Genetic Material: Structure and Function

Structure and Function of the Genetic Material

• Genetics studies genes, including how they carry, express, and are replicated
• Chromosomes are DNA-containing structures that carry hereditary information and contain genes
• Genes encode functional products, often proteins, and are segments of DNA or sequences of nucleotides
• A set of rules that dictates how a nucleotide sequence converts to an amino acid sequence is the genetic code.
• The genetic code exhibits degeneracy, meaning multiple codons can code for a single amino acid.

Genotype and Phenotype

• An organism's genetic makeup, or its genes, is the genotype
• The expression of an organism's genes is the phenotype
• Genomics is the molecular study of entire genomes
• The genome constitutes all the genetic information within a cell

DNA and Chromosomes

• Bacteria typically possess a single, circular, double-stranded DNA chromosome along with associated proteins
• A bacterial cell's original genetic information is in its DNA
• Short tandem repeats (STRs) consist of repeating sequences of noncoding DNA

Genetic Information Flow

• Vertical gene transfer involves the passage of genetic information from one generation to the next
• Horizontal gene transfer involves the transfer of genetic information between cells of the same generation

DNA Structure

• DNA forms a double helix structure
• DNA is a polymer of nucleotides, including adenine, thymine, cytosine, and guanine
• The deoxyribose-phosphate forms as the backbone of DNA
• Hydrogen bonds hold two nucleotide strands together, with A-T and C-G pairings
• Strands are arranged in an antiparallel manner
• The order of nitrogen-containing bases provides the genetic instructions

DNA Replication

• One strand serves as a template for the production of a second strand
• Topoisomerase and gyrase function to relax the DNA strands
• Helicase separates the DNA strands
• When helicase separate the DNA strands a replication fork is created
• Transposase enzymes cut the DNA backbone, resulting in single-stranded "sticky ends"

DNA Replication Elaboration

• DNA polymerase adds nucleotides to the growing DNA strand, exclusively at the 3' end
• Synthesis proceeds in the 5' to 3' direction
• DNA replication is initiated by an RNA primer
• The leading strand undergoes continuous synthesis
• The lagging strand is synthesized discontinuously, forming Okazaki fragments
• To complete replication, DNA polymerase removes RNA primers, and DNA polymerase/ligase join Okazaki fragments

Enzymes in DNA Replication

• DNA gyrase relaxes supercoiling ahead of the replication fork
• DNA ligase makes covalent bonds to join DNA strands, Okazaki fragments, and new segments in excision repair
• DNA polymerases synthesizes DNA; proofreads and repairs DNA
• Endonucleases cuts DNA backbone in a strand of DNA to facilitate repair and insertions
• Exonucleases act to cut DNA from an exposed end of DNA and facilitate repair
• Helicase unwinds double-stranded DNA
• Methylase adds methyl group to selected bases in newly made DNA
• Photolyase uses visible light energy to separate UV-induced pyrimidine dimers
• Primase is a RNA polymerase that makes RNA primers from a DNA template
• Ribozyme is an RNA enzyme that removes introns and splices exons together
• RNA polymerase copies RNA from a DNA template
• snRNP is a RNA-protein complex that removes introns and splices exons together
• Topoisomerase relaxes supercoiling ahead of the replication fork; separates DNA circles at the end of DNA replication
• Transposase cuts DNA backbone, leaving single-stranded sticky ends

DNA Replication Steps Summary

• Enzymes unwind the double-stranded DNA molecule
• Proteins stabilize the unwound DNA
• The leading strand is synthesized continuously by DNA polymerase in the 5' to 3' direction
• The lagging strand is synthesized discontinuously
• RNA primers are synthesized by RNA polymerase and then extended by DNA polymerase
• DNA polymerase digests RNA primers and replaces them with DNA
• DNA ligase joins discontinuous fragments to the lagging strand
• DNA polymerase is typically accurate, with an error rate of only 1 in 10^9 or 10^10 bases due to the proofreading mechanism

Additional DNA Replication Details

• Energy to replicate the strand is supplied by nucleotides
• The hydrolysis of two phosphate groups on ATP provides energy
• Most bacterial DNA replication is bidirectional
• Each offspring cell receives one copy of the DNA molecule
• The capabilities of proofreading of DNA polymerase create high accuracy of replication

RNA and Protein Synthesis

• Ribonucleic acid (RNA) exists as:
• Single-stranded nucleotide
• Containing a 5-carbon ribose sugar
• Containing uracil (U) instead of thymine (T) nucleotides
• Ribosomal RNA (rRNA) forms an integral part of ribosomes
• Transfer RNA (tRNA) transports amino acids during protein synthesis
• Messenger RNA (mRNA) carries coded information from DNA to ribosomes for protein formation

Transcription in Prokaryotes

• Transcription involves synthesizing a complementary mRNA strand from a DNA template
• Transcription initiates when RNA polymerase binds to the promoter sequence on DNA
• Transcription proceeds in the 5' to 3' direction, transcribing only one of the two DNA strands due to the DNA polymerase's 3' start point limitation
• Transcription terminates upon reaching the terminator sequence on DNA

Steps of Transcription Summarized

• RNA polymerase attaches to a DNA sequence termed the promoter, often the TATA box
• RNA polymerase constructs an RNA copy of the gene, known as the transcript
• RNA synthesis continues until RNA polymerase encounters a terminator sequence
• The newly formed RNA molecule and RNA polymerase are then released

Transcription in Eukaryotes

• In eukaryotes, transcription occurs exclusively within the nucleus, while translation takes place in the cytoplasm
• Exons are regions of DNA that code for proteins
• Introns are regions of DNA that do not code for proteins
• Small nuclear ribonucleoproteins (snRNPs) function to remove introns and join exons together

Translation Process

• During translation, mRNA is translated into the "language" of proteins
• mRNA serves as the template from which protein chains are assembled
• Codons, consisting of three mRNA nucleotides, specify particular amino acids
• The 61 sense codons encode the 20 amino acids
• Antisense codons function as stop signals and do not code for any amino acid

Translation Notables

• Translation of mRNA begins at the start codon, AUG (methionine)
• Translation concludes at nonsense or stop codons: UAA, UAG, UGA
• mRNA codons are processed or "read" sequentially
• Translation occurs on ribosomes, which are composed of two subunits (large and small)
• tRNA molecules contain an anticodon that recognizes mRNA codons and carry specific amino acids to the developing polypeptide chain

Translation, additional info

• tRNA molecules transport the necessary amino acids to the ribosome
• tRNA molecules also possess an anticodon that base-pairs with the mRNA codon
• Amino acids join together through peptide bonds
• The nucleic acid sequence within a gene determines the primary protein structure
• 2º, 3º, and 4º structures are defined by folding of the protein as a result of bond formation in amino acid side groups

Translation Steps Simplified

• Initiation: Ribosomal subunits and mRNA assemble together
• The start codon, AUG, binds to tRNA carrying methionine or formylmethionine in the case of bacteria
• Elongation: Subsequent amino acids are added as the ribosome translates each codon
• Ribosomes catalyze the attachment of amino acids to the growing protein chain through peptide bond formation
• Termination: Upon reaching a stop codon, translation ceases, and the ribosome-mRNA complex separates

Bacterial Translation Specifics

• In bacteria, translation initiation occurs before transcription is complete