Genes are sequences of DNA nucleotides that carry and transmit the information specifying amino acid sequences for protein synthesis. Each DNA molecule contains many genes. The genome refers collectively to the total genetic information coded in a cell. With the exception of reproductive cells, all human cells contain 46 DNA molecules in each cell nucleus. Each DNA molecule corresponds to a chromosome. Each chromosome is packaged with proteins called histones. The complex of chromosome and histones are called nucleosomes.
RNA molecules are responsible for transferring information from DNA to the site of protein synthesis. RNA molecules themselves are synthesized according to the information coded in DNA.
DNA -> mRNA -> Protein
Recall that DNA nucleotides are composed of long chains of bases. A triplet code is a sequence of three bases along a single strand of DNA. Each triplet code is ‘read’ and calls for a specific amino acid. Recall that there are 4 bases in DNA (Guanine, adenine, cytosine, thymine) and 20 amino acids that are linked together in different arrangements to make various proteins. The 4 bases can be arranged into 64 different triplet codes (sequence of three bases). Sixty-one (61) of the codes are matched up to one of the 20 amino acids, a given amino acid can be specified by more than one triplet code, while the remaining three triplet codes act as stop signals and end the protein chain rather than adding an amino acid. As the triplet codes are read, the appropriate amino acid is added to the growing chain, the final result being a protein as determined by the DNA information. The genetic code is universal in all cells.
Transcription: mRNA Synthesis
The first item of business in protein synthesis is the unraveling of the DNA double helix and separation of the two strands of nucleotides. One of the strands will act as a template and will determine the sequence of RNA nucleotides. The template strand is determined by the presence of a specific sequence of DNA nucleotides called the promoter. The sequence is located near the beginning of the gene. RNA polymerase is the enzyme that joins together the aligned ribonucleotides into a strand. When the triplet codes reach a stop sequence or stop signal, the RNA polymerase ends the chain and releases then RNA transcript. As a final touch a series of adenine nucleotides called the poly A tail is added to the end of the transcribed RNA strand. The tail is vital in that it gives the signal necessary to allow the RNA to move out of the nucleus and then bind to ribosomes in the cytoplasm where proteins will be synthesized from the encoded information.
In DNA the three base sequences are called triplet codes, while in RNA the three bases sequences that specify one amino acid are called codons. Therefore, triplet codes and codons are analogous in function. The entire sequence of nucleotides in the entire template strand is transcribed into a primary RNA transcript. Only certain segments of this gene actually code for amino acids. The segments are called exons while the non-coding segments in between exons are called introns. The introns are spliced off of the gene by a spliceosome to form a continuous sequence of exons; the sequence is now called mRNA.
Translation: Polypeptide Synthesis
After the introns are removed, the mRNA moves out into the cytoplasm through the nuclear pores and binds to a ribosome. Each ribosome is composed of proteins and a class of RNA called ribosomal RNA (rRNA), which is a strand transcribed from the DNA in the nucleolus.
Transfer RNA (tRNA) is the link between an amino acid and its mRNA codon since the clover-leaved shaped molecule of tRNA can combine with both. Transfer RNA is synthesized in the nucleus before it moves out into the cytoplasm. An enzyme called aminoacyl-tRNA synthetase (there are 20 of these, specific to each amino acid) links specific amino acids to tRNA molecules. The tRNA molecule and amino acid are then base paired to mRNA with a three base sequence called the anti-codon. The anti-codon specifies the amino acid.
Protein assembly is a three-stage process:
- Initiation of the polypeptide chain begins by binding an anti-codon in an amino acid-tRNA complex to the corresponding codon in the mRNA –ribosome complex. This initial binding is driven by enzymes called initiation factors; the activity of these enzymatic factors regulate the rate of protein synthesis. The initiation phase is the slowest of the three phases in the assembly process.
- Elongation of the polypeptide chain is the second phase. Each amino acid brought to the chain on a tRNA molecule is linked by a peptide bond to the end of the growing protein chain; the free tRNA is then released from the ribosome and will go attach to another amino acid.
- The ribosome acts as a ‘reader’ and when it reaches a termination sequence in the mRNA, the link between the polypeptide chain and tRNA is broken. The completed protein is then released from the ribosome and the ribosome is available for the next mRNA strand coming from the nucleus.
As small protein emerge from the ribosome they undergo folding. Larger proteins will fold within the recess of a small, hollow protein chamber called chaperones. If anything is to be added to the protein chain, such as carbohydrate or lipid derivatives, these occur at the chaperone site. Eventually, mRNA molecules are broken down into nucleotides by cytoplasmic enzymes.
Mitochondrial DNA does not have introns. Mitochondria each have the complete set of machinery to produce its own proteins, the nuclear DNA supplies the rest.
Regulation of Protein Synthesis
Signals from within or outside the cell can turn on or off the transcription of genes. This regulation is performed through allosteric or covalent modulation of a class of enzymes called transcription factors. A pre-initiation complex at the promoter region forms these factors and activates or represses the initiation process (such as the separation of DNA strands, activation of RNA polymerase).
Proteins to be secreted from a cell have a signal sequence that binds to a specific membrane protein on the surface of the granular endoplasmic reticulum and is fed into its lumen, within which the signal sequence is removed and carbohydrate groups are attached (almost all secreted proteins are glycoproteins). Portions of the reticulum bud off, forming vesicles containing the proteins. The vesicles migrate to the golgi apparatus and fuse with the golgi membrane. Within the golgi, groups may be added or removed according to final destinations of the proteins. The proteins are then packaged into vesicles that bud off the surface of the golgi membrane and travel to the plasma membrane, where they fuse and release their contents in the extracellular fluid through a process called exocytosis.
Replication and Expression of Genetic Information
Each cell has 44 autosomes, chromosomes that contain genes that produce the proteins governing cell structure and function, and 2 sex chromosomes containing the genes
which determine sex. Each parent contributes half of these (22) autosomes and (1) sex chromosome. Each pair of autosomes has homologous genes coding for the same protein.
Each time a cell divides, all the 46 chromosomes, each corresponding to a DNA molecule, must be replicated and identical copies passed to each of the new daughter cells. Therefore, all cells (except sperms and eggs) have an identical set of DNA (and therefore genes). What makes one cell different from another is the differential expression of various sets of genes.
DNA is the only molecule in a cell able to duplicate itself without information from some other cell component. During replication, the two strands of double helix separate and each exposed strand acts as a template to which free deoxyribonucleotide triphosphates are base paired. The enzyme DNA polymerase then links the free nucleotides forming a strand complementary to each template strand, forming two identical DNA molecules.
Enzymes that assist in replication are anchored to the DNA just ahead of the site where the strands are separating. So that the enzymes find an anchoring site when the replication process reaches the terminal segment of the DNA molecule, an enzyme called telomerase adds a repeating sequence, called telomere, at the end of the DNA molecule. In the absence of telomerase, each replication results in the shortening of the DNA molecule. Any error in the base sequence during replication is corrected by a mechanism called proofreading.
Cell Division and Cell Cycle
The period between the end of one division and the beginning of the next division is called interphase. A cell spends most of its time in interphase that can be further divided into:
(1) Gl (Gap 1): Period from end of one division to the S phase.
(2) S (Synthesis): Period when DNA replication takes place after G1 phase.
(3) G2 (Gap 2): A brief interval between end of S phase and actual cell division.
M phase is the actual cell division consisting of a nuclear division, mitosis, and a cytoplasmic division, cytokinesis.
The two critical checkpoints that control the progress of the cell cycle are the GI - S and the G2 - M boundaries.
Some cells, e.g., stem cells, divide continuously and proceed continuously through successive cell cycles while some cells, e.g., nerve cells rarely divide and spend most of their time in a phase called G0, which is an arrested G1 with no entry into the S phase. Go can be a temporary phase and a cell can reenter the active cell cycle upon receipt of suitable signals from proteins called growth factors that control the synthesis of the enzymes, cell division cycle kinases (cdc kinases) and cyclins.
The replication of a DNA molecule results into two identical chains called sister chromatids; joined together at a point called the centromere. Just prior to cell division, there are 46 chromosomes, each consisting of two chromatids. The nuclear membrane breaks, the centromeres of the chromosomes become linked to spindle fibers, composed of microtubules, emerging from the centrosome. The 2 centrioles of the centrosome divide and a pair moves to opposite sides of the cell.
The sister chromatids separate at the centromere and move toward opposite centrioles. Cytokinesis finally divides the cell into two. The spindle fibers dissolve, nuclear membrane reappears and the chromatids uncoil.
Any alteration in the DNA nucleotide sequence, produced by factors called mutagens, which break the chemical bonds in DNA and results in loss or incorporation of segments. Also occurs naturally due to errors during replication.
Types of Mutations:
(1) Point mutation - A single base is replaced by a different one. May or may not change an amino acid sequence due to redundancy of genetic code.
(2) Addition/deletion - Whole sections of DNA are added or deleted resulting in misreading of a code or a loss of a set of genes.
A mutation may not have any effect if:
(1) The mutation occurs within an intron segment
(2) The changed amino acid does not influence the structure and function of the polypeptide
(3) The homologous gene is intact and able to produce an intact protein
(4) The amino acid can be obtained from external sources.
Mutation in a sperm or an egg cell does not affect the individual but affects the offspring.
Mutations can contribute by introducing variation, some of which may be competitively better.
DNA Repair Mechanisms
Cells have a number of enzymatic mechanisms that can repair one altered DNA strand based on the template provided by the undamaged strand.
Alleles are variants of the same gene. One allele of each gene is received from each parent. If both alleles are identical the individual homozygous for that gene, if the two are different the individual is heterozygous. The set of alleles in an individual is called its genotype. The expression of the genotypes into proteins producing a specific structural and functional form is called the phenotype.
Each homologous allele for a gene (except for genes in the sex chromosomes) can be translated into proteins. If only one of the alleles is active and produces a character, it is called a dominant allele. If both the alleles need to be active to produce a specific character, these alleles are called recessive.
Genetic disease can result from the inheritance of mutant genes, which produce abnormal structure or function. Familial hypercholesterolemia, cystic fibrosis, sickle-cell anemia, hemophilia, muscular dystrophy are single gene diseases. Polygenic diseases result from several defective genes, each of which by itself has little effect. Examples are diabetes, hypertension, and cancer.
Chromosomal diseases result from addition or deletion of whole or portions of chromosomes during meiosis. Example is Down's syndrome or trisomy 21 in which the egg has an extra copy of chromosome 21.
Cancer is a genetic disorder that is not generally inherited. Arise from mutations in the somatic cells. Results in the failure of the control system that regulates cell division and results into uncontrolled growth.
Dominant cancer-producing genes, called oncogenes, code for abnormal forms of cells surface receptors that bind growth factors and produce a continuous growth signal. Recessive cancer-producing genes, called tumor suppressor genes, fail to produce proteins that inhibit various steps in cell replication.
Abnormal replication of cells forms a tissue mass called tumor. If these cells remain localized it is called a benign tumor, if they invade the surrounding tissue it is called a malignant tumor.
Cancers that develop in epithelial cells are called carcinomas, ones in muscle cells are called sarcomas and ones in white blood cells are called lymphomas. Lung, colon, and breast are the organs most commonly affected. Incidence of cancer increases with age due to the accumulation of defective mutations.
Mutagens that increase the probability of cancerous transformation of a cell are called carcinogens.
Modification of the base sequence of a DNA molecule by addition or deletion of bases. Involves:
(1) Cutting the DNA strands at specific sites, called restriction sites, by bacterial enzymes called restriction nucleases.
(2) Linking the resulting fragments of interest to another DNA molecule using an enzyme called ligase.
The process of transferring DNA from one organism to another is called transfection and the organism into which such a transfer has taken place is called a transgenic organism.
Bacteria can be transfected with human genes to produce large quantities of human proteins. Involves the production of DNA without introns, called complementary DNA (cDNA) by using a viral enzyme called reverse transcriptase on an mRNA template. The requirement for cDNA results from the fact that bacterial DNA does not have introns, nor the mechanism to splice them.