DNA Replication: Semiconservative Nature and Process

• DNA structure and function

DNA Structure

• DNA is a helical double-stranded molecule
• DNA occurs bound to proteins in chromosomes within the nucleus, and as unbound circular DNA in the cytosol of prokaryotes, and in the mitochondria and chloroplasts of eukaryotic cells

Discovery of DNA

• In 1952, Rosalind Franklin took the first clear X-ray diffraction image of DNA
• Franklin's photograph helped confirm the spiral nature of DNA
• Without her consent, her colleague Maurice Wilkins took her photographs to James Watson and Francis Crick
• Watson and Crick suggested that DNA consists of two strands, resembling the uprights of a ladder, linked by 'rungs' which are made of the four types of nucleotides, twisted to form a double helix
• Erwin Chargaff worked out the ratios of the four types of nitrogenous bases [adenine (A), cytosine (C), guanine (G) and thymine (T)] present in the nucleotide subunits
• The amount of guanine was equal to the amount of cytosine, and the amount of adenine was equal to the amount of thymine
• Guanine always hydrogen bonds with cytosine, and adenine always hydrogen bonds with thymine
• Guanine and cytosine share three hydrogen bonds, and adenine and thymine share two hydrogen bonds
• Nucleotides are the base units of DNA

Where DNA is found

• DNA occurs bound to proteins in chromosomes within the nucleus of eukaryotic cells
• DNA is also found in prokaryotes, but as unbound circular DNA in the nucleoid region of the cytosol
• Unbound, circular DNA is also found in the mitochondria and chloroplasts of eukaryotic cells

Structural Properties of DNA Molecule

• Each nucleotide consists of three parts: a five-carbon (pentose) sugar known as deoxyribose sugar, a phosphate group and a nitrogenous base (adenine, cytosine, guanine or thymine)
• Each phosphate group is attached to two sugar molecules by ester' bonds called a phosphodiester bond
• A strand of nucleotides has directionality described using the phrase 5' to 3'
• The 5' end starts with a phosphate and the 3' end finishes with a sugar
• DNA and RNA synthesis occurs in the 5' to 3' direction
• The shape of a DNA molecule is a double helix
• The term 'double' refers to the two strands, which are joined by the weak hydrogen bonds between complementary pairs of nitrogenous bases
• Adenine always pairs with thymine, and cytosine always pairs with guanine
• The term 'helix' describes the helical (spiral) molecular shape: the two linear strands run in opposite directions to each other and are twisted into a helix
• RNA (ribonucleic acid) has a similar structure to DNA, except deoxyribose sugar is replaced with ribose sugar

DNA Function

• DNA carries information coded in segments of its molecule known as genes
• DNA thus enables certain traits to be passed on to the next generation
• A trait is an inheritable characteristic
• DNA stores the code for making proteins
• the inheritance of particular gene variants causes an individual to have a specific combination of proteins in its makeup
• A section of DNA that codes for a specific protein (or polypeptide) is called a gene
• Genes may code for more than one kind of polypeptide, and that genes interact with one another, causing changes in their expression (i.e. in the production of proteins)
• DNA, therefore, controls the growth and development of an organism
• The structural properties of the DNA molecule are what allow DNA replication to occur
• The DNA strands can function as template strands

DNA Replication

• DNA contains the genetic code that determines the structure and function of all living things
• The product of DNA replication is two identical, double-helix DNA molecules, each consisting of one parental strand and one new strand
• DNA replication is referred to as semi-conservative replication because one of the two strands is conserved, or retained, from one generation to the next, while the other strand is new
• DNA replication occurs during the S phase of interphase during the cell cycle
• The purpose of DNA replication is to duplicate the code it carries so that it then can be passed on to daughter cells
• In eukaryotic cells, the chromosomes gain a sister chromatid and become double stranded
• DNA replication occurs in preparation for mitosis and meiosis
• Begins with an enzyme called DNA helicase which unzips' the long molecule of double-stranded DNA by breaking the weak hydrogen bonds between the nucleotides and thus exposing the nucleotide bases
• Hydrogen bonds that hold the two strands of the DNA molecule together are weak, and the enzyme is easily able to separate them
• The junction between the unwound single strands of DNA and the intact double helix is called the replication fork
• DNA polymerase, helps free nucleotides attach to the exposed bases, according to the base-pairing rule
• DNA ligase seals the new short stretches of nucleotides into a continuous double strand that rewinds
• DNA strands are antiparallel, so DNA polymerase moves in opposite directions on the two strands during synthesis
• On the leading strand, DNA polymerase is moving towards the replication fork and synthesises continuously
• On the lagging strand, DNA polymerase is moving away from the replication fork and synthesises in pieces called Okazaki fragments

Coding and Non-Coding DNA

• DNA is a molecule consisting of a sequence of nucleotides
• The entire order of the nucleotides in a human cell's DNA have been sequenced, which is known as the genome sequence
• Coding DNA are regions of DNA sequence which code for proteins
• These sections are also called genes
• The coding DNA specifies sequences of amino acids, which are the building blocks of proteins
• Humans have around 20 000 protein-coding genes
• The majority of the human genome is comprised of non-coding DNA
• The sections of DNA that do not code for a protein are classified as non-coding DNA
• Some non-coding DNA is transcribed into functional non-coding RNA molecules, such as transfer RNAs and regulatory RNAs

Genetic Code

• The genetic code is the term used for the way that the four nitrogenous bases of DNA, adenine, thymine, guanine and cytosine, are ordered
• The base order is read' by cellular machinery and turned into a protein via a process called protein synthesis
• Cellular machinery consist of biological machines' that work to manufacture a biological molecule, such as the transcription machinery
• The translation machine is the ribosome
• In the genetic code, each set of three DNA nucleotides in a row counts as a triplet and codes for an mRNA (messenger RNA) triplet called a codon

Protein Synthesis

• Protein synthesis is the process of making new proteins from the genetic information encoded in DNA
• There are two main processes that facilitate the flow of information from gene to protein: transcription and translation
• Transcription is the synthesis of mRNA using the stored DNA code
• The synthesised mRNA is a chain of RNA nucleotides complementary to the DNA strand, except uracil (rather than thymine) is the base pair of adenine in RNA
• Translation is the synthesis of a polypeptide using the information in the mRNA
• The RNA nucleotide code is translated into an amino acid sequence
• Transcription, a process that produces mRNA from DNA, occurs in the nucleus in eukaryotes
• RNA polymerase moves step by step along the DNA molecule, separating the two strands
• Only the template strand is copied
• The template strand is also known as the antisense or non-coding strand
• The other strand is known as the non-template, sense or coding strand
• The coding strand has the same code as the mRNA, except in RNA uracil replaces thymine
• A promoter attaches help the DNA template strand to locally separate from the non-template strand, initiating transcription
• After the RNA polymerase enables elongation of the strand, the mRNA molecule detaches as pre-mRNA'
• Pre-mRNA requires processing before it exits the nucleus via the nuclear pore
• Stretches of non-coding DNA (known as introns) are removed and the remaining stretches of DNA (known as exons) join to form mature mRNA
• The final process of protein synthesis is translation, which primarily occurs at ribosomes, which are mostly composed of ribosomal RNA (rRNA)
• Translation occurs when mRNA moves out of the nucleus through a nuclear pore, enters the cytoplasm, and travels to a ribosome

Translation Stages

• First stage is initiation.
• Second stage is elongation
• Final stage is termination

Proteins

• Proteins are built of their basic units or monomers (known as amino acids) and are essential to cell structure and functioning
• Enzymes (e.g. lipase and trypsin) are catalysts that increase the rate of virtually all of the chemical reactions within cells
• The protein shape at the active site of an enzyme determines the specificity of the enzyme: only specific enzymes can fit with specific substrates
• In addition to providing mechanical support and functioning as catalysts, proteins transport and store other molecules (such as oxygen), provide immune protection, generate movement, transmit nerve impulses, and control growth and differentiation
• Proteins are built from a selection of 20 different amino acids
• The amino acids are linked together by peptide bonds to form polypeptide chains, which fold and/or are modified to form the protein
• The sequence of amino acids in a polypeptide is determined by the sequence of mRNA codons in a strand of mRNA

Explore DNA replication's semiconservative nature and the crucial role of each enzyme involved. Understand the importance of the replication fork, the directionality of DNA polymerase, and the effect of mutations on the replication process, along with the role of hydrogen bonds.