Nucleic Acids, DNA Replication and ATP

• Nucleic acids:

  • DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are important information-carrying molecules. They are both examples of a group of biological molecules called nucleic acids
  • In all living cells, DNA is the molecule that provides long term storage of genetic information. RNA transfers genetic information from DNA to ribosomes. Ribosomes themselves are formed from RNA, as well as protein
  • Both DNA and RNA are polymers of a monomer units called nucleotides
• Components of a nucleotide:

  • a nucleotide is made up of 3 components

  -a 5-carbon pentose sugar

  -a nitrogen-containing organic base

  -a phosphate group (comprising a phosphate ion)
• Nucleotides:

  • nucleotides are nitrogen-containing organic molecules. They are monomers that join to form polynucleotide strands. The chain is held together because the phosphate group of each nucleotide is linked to the sugar of the next by phosphodiester bonds (strong covalent bonds). The phosphate group and the sugar are identical throughout the chain, so they're called the the sugar-phosphate backbone
  • The only way in which one polynucleotide chain can differ from another is the sequence of bases in the polynucleotide
• Formation of nucleotides:

  • nucleotides are formed by condensation reactions (a water molecule is released)
  • the bonds can be broken in hydrolysis reactions
• Functions of DNA:

  • DNA is important as its structure enables it to play a key role in two essential features of all organisms:
  • inheritance - ensuring that all DNA is passed on, unaltered, onto the next generation
  • protein synthesis
• Components of DNA:

  • the components of a DNA nucleotide are;

  -deoxyribose is the pentose sugar

  -the nitrogen-containing organic base is either adenine (A), thymine (T), guanine (G) or cytosine (C)

  -a phosphate group
• DNA:

  • DNA molecules are huge and consist of 2 polynucleotide chains, one running the opposite way to the other (antiparallel), twisting to form a double-helix
  • because of the complementary pairing, the sequence of bases along one polynucleotide chain determines the sequence along the complementary strand
  • the bases in each strand are held together by hydrogen bonding
  • individually, hydrogen bonds are weak, but in a combination they can be strong
  • hydrogen bonds break and reform, allowing strands to seperate during replication and protein synthesis
• Bases:

  • hydrogen bonding only occurs between certain bases in 2 strands of DNA
  • adenine is complementary to thymine, so binds with 2 hydrogen bonds
  • cytosine is complementary to guanine, so binds with 3 hydrogen bonds
  • in a sample of DNA, the number of adenine bases is equal to the number of thymine bases, and the number of cytosine bases would equal the number of guanine bases
• Components of RNA:

  • a 5-carbon pentose sugar called ribose
  • a nitrogenous organic base - either guanine (G), cytosine (C), adenine (A) or uracil (U)
  • a phosphate group
• RNA:

  • the DNA of a eukaryotic organism is stored in the nucleus, but protein synthesis occurs on ribosomes found in the cytoplasm and the rough endoplasmic reticulum
  • this means that the genetic code on the DNA must be transferred from the nucleus to the cytoplasm
  • sections of DNA that code for polypeptides (genes) are copied onto a single-stranded molecule known as RNA
  • RNA is a ribonucleic acid. It's a relatively short single-stranded polynucleotide made up of RNA nucleotides
• Messenger RNA (mRNA):

  • long single strand
  • made during transcription (1st stage of protein synthesis)
  • complementary copy of the gene but shorter
  • 3 bases = a codon
  • relatively unstable
• Ribosomal RNA (rRNA):

  • ribosomes are made of 2/3 RNA and 1/3 protein
  • ribosomes are responsible for protein synthesis
• Transfer RNA (tRNA):

  • single-stranded chain folded into a clover shape, held by hydrogen bonds
  • has an amino acid binding site
  • 3 bases = an anticodon
  • used in translation(2nd stage of protein synthesis)
• Purpose of DNA replication:

  • DNA replication is needed because: multi-cellular organisms are constantly losing cells which need to be replaced, more cells are needed when the organism grows, extra cells are produced when the parent cell divides, new cells must contain the same genetic information as the parent cell or they would not be able to make the same proteins needed by the cell
• DNA replication:

  • DNA must be able to replicate itself exactly
  • scientists proposed that DNA 'unzipped' as hydrogen bonds between base pairs were broken
  • new polynucleotide strands could then be synthesised using the originals as a template
  • several hypothesis were proposed as to the specific mechanism by which new strands are created
• Conservative replication:

  • the original double helix DNA molecule remains intact and a new DNA molecule is synthesised that contains no part of the original. It is a completely new molecule
• Semi-conservative replication:

  • each of the 2 DNA molecules is composed of 1 strand from the original molecule and 1 newly synthesised strand
  • Meselson and Stahl in 1958 used the results from their experiment with the bacteria E coli and determined that DNA replicated by semi-conservative replication
• Dispersive replication:

  • each of the 2 DNA molecules is composed of sections of the original DNA and newly synthesised DNA randomly interspersed along each strand
• Semi-conservative replication:

  • an enzyme called DNA helicase is required to unwind the double-helix, by breaking the weak hydrogen bonds between the complementary bases in the polynucleotide strands. This separates the strands
  • each exposed strand of DNA can now act as a template for the formation of a new strand
  • free DNA nucleotides (avaliable in the nucleus) are attracted to the exposed bases on the template strands and attach by complementary base pairing
• Semi-conservative replication:

  • through condensation reactions, an enzyme called DNA polymerase joins the adjacent nucleotides together by forming phosphodiester bonds between the deoxyribose of one nucleotide and the phosphate group of the next, forming a new polynucleotide strand
  • the DNA molecule rewinds into a double helix and the process is complete
  • each DNA molecule is comprised of one old/original strand and one newly synthesised strand. This is semi-conservative replication
• Structure of DNA:

  • sugar phosphate backbone/ double-stranded/helix - provides strength/stability/protects bases and hydrogen bonds
  • long/large molecule - can store lots of genetic information
  • helix/coiled - compact/can store lots of DNA in a small amount of space (nucleus)
  • base sequence - allows infromation to be stored and gives a precise genetic code so codes for amino acids/protein
• Structure of DNA;

  • double stranded - replication can occur semi-conservatively/strands act as templates/complementary base pairing/A-T and G-C so accurate replication/identical copies can be made
  • weak hydrogen bonds - replication/unzipping/strand separation/many hydrogen bonds so stable/strong
  • complementary base pairing - allows DNA to replicate itself exactly when cells divide. The weak H bonds allow strands to seperate in this process
  • covalent/phosphodiester bonds in the sugar-phosphate backbone - provides strength/protection
• The 5' and the 3' ends:

  • a polynucleotide has 2 distinct ends; a 3-prime (3') and a 5-prime (5') end
  • the carbons in the sugar are given numbers 1 to 5
  • at the 3' end, carbon 3 of the deoxyribose sugar is closest to the end. At the 5' end, carbon 5 closest to the end
  • each of the 2 polynucleotide chains runs antiparallel (in opposite directions)
  • a new DNA strand is made in a 5' to 3' direction. This is due to the active site of DNA polymerase enzyme only being complementary to the 5' end of the new strand
  • DNA polymerase, therefore, works on opposite directions on each DNA strand
• Evidence for semi-conservative replication:

  • this came from experiments carried out by Meselson and Stahl in 1958, using the bacteria E.coli
  • these have a circular DNA molecule and when cultures of these cells were grown in a medium containing the heavy isotope (15N) all the DNA became labelled with 15N
  • these cultures were then transferred to a medium containing the normal light isotope of nitrogen (14N) and allowed to grow. After some time, samples were taken and the DNA extracted
  • they then measured the density of the DNA (and, indirectly, its 15N and 14N) using density gradient centrifugation
• Density of DNA:

  • the 'lighter' 14N labelled DNA will form a band towards the top of the test tube as it has a lower density
  • the 'heavier' 15N labelled DNA will form a band towards the bottom of the test tube as it has a higher density
  • DNA that was a 'mixture' of 15N and 14N would form a band in between these two
• Summary of the evidence for semi-conservative replication:

  • generation 0 (the parents) - all DNA is 'heavy' (15N), so a single band forms lower down
  • generation 1 - two hybrid molecules of DNA (one strand of each molecule is 'heavy' and one strand is 'light' - newly synthesised), so a single intermediate band forms
  • generation 2 - two hybrid molecules and two all new 'light' DNA (50% hybrid : 50% light) so 2 separate bands from - one intermediate (hybrid) and one 'light' (near the top)

  With each successive generation the proportion of hybrid DNA halves and all the remain DNA is 'light'
• Energy:

  • energy is needed in cells as it allows chemical reactions to take place for the synthesis or breakdown of molecules. In order to do this, energy is required to make and break chemical bonds
  • all living organisms require energy to carry out processes that are essential to life
• Purpose of ATP:

  • active transport - energy is required to move substances against a concentration gradient
  • synthesis of substances (biosynthesis) -energy is required to make large molecules (polymers) from smaller ones (monomers), e.g. synthesis of proteins from condensation of amino acids
  • DNA replication and cell division - energy required for synthesis of new DNA molecules (by DNA replication) prior to cell division. Mitosis and meiosis also require ATP
• Purpose of ATP:

  • muscle contraction/movement
  • photosynthesis - the Calvin cycle in photosynthesis requires ATP for the production glucose
  • maintenance of body temperature (animals) - in the process of ATP production by cells throughout the body, approximately 60% of the energy released is in the form of heat used to maintain body temperature
• ATP (adenosine triphosphate):

  • respiration is the process by which organisms extract the energy stored in complex molecules (e.g. glucose and use it to generate ATP)
  • in this way they obtain energy to fuel their metabolic pathways
  • ATP is the immediate source of energy used by all cells to provide the energy to drive their metabolic reactions
  • metabolism = all the chemical processes that occur in an organism
  • ATP is common to all living things (it is a universal energy currency)
• Components of ATP:

  • ATP is a nucleotide-derivative (modified nucleotide). These are nitrogen containing organic substances
  • ATP occurs as a single molecule (a mononucleotide)
  • ATP is made from 3 components; adenine (a nitrogen containing organic base), ribose (a 5-carbon sugar) and 3 phosphate groups
  • the majority of the chemical energy is stored in the bond between the 3rd and 2nd phosphate - breaking this bond releases the energy
  • any chemical that interferes with the production or breakdown of ATP is fatal to the cell and therefore the organism
• The ATP cycle:

  • ATP is formed from adenosine diphosphate (ADP) and inorganic phosphate (Pi) in a condensation reaction (ATP synthase). This mainly occurs during respiration
  • ATP is hydrolysed back into ADP and Pi in a hydrolysis reaction (ATP hydrolase). This releases the the energy contained in the bond between the phosphates
  • This is a constant cycle in cells as the reactions are reversible
• Synthesis of ATP:

  the synthesis of ATP can occur in 3 ways;

  • photophosphorylation - this takes place in plant cells (chloroplasts) during the reactions of photosynthesis
  • oxidative phosphorylation - this occurs in the mitochondria of plant and animal cells as a result of the process of electron transport in respiration
  • substrate level phosphorylation - this occurs when phosphate groups are transferred from donor molecules to ADP to make ATP
• ATP as an energy source:

  • ATP hydrolysis can be coupled to other energy-requiring reactions in the cell which means that the energy released can be used directly to make the reaction occur and less is lost as heat
  • ATP is not good for long term energy storage due to the instability of its phosphate bonds. Cells can maintain only a few second's supply. ATP is therefore the immediate energy source. This is not a problem as ATP is rapidly reformed from ADP and inorganic phosphate (Pi)
• Comparison of ATP and glucose:

  • in ATP energy is released in a single reaction. In glucose energy release needs several stages
  • therefore in ATP, energy release is immediate. In glucose, energy is not immediately available
  • breaking down ATP releases a small amount of energy - ideal for cells reactions. This prevents energy being wasted as heat. The breakdown of glucose may produce more energy than is required at one time (inefficient - a lot of the energy would be wasted as heat)
• Comparison of ATP and glucose:

  • in ATP, the components are rapidly resynthesised (reusable). In glucose, the components are not resynthesised
  • ATP is soluble and easily moved around inside cells but cannot pass through cell membranes. Glucose is soluble and easily moved around inside cells but can also pass through cell membranes
  • ATP can transfer its phosphate group to other molecules, phosphorylating them and making them more reactive. Glucose cant phosphorylate other molecules