of synthesis, always with the amino acid methionine (Met). AUG also codes for Met in the interior of polypeptides.
d. Many amino acids are coded by several codons. Therefore, the genetic code is degenerate.
e. All forms of life use the same genetic code; it is universal.

C. In polypeptide synthesis, a ribosome binds to the 5' end of the mRNA and moves toward the 3' end.
1. The first AUG is the initiation codon and starts the assembly of the polypeptide chain from the N-terminal end. Only a tRNA with a complementary sequence (UAC) in the anticodon region will bind, starting the polypeptide with the amino acid Met.

2. The ribosome then moves to the next codon. The tRNA with the matching anticodon binds. The covalent bond that the Met formed with its tRNA is transferred to the amino group of the second amino acid, forming a peptide bond.

3. With its amino acid gone, the first tRNA is now released and recycles by picking up another Met.

4. The ribosome now moves to the third codon, and the process repeats.

5. If the ribosome encounters a termination codon (UAA, UAG, or UGA) as it moves toward the 3' end of the mRNA, the growing polypeptide chain is released and synthesis is over.

6. The initiation codon sets the reading frame. Thereafter, nucleotides are read three at a time.

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