Nucleotides and Nucleic acids

Nucleotides and Nucleic acids

Nucleotides are nitrogen containing organic substances wich play a vital role in every espect of an organisms life.Nucleotide molecules occur singly(mononucleotides) or combined in numbers frol two to many thousands(polynucleotides).
Nucleotides are made of three parts:

1. a nuitrogen-containing organic base
2. a five-carbon sugar ( pentose)
3. one or more phosphate groups

ATP is energy to drive reactions.(Adenosine triphosphate or ATP) is a mononucleotide.It is vital because ir the main source of chemical energy. The base is adenine and the sugar is ribose. Attached to the ribose are three phosphate groups.The covalent bond linking the second and third phosphate groups is unstable, and is easily broken by hydrolysis.

When this bond is broken a phosphate group(Pi) is removed, and ATP becomes ADP (adenosibne diphpsphate).Energy is release so it is calle exergonic reaction.This reaction can be reversible because from ADP it can be obtained ATP by resynthesis and the inorganic phosphate by a condensation reaction.(energy for this reaction comes from respiration).

Nucleic acids: DNA

Nucleotides are combined by condensation reactions to form long chains wich are called nucelic acids.DNA plays the key role in inheritance and protein synthesis. The basic structure of DNA seems simple because it is made of only four type of nucleotide.Each DNA nucleotide has a phosphate group, a pentose sugar (deoyribose,and one of four types of base ( all of wich containing nitrogen) adenine, cytosine,guanine or thymine.

DNA FORMS A DOUBLE-HELIX

• The DNA molecule consists of two strands, each of wich is a polynucleotide chain
• Each strand has a helical (spiral) shape, so that DNA has become known as the "double helix"
• The polyunucleotide chains run in opposite directions and are joined by pairs of bases.
• The bases are held together by hydrogen bonds between the hydrogen atoms of a base in one chain and the oxygen and nitrogen atoms of a base in the other chain

Introduction to Proteins

Proteins

Type of proteins

• Enzymes, biological catalysts that control biochemical reactions.
  


• structural proteins, for example collagen that make up tendons.
  


• signal proteins, carry a message around the body, for example insulin.
  


• storage proteins, protein store that form the white of egg.


• defensive proteins, for example, antibodies that fight infections.


• Transport proteins, for example haemoglobin, the carrier of oxygen in blood.

Proteins are polymers formed of amino acids, there are thousands of proteins bu only 20 differents amino acids.

Amino Acids

The amino acids have an amino group(-NH2) and a carboxyl group(-COOH). The amino group is attached by a covalent bond to the central carbon atom called the alpha carbon. In the amino acids the R varies for each different amino acid. The R groups are non-polar and hydrophobic but others are polar and hidrophilic.

Amino Acids as buffers

Amino acids are amphoteric, they have both acidic and basic properties when they dissociate in water. The acidic properties are derived from the carboxyl group, which can donate a proton and being negatively charged in an alkiline solution. The basic properties are derived from the amino group, which can take a proton to be positively charged in an acidic solution. Ions with both, negative and positive charges are called zwitterions. The ability to donate and receive protons allow amino acids to behave as buffers. A buffer solution tends to resist changes in ph. Buffer systems play an essential role in the human body, keeping the ph of blood in tolerable levels.

Peptide bonds

Two amino acids can combine to form a dipeptide by a condensation reaction , this bond is called peptide bond. Further amino acids can combine with the dipeptide to form a polypeptide chain. Proteins consist of one or more polypeptide chains.

Proteins

Proteins

Proteins consist of one or more chains of amino acids folded into a unique three-dimentional shape. The shape is determined by by up to four levels of structure(each level of structure determines the next):

• Primary structure: a proteins primary structure is the sequence of amino acids that make up its polypeptide chains.In order for a protein to carry out its specific function, it must contain the correct amino acids arranges in a precise order.
  
• Secondary structure: Is the coil into an alpha-helix or beta-pleated sheet by hydrogen bonding.
• Tertiary structure: Refers to the overall three-dimensional shape of a polypeptide chain.they are classified into two main groups depending on the basis of their tertiary structure:

Fibrous proteins consist of parallel polypeptide chains cross-linked at intervals of from long fibres or sheets. In globular proteins the polypeptide chains are tightly folded to form a spherical shape. Breaking down the tertiaty structure:denatiration. if the bons holding the proteins chape are broken, a proces called denaturation occurs. the polypeptide chains unravel and lose their specific shape,as a result they lose their specific function.Denaturation is nearly irreversible. It can be cause by:

1. changes in ph
2. salt concentration
3. temperature

• Quaternary structure: the association of polypeptide chains.Many proteins consist of more than one polypeptide chain bonded to each other. It refers to the way these polypeptide chains are arranged.

Lipids

Lipids

Compounds wich are insoluble in water but dissolve readily in other lipids or organic solvents (ethanol,chloromethanol). All lipids contain carbon,hydrogen and oxygen wich is lower than in carbohydrates.

Fats and oils


Triglycerides, are also known as true fats, are lipids made from a molecule of glycerol and three molecules of fatty acids. They are formed by a condensation reaction, water is removed forming a bond called "ester bond".

Saturated and unsaturated fatty acids

Fatty acids may be saturated or unsaturated. The saturated fatty acids are the ones that have no any free electrons to form any new bond, they have only single bonds. The unsaturated fatty acids have double bonds of carbo that could break for creating new bonds, they are qualified into monounsaturated fatty acids that have only one double bond, and the polyunsaturated fatty acids that have two or more doble bonds.

In the unsatureted fatty acids there are the cis-fatty acids that is liquid because the hidrocarbon chain is not totally straight so the atracctions between the molecules is very weak. And there are also the trans-fatty acids which are much more solid because hidrocarbon chains are satright so it leads to the properties of saturated fatty acids.

Functions of Fats and Oils in living organisms

Tryglicerols, for example, they have the higher proportion of hidrogen either carbohydrates or proteins, so they are the a more concentrated source of energy. Under the skin is the adipose tissue which is a special connective tissue for the storage of fats.

• heat insulation, it manteins the heat and prevent it to go out, in winter the adipose tissue increase
• shock absorption, some organs that are delicate have a thick layer of fats for protection
• buoyancy, oil produced for single-celled aquatic organisms to aid buoyancy

Phospholipids

They form a major part of cell membranesincluding myelin which allows a fast conduction of nerve impulses. Phospholipids consist of a glycerol and two fatty acids chains. The third hydroxyl group combines with phosphoric acid to form a polar phophste group. The polar group is hydrophilic, and the non-polar tail is hydrophobic, that's why it is called amphipathic.

In water they join together forming a layer, in the cells mostly all is water so they form a double layer , with the hydrophobic tails inwards.

Carbohydrates

Carbohydrates

are a group of substances that are important in many biological processes. they provide energy-rich nutrients to organisms and are used to build their body structure.
Monosacharides are simple sugars, and they have the common formula (CH2O)n Where letter can be any number from 3 to 7. Glucose is a simple sugar where n is 6 so the formula is C6H12O6.Plants produce glucose with photosynthesis.

Glucose has different issomers, they are alpha glucose and beta glucose. The figure in the left shows the difference in the structures. Beta Glucose can be digested by herbivores because they produce cellulase,so carnivores can not digest beta glucose.


Disacharides are the combination of two monosacharides, they are produced by a condensation reaction . The bond formed is called glycosidic bond.

1. Maltose: (malt sugar) is a disacharide made up of two glucose molecules


2. Sucrose: (table sugar) is made up of a glucose and fructose.


3. Lactose: (milk sugar) is made up of a glucose and a galactose.

Disacharides can be broken down to the constituent monosacharide by hydrolisis.
A reducing sugar is any sugar that, in basic solution, forms some aldehyde or ketone. This allows the sugar to act as a reducing agent, for example in the Maillard reaction and Benedict's reaction.
Here are some of them: Glucose, fructose, glyceraldehyde, lactose, arabinose and maltose

The non reducing sugars are: sucrose and trehalose

Functions of simple sugars in living organisms

Lactose is the main sugar of the milk

• maltose it is produced by the breakdown of amylose in many germinating seeds.
• sucrose is the form in which carbohydrates are transported in plants.
• glucose is the main source of energy for most animals (19kj of energy), and it is also the main form in which carbohydrates are transported in animals
  

Reducing sugars:

• glucose

• fructose

(alpha & beta)

• glyceraldehyde

• lactose

• arabinose

• maltose

Polysacharides A molecule with between 3 and 10 monosacharides units is called an oligosacharides. If more and more units are added, it is called a polysacharides, this happens by a process called polymerisation. A polymer is a large molecule of repeating units that are called monomers. Conjugated molecules are molecules formed by monosacharides monomers with other type of molecules. They have the general formula of (C6H10O5)n

There are two differents glycosidic bonds: the 1-4 glycosidic bond is the condensation reaction between the hydroxl groups at carbon 1 of one monosacharide and carbon 4 of an other. The 1-6 glycosidic bond is formed y the condensation reaction of teh hydroxyl group atcarbon 1 and at 6 of the other.

• Straight chains are formed by monomers linked by 1-4 glycosidic bonds
• Branched chains are formed by monomers linked by 1-6 glycosidic bonds
  

Starch: is the way in which energy is storage in plants. It is a polysacharide formed by alpha glucose units. Starch consist in two components, amylose and amylopectin. In amylose, the units are linked by 1-4 glycosedic bonds forming a straight chain. In amylopectin, the units are linked by 1-6 glycosidic bonds forming a branched chain. Because of the compact structure, starch is ideal for storage. It is a helical molecule with the hydroxil groups pointing inwards.

Glycogen is the way in which energy is storage in animals. It is abundant in liver and muscle cells. It is very similar to starch but it is much more branchd because it has more 1-6 glycosidic bonds.

Cellulose is the the main components of the cell walls. It carries a structural functions in plants. Cellulose is completely permeable. In comparison with starch and glycogen, cellulose isn't easy to hydrolysed so herbivores are the only animals that can digest it because it have microorganisms that produce an enzime called cellulase.

Lignin is what makes cellulose further strengthened in wood. It is a highly complex non carbohydrate polymer. It impregnates in th cell walls of the xylem vessels in a process called lignification, when the cell wall is completely lignificated, it dies. Also this prevent decay and rot infections.