DNA structure and properties

• DNA and RNA are polymers of nucleotides

DNA/RNA Chemical Structure

• DNA and RNA consist of long polymer chains of chemical units called nucleotides
• DNA has a 3D structure which allows it to store, copy and pass on genetic information
• Each nucleotide has a nitrogen-containing base; adenine (A), cytosine (C), thymine (T), or guanine (G)
• The number of possible polynucleotides is enormous due to the variability in length and sequence of nucleotides
• Each nucleotide consists of a nitrogenous base, sugar, and phosphate group
• Nucleotides are joined by covalent bonds between the sugar of one and phosphate of the next, forming a sugar-phosphate backbone
• Nitrogenous bases project like ribs from the backbone
• A single nucleotide contain a phosphate group, a five carbon sugar and four of its carbon lie in its ring with the 5th sticking above the ring plus a oxygen atom
• The sugar in DNA is deoxyribose which is missing an oxygen atom compared to ribose
• DNA full name is deoxyribonucleic acid, the nucleic portion of the word referring to DNA's location in the nuclei of eukaryotic cells
• Functional groups are responsible for the hydrogen-bonding between particular bases

Purines and Pyrimidines

• Thymine (T) and cytosine (C) are single-ring structures called pyrimidines
• Adenine (A) and guanine (G) are double-ring structures called purines

RNA Structures

• RNA is called ribonucleic acid because its sugar is ribose rather than deoxyribose
• Instead of thymine, RNA has a nitrogenous base called uracil (U)
• RNA has a -OH group attached to the C atom at its lower-right corner
• An RNA polynucleotide chain is identical to a DNA polynucleotide chain except for the presence of ribose and uracil

DNA Replication

• Specific pairing of bases is key to the correct structure of the double helix
• There is functional significance of the base-pairing rules
• A pairs with T, and G pairs with C
• Watson and Crick proposed a copying mechanism for DNA by specific pairing of complementary bases
• Each strand becomes a template for the assembly of a complementary strand from available free nucleotides
• Enzymes link the nucleotides to form the new DNA strands
• The completed new molecules are known as daughter DNA
• When a double helix replicates, each of the two daughter molecules will have one old strand with one newly created strand
• This model for DNA replication is known as the semiconservative model
• The DNA molecule untwists as it replicates and the two new strands are made simultaneously
• E. coli can copy its entire genome in less than an hour and humans can copy theirs in a few hours
• Only one DNA nucleotide per several billion is incorrectly paired
• The DNA molecule of a eukaryotic chromosome has many origins where replication can start simultaneously
• Sugar-phosphate backbones run in opposite directions

DNA Strands

• Each strand has a 3' end and a 5' end
• The primed numbers refer to the carbon atoms of the nucleotide sugars
• At one end of each DNA strand, the sugar's 3' carbon atom is attached to an -OH group
• At the other end, the sugar's 5' carbon is attached to a phosphate group
• DNA polymerases add nucleotides only to the 3' end of the strand and never to the the 5' end
• A daughter DNA strand can only grow in the 5' → 3' direction

Okazaki Fragments & DNA Repair

• One of the daughter strands can be synthesized in one continuous piece by a DNA polymerase working toward the forking point of the parental DNA
• The polymerase molecules must work outward from the forking point, so the new strand are synthesized in short pieces called Okazaki fragments
• DNA ligase then links, or ligates, the pieces together into a single DNA strand
• DNA polymerases carry out a proofreading step that quickly removes incorrectly base-paired nucleotides during replication
• DNA polymerases and DNA ligase are involved in repairing DNA damaged by harmful radiation, and toxic chemicals, DNA replication ensures that all the somatic cells in an organism carry the same genetic information

Transcription Basics

• Transcription is the transfer of genetic information from DNA to RNA
• In eukaryotic cells, transcription occurs in the nucleus
• An RNA molecule is transcribed from a DNA template
• Only one of the DNA strands serves as a template for the newly forming RNA molecule
• RNA nucleotides follow the same base-pairing rules that govern DNA replication, except that U pairs with A
• RNA nucleotides are linked by the transcription enzyme RNA polymerase
• Specific sequences of nucleotides along the DNA mark where transcription of a gene begins and ends
• The "start transcribing" signal is a nucleotide sequence called a promoter
• A promoter is a specific binding site for RNA polymerase and determines which of the two strands of the DNA double helix is used

Transcription Process

• Initiation is the attachment of RNA polymerase to the promoter and the start of RNA synthesis

• Elongation is when the RNA grows longer As RNA synthesis continues, the RNA strand peels away from its DNA template and the two separated DNA strands come back together in the region already transcribed.

• Termination is when the RNA polymerase reaches a sequence of bases in the DNA template called a terminator

• This sequence signals the end of the gene

• The polymerase molecule detaches from the RNA molecule and, in addition to RNA that encodes amino acid sequences, transcription makes two other kinds of RNA that are involved in building polypeptides

• The three kinds of RNA are messenger RNA, transfer RNA, and ribosomal RNA

Translation: from RNA to Protein

• Messenger RNA (mRNA) encodes amino acid sequences and conveys genetic messages from DNA to the translation machinery of the cell
• mRNA is transcribed from DNA, and the information in the mRNA is then translated into polypeptides
• Before leaving the nucleus as mRNA, eukaryotic transcripts are modified, or processed
• RNA processing is the addition of extra nucleotides to the ends of the RNA transcript
• The additions include a small cap (a single G nucleotide) at one end and a long tail (a chain of 50 to 250 A nucleotides) at the other end
• The cap and tail facilitate the export of the mRNA from the nucleus, protect the mRNA from attack by cellular enzymes, and help ribosomes bind to the mRNA

RNA Splicing

• Eukaryotes require RNA processing as noncoding stretches of nucleotides interrupt the nucleotides that actually code for amino acids
• The interruptive sequences include internal noncoding regions called introns, and the coding regions- the parts of a gene that are expressed-are called exons
• Before the RNA leaves the nucleus, the introns are removed, and the exons are joined to produce an mRNA molecule with a continuous coding sequence
• This cutting-and-pasting process, RNA splicing, is catalyzed by a complex of proteins and small RNA molecules

tRNA Structure & Function

• Translation is a conversion between different languages-from the nucleic acid language to the protein language-
• The processed mRNA is required for translation, as well as enzymes and sources of chemical energy, like ATP
• Translation requires ribosomes and a kind of RNA called transfer RNA (tRNA)
• Translation of a genetic message requires an interpreter and a molecular interpreter in the form of tRNA -
• Transfer RNA (tRNA) converts the words of nucleic acids (codons) to the amino acid words of proteins
• tRNA molecules must carry out two functions: (1) picking up the appropriate amino acids and (2) recognizing the appropriate codons in the mRNA
• Each amino acid is joined to the correct tRNA by a specific enzyme
• The amino acid-tRNA complex then furnishes its amino acid to a growing polypeptide chain
• The computer graphic shows a tRNA molecule (green) and an ATP molecule (purple) bound to the enzyme molecule
• Once an amino acid is attached to its appropriate tRNA, it can be incorporated into a growing polypeptide chain and accomplished within ribosomes

tRNA Composition

• A tRNA molecule is made of a single strand of RNA of about 80 nucleotides
• By twisting and folding upon itself, tRNA forms several double-stranded regions
• A single-stranded loop at one end of the folded molecule contains an anticodon of three bases
• The anticodon triplet is complementary to a codon triplet on mRNA.
• During translation, the anticodon on tRNA recognizes a particular codon on mRNA by using base-pairing rules. At the other end of the tRNA molecule is a site where one specific kind of amino acid can attach
• We represent tRNA with the simplified shape to emphasize the anticodon and the amino acid attachment site in modules
• The cell needs mRNA molecules, tRNA, a supply of amino acids and enzymes, and ATP for translation
• The ribosomes are structures which position mRNA and tRNA close together and catalyze the synthesis of polypeptides

Ribosomes

• A ribosome consists of two sub-units, each made up of proteins and a kind of RNA called ribosomal RNA (rRNA)
• Prokaryotic and eukaryotic ribosomes are very similar in function and those of eukaryotes are slightly larger and different in composition
• The ribosome has a binding site for mRNA and the two main binding sites (P and A) for tRNA
• Translation can be divided into initiation, elongation, and termination, as transcription
• The initiation process establishes exactly where translation will begin
• An mRNA molecule binds to a small ribosomal subunit along with the initiator RNA
• An initiator tRNA binds to the start codon, where translation is to begin on the mRNA molecule
• The initiator tRNA fits into the P site, which will hold the growing polypeptide -The A site is vacant and ready for the next amino acid once initiation is complete
• Each addition occurs in a three-step elongation process

1. Codon recognition, when the anticodon of an incoming tRNA molecule, carrying its amino acid, pairs with the mRNA codon in the A site
2. Peptide bond formation, when the polypeptide separates from the tRNA in the P site and attaches by a new peptide bond to the amino acid carried by the tRNA in the A site
3. Translocation, when the P site leaves the ribosome and the site translocates the remaining tRNA to the P site

• Elongation continues until a stop codon reaches the ribosomes A site
• Stop codons do not code for amino acids but instead act as signals to stop translation
• The completed polypeptide is freed from the last tRNA, and the ribosome splits back into its separate subunits.

Mutations

• Mutations can be traced through a difference in a protein to one tiny change in a gene
• An individual with sickle-cell disease has a single different amino acid-wine (Val) instead of glutamate (Glu)
• One nucleotide pair is changed in the coding strand of DNA
• Any change in the nucleotide sequence of DNA is called a mutation

Nucleotide Substitutions

• Mutations within a gene can be divided into nucleotide substitutions, and nucleotide insertions or deletions
• A nucleotide substitution is the replacement of one nucleotide and its base-pairing partner with another pair of nucleotides
• Because the genetic code is redundant, some substitution mutations have no effect at all, causing a silent mutation
• Other substitutions, called missense mutations, do change the amino acid coding
• Some missense mutations have little or no effect on the shape or function of the resulting protein and others prevent the protein from performing its normal function
• Some substitutions, called nonsense mutations, change an amino acid codon into a stop codon
• Mutations involving the insertion or deletion of one or more nucleotides in a gene lead to alter the reading frame of the message.

Mutagenesis

• The production of mutations, called mutagenesis, can occur in a number of ways.
• Spontaneous mutations are due to errors that occur during DNA replication or recombination.
• Other mutations are caused by physical or chemical agents, called mutagens
• High-energy radiation, such as X-rays or ultraviolet light, is a physical mutagen
• Mutations are essential tools for genetic research