Biological molecules part 2

Water and its functions

Water is a major component of cells, although it is the most abundant liquid on Earth.

Specific heat capacity of water

Water molecules stick together as it takes more energy (heat) to separate them than would be needed if they did not bond to one another. The boiling point of water is higher than expected. Without hydrogen bonding water would be a gas (water vapour) at the temperatures commonly found on Earth and life as we know it would not exist. It takes more than more energy to heat a given mass of water; water has a high specific heat capacity. It acts as a buffer against sudden temperature variations, making the aquatic environment a temperature-stable one. As organisms are mostly water it also buffers them against sudden temperature changes especially in terrestrial (land) environments.

Water as a solvent

Water readily dissolves other substances: • Gases (oxygen and carbon dioxide) • Wastes (ammonia and urea) • Inorganic ions and small hydrophilic molecules (amino acids, ATP and monosaccharides) • Enzymes whose reactions take place in solution

DNA replication the process

Watson and Crick also came up with the theory of semi-conservative DNA replication. Meselson and Stahl's experiment proved that DNA was semi-conservative with this experiment. However if DNA was conservative, the original DNA strands would stay together and the new DNA molecules would contain two new strands. Used 2 isotopes of nitrogen - heavy nitrogen 15N and light 14N.

ATP is used in energy-requiring processes in cells including:

• Metabolic processes- ATP provides energy needed to build up macromolecules from their basic units. Making starch from glucose • Movement- ATP provides energy for muscle contraction. In muscle contraction ATP provides the energy for the filaments of muscle to slide past one another and therefore shorten the overall length of muscle fibre • Active transport - ATP provides the energy to change the shape of carrier proteins in plasma membranes . This allows molecules/ions to be moved against a concentration gradient • Secretion- ATP is needed to form lysosomes necessary for the secretion of cell products • Activation of molecules - the inorganic phosphate released during the hydrolysis of ATP can be used to phosporylate other compounds in order to make them more reactive thus lowering the activation energy in energy-catalysed reactions. Addition of phosphate to glucose molecules at the start of glycolysis Activation of molecules, Secretion and Active transport are all used in plant cells.

RNA structure

• Polymer made up of nucleotides • Single, relatively short polynucleotide chain in which the pentose sugar is always ribose and the organic bases are au and cg. • One type of RNA transfers genetic information from DNA to ribosomes • The ribosomes themselves are made up of proteins and another type of RNA • A third type of RNA is involved in protein synthesis

Semi conservative replication the process:

• The enzyme DNA helicase breaks the hydrogen bonds linking the base pairs of DNA • The double helix separates into its two strands and unwinds • Each exposed polynucleotide strand then acts as a template to which complementary free nucleotides bind by specific base pairing • Nucleotides are joined together in a condensation reaction by the enzyme DNA polymerase to form the "missing" polynucleotide strand on each of the two original polynucleotide strands of DNA • Each of the new DNA molecules contains one of the original DNA strands that is half the original DNA has been saved and built into each of the new DNA molecules. This is called semi conservative replication

Phosphate ions are an essential component of ATP and DNA

• When a phosphate ion (PO43-) is attached to another molecule its known as a phosphate group • DNA, RNA and ATP all contain phosphate groups • It's the bonds between phosphate groups that store energy in ATP • The phosphate groups on DNA and RNA allow nucleotides to join up to form the polynucleotides

The dipolar water molecule

A water molecule is made up of two atoms of hydrogen and one of oxygen. Although the molecule has no overall charge the oxygen atom has a slight negative charge while the hydrogen atoms have a slight positive one. It is dipolar.

Energy and ATP

All living organisms require energy to remain alive. This energy initially comes from the Sun and plants use solar energy to combine water and carbon dioxide into complex organic molecules by photosynthesis. Both plants ten oxidise these organic molecules to make ATP which is used as the main energy source to carry out processes in cells.

DNA replication

Cell division occurs in 2 main stages: Nuclear division- nucleus divides and there are two types meiosis and mitosis Cytokinesis-follows nuclear division and is when the whole cell divides Before a nucleus divides its DNA must be replicated, so that all the daughter cells have the genetic information to produce the enzymes and other proteins that they need. The process is very precise because all the new ones cells are more/less genetically identical.

Water and hydrogen molecule

Different poles attract and so the positive pole of one water molecule will be attracted to the negative pole of another water molecule. The attractive force between these opposite charges is a hydrogen bond. Although each bond is fairly weak (about 1/10th as strong as a covalent bond) together they form important forces that cause the water molecules to stick together giving water its unusual properties.

3' and 5'

Each end of a DNA structure is slightly different in structure one end is called 3' (3 prime) and the other is 5' (5 prime). In a DNA helix the strands run in opposite directions, they are antiparallel. The active site of DNA polymerase is only complementary to the 3' end of the newly forming DNA strand, so the enzyme can only add nucleotides to the new strand at the 3' end. The new strand is made in a 5' to 3' end that DNA polymerase moves down the template group in a 3' to 5' direction and as the strands in the double-helix are antiparallel the DNA polymerase working on one of the template strands moves in the opposite direction to the DNA polymerase working on the other template strand.

Latent heat of vaporisation of water

Hydrogen bonding between water molecules means that it requires a lot of energy to evaporate 1 gram of water, this energy is called latent heat of vaporisation. Evaporation such as sweat in mammals is an effective means of cooling down as the body heat is used to evaporate water.

Nucleotide structure

Individual nucleotides are made up of three structures: 1. Pentose sugar (five carbon atoms) 2. Phosphate group 3. Nitrogen containing organic base. These are cytosine (C), adenine (A), thymine (T), guanine (G) and uracil (U). The pentose sugar, phosphate group and organic base are joined, due to a condensation reaction to form a mononucleotide (single nucleotide). Two mononucleotides may in turn be joined as a result of a condensation reaction between the deoxyribose sugar of one mononucleotide and the phosphate group of another. The bond formed between them is called a phosphodiester bond. The new structure is called a dinucleotide. The continued linking of mononucleotides in this way forms a long chain (polynucleotide). In addition to RNA and DNA some other biologically important molecules contain nucleotides.

Structure of ATP (adenosine triphosphate)

It is a phosphorylated molecule. It is made up of: adenine (nitrogen containing organic base) ribose (sugar molecule with a 5 carbon ring structure (pentose sugar) that acts as the backbone to which the other parts are attached) phosphates (chain of three phosphate groups)

The importance of water to living organisms

Main constituent of all organisms- up to 98%of jellyfish and 65% of mammals. It is where life on earth arose.

Base pairing

The bases on the two strands of DNA attach to each other by hydrogen bonds. It is these hydrogen bonds that hold the two strands together. Adenine always pairs with thymine and guanine always pairs with cytosine As a result of these pairings, adenine is said to be complementary to thymine. It follows that the quantities of adenine and thymine in DNA are always the same and so are the quantities of cytosine and guanine. However the ratio of adenine and thymine to guanine and cytosine varies between different species.

Synthesis of ATP

The conversion of ATP to ADP is a reversible reaction and therefore energy can be used to add an inorganic phosphate to ADP to re-form ATP according to the reverse of the equation above. This reaction is catalysed by ATP synthase, as water is removed in this process it is a condensation reaction. The synthesis of ATP fro ADP involves the addition of a phosphate molecule to ADP. It occurs in three ways: • Chlorophyll-containing plant cells during photosynthesis (phosphorlyation) • Plant and animal cells during respiration (oxidative phosphorylation) • Plant and animal cells when phosphate groups are transferred from donor molecules to ADP (substrate-level phosphorylation)

The stability of DNA

The phophodiester backbone protects the more chemically reactive organic bases inside the double helix. Hydrogen bonds link the organic base pairs forming bridges (rungs) between the phosphodiester uprights. As there are three hydrogen bonds between cytosine and guanine, the higher the proportion of C-G pairings, the more stable the DNA molecule. There are other interactive forces between the base pairs that hold the molecule together (base stacking).

Roles of ATP

The same feature that makes ATP a good energy donor (instability of phosphate bonds) also is the reason why it is not a good long-term energy store. Fats and carbs (glycogen) serve this purpose better so ATP is the immediate energy source of a cell. As a result cells do not store large quantities of ATP but a few seconds supply. This is not a problem as ATP is rapidly reformed from ADP and inorganic phosphate.

Cohesion and surface tension in water

The tendency of molecules to stick together -cohesion Water molecules have large cohesive forces due to its hydrogen bonds and these forces allow it to be pulled up through a tube (xylem vessels in plants). Where water molecules meet air they tend to be pulled back into the body of water rather than escaping from it (surface tension force). The water acts like a skin and is able to support small organisms (pond skaters).

The double helix

The uprights of phosphate and deoxyribose wind around one another to form a double helix. They form the structural backbone of the DNA molecule.

Hydrogen ions (H+) determine pH

pH is calculated on the concentration of hydrogen ions in the environment. The more H+ present, the lower the pH and the more acidic the environment. Enzyme-controlled reactions are all affected by pH.

Other important features of water

• Evaporation-cools organisms and allows them to control their temperature • Not easily compressed-provides support (hydrostatic skeleton of animals eg: earthworm and turgor pressure in herbaceous plants) • Transparent and so aquatic plants can photosynthesise and also light rays can penetrate the jelly-like fluid that fills the eye and so reach the retina

Sodium ions (Na+) help transport glucose and amino acids across membranes

• Glucose and amino acids need a bit of help when crossing cell membranes • A molecule of glucose or an amino acid can be transported into a cell (across the cell-surface membrane) alongside sodium ions (Na+). This is co-transport

Iron ions are an important part of haemoglobin

• Haemoglobin is a large protein that carries oxygen around the body in red blood cells • Made of four different polypeptide chains each with an iron ion in the centre (Fe 2+) • Fe2+ actually binds to the oxygen • When oxygen is bound the Fe2+ ion temporarily becomes an Fe3+ ion until the oxygen is released

Water in metabolism

• Used to break down many complex molecules by hydrolysis (proteins to amino acids) • Produced in condensation reactions • Chemical reactions take place in an aqueous medium • Major raw material in photosynthesis

How ATP stores energy

ATP is a nucleotide so has three phosphate groups. The bonds between the phosphate groups are unstable so have a low activation energy, so they are easily broken. When they do break a considerable amount of energy is released. Usually in living cells it is the final/terminal phosphate that is removed: ATP + H2O -> ADP + Pi + E Adenosine triphosphate + water -> adenosine diphosphate + inorganic phosphate + energy It is a hydrolysis reaction, the reaction is catalysed by the enzyme ATP hydrolase.

DNA structure

• 1953 James Watson and Francis Crick worked out the structure of DNA following pioneering work by Rosalind Franklin on the x-ray diffraction patterns of DNA • The pentose sugar is deoxyribose • Organic bases are at and cg • Made up of two strands of nucleotides (polynucleotides) • Each of the two strands is extremely long and they are joined together by hydrogen bonds formed between certain bases • Can be thought of as a ladder where the phosphate and deoxyribose molecules alternate to form the uprights and organic bases pair together to form the rungs

Function of DNA

DNA is the hereditary material responsible for passing genetic information from cell to cell and generation to generation. There is almost an infinite variety of sequences of bases along the length of the DNA molecule. It is this variety that provides the genetic diversity within living organisms. It's adapted to carry its function out: • Very stable structure which normally passes from generation to generation without change. Only rarely does it mutate • Its two separate strands are joined only with hydrogen bonds which allow them to separate during DNA replication and protein synthesis • Extremely large molecule and so carries an immense amount of genetic information • By having the base pairs within the helical cylinder of the deoxyribose-phosphate backbone the genetic information is to some extent protected from being corrupted by outside chemical and physical forces • Base pairing leads to DNA being able to replicate and to transfer information such as mRNA

Inorganic ions

1. An ion is an atom/ group of atoms that has an electric charge 2. Positive charge-cation 3. Negative charge-anion 4. An inorganic ion doesn't contain carbon - although there are a few exceptions 5. There are inorganic ions in solution, in cytoplasms of cells and in the bodily fluids of organisms. Each ion has a specific role depending on its properties. An ion's role determines whether it's found in high/low concentrations

Semi conservative replication Four requirements:

1. The four types of nucleotide each with their bases of adenine, guanine, cytosine or thyomine must be present 2. Both strands of the DNA molecule act as a template for the attachment of nucleotides 3. The enzyme DNA polymerase 4. A source of chemical energy is required to start the process

actual semi conservative experiment

1. Two samples of bacteria were grown - one in a nutrient broth containing light nitrogen and one in a broth containing heavy nitrogen. As the bacteria reproduced they took up nitrogen from the broth to help make nucleotides for new DNA. So the nitrogen gradually became part of the bacteria's DNA. 2. A sample of DNA was taken from each batch of bacteria, and spun in a centrifuge. The DNA from the heavy nitrogen bacteria settled lower down the centrifuge tube than thr DNA from the light nitrogen bacteria- as it is heavier. 3. Then the bacteria grown in the heavy nitrogen broth were taken out and put in a broth containing only light nitrogen. The bacteria were left for one round of DNA replication and then another DNA sample was taken out and spun in the centrifuge. 4. If replication was conservative the original heavy DNA which would still be together would settle at the bottom and the new light DNA would settle at the top 5. If replication was semi-conservative the new bacterial DNA molecules would contain one strand of the old DNA containing heavy nitrogen and one strand of new DNA containing light nitrogen. So the DNA would settle out between where the light nitrogen DNA settled out and where the heavy nitrogen DNA settled out. 6. As it turned out the DNA settled out in the middle, showing that the DNA molecules contained a mixture of heavy and light nitrogen. The bacterial DNA had replicated semi-conservatively in the light nitrogen

hydrogen bonds between a and t

2 hydrogen bonds

hydrogen bonds between c and g

3 hydrogen bonds

Structure of RNA and DNA

Nucleic acids are a group of the most important molecules of which are RNA (ribonucleic acid) and DNA (deoxyribonucleic acid). The double helix of DNA makes it instantly recognisable. DNA carries genetic information and it is made up of nucleotides.

ATP is a better immediate energy source than glucose as:

• Each ATP molecule releases less energy than each glucose molecule. The energy for reactions is therefore released in smaller, more manageable quantities rather than the much greater and less manageable release of energy from a glucose molecule • 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 the energy release takes longer ATP cannot be stored and so has to be continuously made within the mitochondria of cells that need it. Cells (muscle fibres and epithelium of small intestine) which require energy for movement and active transport respectively possess many large mitochondria.