biology - nucleic acids

what are nucleic acids?

• ribonucleic acid (RNA)

• deoxyribonucleic acid (DNA)

features of DNA:

• double helix

• carries genetic information

• made up of nucleotides with just 3 basic components

what are the 3 components of nucleotides?

• pentose sugar (5 carbons)

• phosphate group

• nitrogen containing organic base (cytosine, thymine, uracil, guanine, adenine

how are these 3 components joined?

condensation reactions

what does this form?

a mononucleotide

how might 2 mononucleotides be joined to make a dinucleotide?

condensation reaction between deoxyribose sugar and phosphate group 

what is the bond that forms between these?

phosphodiester bond

what does the continued linking of mononucleotides form?

a polynucleotide

do other biologically important molecules besides DNA and RNA have nucleotides?

yes

symbols for simplicity to show components of nucleotides:

what is the structure of RNA?

• polymer of nucleotides

• single polynucleotide chain in which then pentose sugar is always ribose

what are the organic bases of RNA?

adenine, guanine, cytosine and uracil

3 types of RNA?

1. transfers genetic info from DNA to the ribosomes

2. ribosomes made up of proteins and another type of RNA

3. involved in protein synthesis

structure of DNA?

• pentose sugar: deoxyribose 

• made up of 2 strands of nucleotides

• strands joined by hydrogen bonds at certain bases

what are the organic bases for DNA?

adenine, thymine, guanine and cytosine

complementary base pairing? (joined by hydrogen bonds)

• adenine with thymine

• guanine with cytosine

double helix structure:

• 2 polynucleotide chains are twisted

• phosphate and deoxyribose form structural backbone of DNA molecule

why is DNA a stable molecule?

• phosphodiester backbone protects the more chemically reactive organic bases in the double helix

• hydrogen bonds link the bases forming bridges between the phosphodiester backbone (3 hydrogen bonds between C-G, 2 hydrogen bonds between A-T)

what is DNA responsible for?

passing genetic info from cell to cell. 3.2 bill base pairs in a typical cell, leading to great genetic variety

how is DNA adapted to carry out its functions?

• stable structure which passes from gen to gen without big change. most mutations are repaired, so persistent mutations are rare

• 2 separate strands joined with hydrogen bonds, which allow them to separate during DNA replication and protein synthesis

• carried lots of genetic info from large size

• base pairs in the helical cylinder of the deoxyribose phosphate backbone which protects the genetic info from being corrupted by outside forces

• base pairing leads to DNA being able to replicate and transfer info as mRNA

what are the important carbon atoms in a pentose sugar in the structure of DNA?

3’ and 5’ carbon atoms (5’ attached phosphate, 3’ attached hydroxyl)

what are the DNA strands?

antiparallel to one another (one runs 5’ to 3’ and the other runs 3’ to 5’

what are the 2 main stages of cell division?

• nuclear division (mitosis or meiosis)

• cytokinesis 

what must happen before this can take place?

DNA replication, which must be precise to ensure that the cells are genetically identical

what are the 4 requirements for semi conservative replication?

• the 4 types of nucleotide with their bases must be present

• both strands of the DNA molecule act as a template for the attachment of these nucleotides

• the enzyme polymerase

• chemical energy to drive the process

what is the process of semi conservative replication?

• helicase breaks hydrogen bonds linking the base pairs of DNA

• double helix separates and unwinds

• each exposed polynucleotide acts as a template to free complimentary nulceotides by specific base pairing

• nucleotides joined together in condensation reaction by polymerase to form the template polynucleotide

• each new DNA molecule has one original DNA strand and one template

summary of the semi conservative replication of DNA

summary of DNA polymerases’ role:

what is ATP?

adenosine triphosphate (main energy source in cells)

what is an ATP molecule?

a phosphorylated macromolecule

what are the 3 parts of ATP?

• adenine - nitrogen containing organic base

• ribose - pentose sugar that acts as a backbone

• chain of 3 phosphate groups

is ATP a nucleotide?

yes

what is the issue about the bonds between the 3 phosphate groups?

they are unstable and so have a low activation energy, being broken easily

what happens when broken?

they release a considerable amount of energy

what is the reaction above known as?

hydrolysis, as it uses water to convert ATP into ADP

what is the reaction catalysed by?

ATP hydrolase

can ADP be made back into ATP?

yes, as it is reversible, via a condensation reaction and the catalyst ATP synthase

summary of the equations:

where does the synthesis of ATP from ADP involving the addition of a phosphate molecule occur?

• in chlorophyll containing plant cells in photosynthesis (phosphorylation)

• in plant and animal cells during respiration (oxidative phosphorylation)

• in plant and animal cells when phosphate groups are transferred from donor molecule to ADP (substrate level phosphorylation)

why is ATP not a good long term energy store?

the instability of its phosphate bonds

what is ATP therefore?

an immediate energy source

why is this not an issue?

ATP is rapidly reformed from ADP and inorganic phosphate

why is ATP a better immediate energy source than glucose?

• each ATP molecule releases less energy than each glucose molecule. The energy for reactions is therefore released in smaller, more manageable quantities

• the hydrolysis of ATP to ADP is a single reaction that releases immediate energy. the breakdown of glucose is a long series of reactions and therefore takes longer

what has to happen because ATP cant be stored?

has to be continuously made in the mitochondria of cells that need it

what is ATP used in?

• metabolic processes

• movement

• active transport

• secretion

• activation of molecules

metabolic processes:

provides energy to build up macromolecules from their basic units, eg. starch from glucose

movement:

provides energy for muscle contraction, by providing the energy for the filaments of muscle to slide past one another and shorten the overall length of a muscle fibre 

active transport:

provides energy to change the shape of carrier proteins in plasma membranes, which allows molecules to be moved against a concentration gradient

secretion:

ATP is needed to form the lysosomes necessary for the secretion of cell products

activation of molecules:

the inorganic phosphate released during the hydrolysis of ATP can be used to phosphorylate other compounds to make them more reactive, therefore lowering the activation energy in enzyme catalysed reactions, eg. addition of phosphate to glucose molecules at the start of glycolysis

what is water made up of?

2 hydrogen atoms and one oxygen atom. the molecule has no overall charge, but the oxygen is slight negative, and the hydrogen atoms are slight positive

what is it therefore described as?

dipolar

how do different water molecules attract?

the positive pole of one water molecule will be attracted to the negative poles of another water molecule. this forms the weak attraction of a hydrogen bond

is the hydrogen bond weak?

yes, but there are thousands, giving overall important forces

why is the boiling point of water higher thsn expected?

takes more energy to separate them as the water molecules are bonded to each other 

what does it therefore also have?

a high specific heat capacity

what does water act as?

a buffer against sudden temp variations, making the aquatic environment a temp stable one

why does water have a high latent heat of vaporisation?

hydrogen bonding between water molecules means that it requires a lot of energy to evapourate 1 gram of water

what is cohesion?

the tendency of molecules to stick together

what does waters hydrogen bonding mean?

water has large cohesive forces which allow it to be pulled up through a tube, eg. a xylem vessel

other example of waters cohesive forces:

tends to be pulled back to body of water rather than escaping at water surface. this is surface tension

why is water important to living organisms?

water is the main constituent of all organisms - 65% water is humans. it is also where life arose and where many species live

role of water in metabolism:

• used to break down many complex molecules by hydrolysis, alongside being produced in condensation reactions

• chemical reactions take place in an aqueous medium

• water is a major raw material in photosynthesis

role of water as a solvent:

DISSOLVES:

• gases, eg. oxygen and CO2

• waste (ammonia and urea)

• inorganic ions and small hydrophillic molecules, eg. amino acids

• enzymes

other important features of water:

• its evaporation cools organisms and allows for temp control

• its not easily compressed and provides support

• it is transparent and therefore aquatic plants can photosynthesise and light rays can penetrate jelly like fluid that fills the eye and reaches the retina

where are inorganic ions found?

in organisms where they occur in solution in the cytoplasm of cells and in body fluids as well as part of larger molecules. they may be in concentrations that range from high to low

what do inorganic ions perform?

a range of functions based on the particular ion

eg. iron ions:

found in haemoglobin and play a role in the transport of oxygen

eg. phosphate ions:

form a structural role in DNA molecules, and have a role in storing ATP molecules

eg. H+ ions:

determine the pH of solutions and functioning of enzymes