biology topic 1.2

• what are nucleic acids?

  • neucleic acids are biopolymers
  • they are composed of nucleotides which are their monomer component
  • each monomer contains a pentose or 5-carbon sugar (ribose or deoxyribose), a phosphate group and a nitrogeous base.
  • if the sugar is ribose, the polymer is RNA
  • if the sugar is deoxyribose (a version of ribose that is missing an oxygen at carbon 2) then the polymer is DNA
• what are the two types of nitrogenous bases?

  • the two types of nitrogenous bases are purine and pyrimidine
  • in order to form a correct length bond purines must bind with pyrimidines rather than two purines or two pyrimidines binding together
  • the purines are: Guanine (DNA, RNA) and Adenine (DNA, RNA)
  • the pyrimidines are: Cytosine (DNA, RNA), Thymine (DNA) and Uracil (RNA) (Uracil is similar to Thymine but it lacks the methyl group (CH3))
• what are the different types of RNA?

  messenger RNA (mRNA)

  • a complementary copy of a portion of DNA, it carries a fraction of DNA code (called a codon (three section/bases/nucleotides in a codon form an amino acid which form proteins)) to the ribosomes for processing and are linear in shape.

  transfer RNA (tRNA)

  • decodes mRNA into a polypeptide, brings amino acids to the ribosomes, they are clover shaped and carry anticodons.

  ribosomal RNA (rRNA)

  • forms the ribosomes and is the structure for translation, they are spherical in shape and there are no codons/anticodons present.
• how do DNA nucleotides bond with together?

  • the DNA nucleotides join to one another with phosphodiester bonds that form between the phosphate group of one nucleotide and the sugar of the next. this forms a strand that is known as the sugar-phosphate backbone
  • the two strands of DNA join together with hydrogen bonds at the bases of the two strands
  • these two strands run in opposite directions, so are said to be anti-parallel
• how do RNA nucleotides join together?

  • RNA nucleotides join together with phosphodiester bonds that form between the phosphate group of one nucleotide and the sugar of the next. this forms a strand which is also know as the sugar-phosphate backbone
  • RNA is single stranded so there are no hydrogen bonds between the bases
• what is the role of the phosphodiester backbone

  • the phosphodiester backbone protects the more chemically reactive organic bases in the helix (protects the chemicals inside the helix from reacting)
• what are the three types of DNA replication?

  • conservative
  • semi conservative
  • dispersive
  • the semiconservative model is universally accepted
• what are the four requirements of DNA repliaction?

  • the four types of nucleotides and bases (A, T, G, C) must be present
  • both strands of DNA act as a template for the attachment of these nucleotides
  • the enzyme DNA polymerase
  • a source of chemical energy
• The steps of the semi conservative method of DNA replication involve the separation of the two strands of DNA by an enzyme, DNA helicase, the binding of free nucleotides to their complementary bases by DNA polymerase, the joining of these nucleotides together by DNA polymerase which makes phosphodiester bonds, and the formation of a polynucleotide chain using DNA polymerase with two identical strands, each retaining half of the original DNA.
• what is the role of DNA helicase?

  • it unzips the DNA by temporarily breaking the hydrogen bonds
• what is the role of primase?

  • makes the primer (which is made of RNA)- this is the starting point for adding a new strand
• what is the role of SSB proteins?

  • SSB (single stranded binding) proteins bind to the bases to prevent the strands from joining back together
• primase + polymerase

  • primase always starts on the 3' end and they look like they are going in opposite directions
  • DNA polymerase always builds the new strand in the 5' to 3' direction
• what are lagging and leading strands?

  • the leading strand is where DNA polymerase follow the helicase
  • the lagging strand is where DNA polymerase has to keep jumping back to the next 5' (new primers have to keeping being placed instead of only one at the start)-these are called okazaki fragments (each 5' to 3' on the lagging strand)
  • ligase joins the gaps in the okazaki fragments together
• what is ATP?

  • eukaryotes oxidise molecules to make adenosine triphosphate (ATP) which is used as the main energy source to carry out processes within cells
  • it is made up of:
  • adenine-nitrogen containing organic base
  • ribose-a pentose sugar
  • a chain of 3 phosphates
• how can we get the extra inorganic phosphate for ATP?

  • ATP can be resynthesised by the hydrolysis of a substance called phosphocreatine(creating phosphate)
  • CP+H2O—>C+Pi+(E)
• What are the three ways for synthesising ATP from ADP

  • synthesis of ATP from ADP, involves the addition of a phosphate molecule to ADP, occurring in three ways:

  1. in chlorophyll-containing plant cells during photosynthesis (photophosphorylation)
  2. in plant and animal cells during respiration (oxidative phosphorylation)
  3. in plant and animal cells when phosphate groups are transferred from donor molecules to ADP (substrate-level phosphorylation)
• Why is ATP not a good long term energy store?

  • the same feature that makes ATP a good energy donor (single step hydrolysis), is also a reason why it’s not a good long term energy store
  • as a result cells do not store large quantities of ATP, but rather a seconds supply
  • it is rapidly reformed from ADP and Pi so a little goes a long way
• What are the differences between ATP and glucose?

  • ATP:
  • releases less energy
  • released in small manageable amounts
  • simple chemical reaction
  • immediate source of energy
  • glucose:
  • releases more energy
  • released in large unmanageable amounts
  • complex chemical reaction
  • slower source energy
• What are the uses of ATP?

  • ATP is used in energy requiring processes in cells including:
  • metabolic processes-building macromolecules from their base units
  • movement-ATP provides energy for filaments in muscles to slide past one another and shorten in length
  • active transport-ATP provides energy to change the shape of carrier proteins in the plasma membrane
  • secretion-ATP is needed to form the lysosomes necessary for the secretion of cell products
• Key feature of water

  • water is dipolar due to electrons orbiting closer to the oxygen (slightly -) atom than the hydrogen (slightly +) atoms
  • oppost poles attract and although individual bonds are weak collectively they give water it’s unusual properties
• what makes water take more energy separate?

  • due to hydrogen bonding more energy than expected is needed to separate water molecules
• why is water important?

  • water is the main constituent of all organisms and it is important for the following reasons:
  • metabolism-hydrolysis and condensation reactions
  • transparent-aquatic plants can therefore photosynthesise
  • solvent-because its charged (dipolar) it is a good solvent, almost all chemical reaction of life take place in aqueous solutions
• what is the specific heat capacity of water?

  • it takes more energy to heat a given mass of water
  • water has a high specific heat capacity (4.2Jg^-1°C^-1)
  • specific heat capacity is the amount of heat energy required to raise the temperature of a unit of mass of a substance by 1°C
  • water therefore acts as a buffer against sudden temperature variations (environmental stability)
• what is the importance of the hydrogen bonding in water?

  • hydrogen bonding also means a lot of energy is required to evapourate-this is known as latent heat of vapourisation
  • this is useful in thermoregulation in mammals
  • with its hydrogen bonding, water has large cohesive forces (attraction to eachother) which aids capillarity
  • cohesion is the hydrogen bonds between water molecules
  • adhesion is the hydrogen bonds between water molecules and other surfaces
• how do water droplets form?

  • when water meets air molecules tend to be pulled back into the body of water
  • this creates a surface tension that acts like a skin forming water droplets
  • as water molecules lose kinetic energy the hydrogen bonds as less likely to break, forming a semi-crystaline structure holding the water molecules apart, lowering its density (<1)
• what is the role of inorganic iron ions?

  • iron ions are found in heamoglobin where they play a role in the transport of oxygen
  • iron is a prosthetic group
  • a prosthetic group is anything that binds to a protein that isnt made out of amino acids that is needed for the proteins to function
• what is the role of inorganic phosphate ions?

  • phosphate ions that form a structural role in nucleic acids, ATP, FAD, NAD, NADP and phospholipids (phospholipid bilayer)
• what is the role of inorganic hydrogen ions?

  • hydrogen ions play a role in the determination of pH and therefor the functioning of enzymes
  • there is an inverse relationship between the pH value and the hydrogen ion concentration (a higher concentration of H+ ions leads to a lower pH and a lower concentration of H+ ion leads to a higher pH)
• what is the role of inorganic sodium ions?

  • sodium ions are important in the transport of glucose and amino acids across cell-surface membranes
  • they transport glucose for respiration
  • and creating an electrochemical gradient