Molecules

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Structure of an amino acid

(http://study.com/cimages/multimages/16/amino_acid_med.jpeg)

An amino acid contains:

  • an amino group (NH2)
  • a carboxylic acid group (COOH)
  • a variable group (this is anything except H, e.g. CH3)
  • a hydrogen (H) 
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Formation of a dipeptide (b)

dipeptide is two amino acids joined together by a condensation reaction

  • In the condensation reaction, a hydrogen from the amine group in one amino acid, and OH from the carboxylic acid group in the second amino acid is removed. i.e a molecule of water is removed. 
  • peptide bond forms between the nitrogen atom and the carbon atom
  • hydrolysis reaction is where a molecule of water is added to the dipeptide and will break the peptide bond. 

(http://swh.schoolworkhelper.netdna-cdn.com/wp-content/uploads/2010/11/peptide.jpg?e6ecea)

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Primary Structure of a protein (c)

The primary structure a protein is the sequence of amino acids held together by peptide bonds, making a polypeptide chain. 

This unique sequence will determine the function of the protein. 

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Secondary structure of a protein (c)

The polypeptide chain can then do two things:

  • Coil into an alpha helix. The structure is maintained by hydrogen bonds between adjacent CO and NH groups. A protein that is entirely alpha-helical is fibrous. An example of a fibrous protein is keratin. 
  • Fold into pleats.This is known as beta pleated sheet. Again, hydrogen bonds are formed, this time between CO and NH groups of one chain, and the NH groups and CO groups of adjacent chains. 
  • Haemoglobin contains both of these structures. 

(http://images.tutorvista.com/cms/images/81/protein-secondary-structure.jpeg)

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Tertiary structure of a protein (c)

The alpha helix or beta pleated sheet will further coil or fold into a specific 3D shape. This shape is maintained by three types of bonds:

  • Hydrogen bonds- between amino acids/side chains. These are relatively weak and easily broken. 
  • Disulphide bridges- are very strong covalent bonds formed between two neighbouring sulfur-containing amino acids.  
  • Ionic bonds- form between charged groups of polypeptide chains. For example, between COO- and NH2+.

Hydrophobic interactions may also form between non-polar parts of the molecule.  (http://alevelnotes.com/content_images/Image85.gif)

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Quaternary structure of a protein (c)

A quaternary structure determines the final 3D structure of a protein. It is made from more than1 polypeptide chain.

  • Haemoglobin has 4 polypeptide chains. 2 alpha helix's and 2 beta pleated sheets. 
  • The prosthetic group is the haem group in each chain. 

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The role of haemoglobin in carrying O2 (d)

Haemoglobin is a globular protein. 

It is round, compact and soluble. This means it can be transported in fluids.

Haemoglobin has 4 polypeptide chains, 2 alpha helix's and 2 beta pleated sheets. 

Each chain contains a haem group, which in itself contains 1 iron ion.

Each Iron ion is able to associate with 1 O2 molecule. Since there are 4 haem groups, haemoglobin can associate with 4 O2 molecules altogether. 

When 1 haem group binds with the first O2 molecule, the next haem group is exposed so it is easier to pick up O2. 

When haemoglobin combines with O2, it is referred to as oxyhaemoglobin

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Plasma, serum, tissue fluid and lymph (e), (f)

Blood plasma

Plasma makes up 55% of the total volume of our blood.

It transports: RBC's, WBC's, platelets, fibrinogen (protein).  O2, CO2, salts and glucose are dissolved.

Tissue Fluid

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Water (g)

Water is a polar molecule. This is bceuase there is unchared charge betweent he oxygen and the hydrogens. Water molecules are able to form hydrogen bondswith other water molecules. This occurs between the lone pair of electrons on the oxygen atom and the hydrogen atom on a nother moleucle of water.

Image result for water polar molecule

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Properties of water (g)

High Specific Heat Capacity

High SHC is due to the hydrogen bonding. Lot's of heat energy is requried to change the temperature of water. This means water remains stable at high temperatures. It is therefore good for homeostasis. It is also a good coolant- evaporating water from an removes heat energy i.e. sweating.

High Cohesion

Each water molecule bonds with 4 others in a tetrahedral arrangement. Because of this, water is cohesive- it will stick to other molecules of water. Water is also adhesive so it will stick to other surfaces. This leads to capilaary action- water will move up the xylem against gravity and high surface tension, supporting insects and allowing droplets to form.

Good Solvent

Water is a polar molecule. It will therefore dissolve polar solutes easily. Ionic solids dissociate in water. Polar attractions form between the water molecule and solutes. Water molecules will surround and isolate the solute molecule, causing it to dissolve.   

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Electrolytes (h)

  • Electrolytes are ions with a positive or negative charge (cations and anions respectively)
  • Responsible for maintaining the water potential balance
  • Contained in the plasma or cells.

Measuring electrolytes

Sodium, potassium, chloride, calcium are all measured. This is because the levels must be kept within a narrow range as it could lead to conditions such as diabetes and kidney disease. 

Potentiometry is used to measure electrolytes. 

  • A small sample of body fluid such as urine or blood plasma is placed in a machine.
  • The voltage is measured between the inner and outer surfaces of an ion selective electrode
  • The electrode is selectively permeable to the ion being measured. 
  • The potential is compared to the potential of a reference electrode which will have a constant potential. Therefore, the difference in potential will be the concentration of the ion. 
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Diffusion (i)

The net movement of molecules from a region where it is in a high concentration to a region where it is in low concentration.

Molecules move randomly and do not require energy,therefore diffusion is a passive process. 

Only molecules that are:

  • lipid-soluble
  • small

Can diffuse across the plasma membrane through the phospholipid bilayer. 

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Facilitated Diffusion (i)

Passive process 

e.g. glucose into erythrocytes through carrier protiens. 

Molecules that:

  • are very large
  • are soluble in water  
  • have a high charge, can't pass thorugh the plasma membrane. 

This is because the fatty acids in the phoshoplipid bilayer repel anything with a charge.

Such molecules require proteins to aid them in passing through the plasma membrane. These proteins are:

Channel proteins: permanantly open. Lined with hydrophillic lining made up of amino acids and water. Allows substances such as chloride ions to pass through. 

Carrier proteins: molecules bind to the carrier protein, casuing it to change shape and release the molecule on the other side. 

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Osmosis (i)

The net movement of water molecules from an area where there is a high water potential, to an area where there is a low water potential, through a partially permeable membrane 

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Active Transport (j)

The movement of molecules against a concentration gradient across a partially permeable membrane, using energy from ATP. 

Molecules bind to an active transport protein. 

The protein chnages shape using energy from ATP. The change in shape 

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Endocytosis (k)

Endocytosis 

Plasma membrane of neutrophill will invaginate to form a depression which envelopes the material.

When the particles or molecules get close enough, the membrane invaginates itself around the substance and seals off. 

A vesicle is formed which moves into the cytosol of the cell. 

Phagocytosis is a type of endocytosis involved in the uptake of large particles compared to pinocytosis which is associated with the uptake of much smaller particles. Phagocytic vesicles are formed containing the particles. It will fise with lysosomes which have digestive enzymes that will digest the particles. A phagocyte is any cell that is capable of absorbing bacteria and other small particles. An example is a neutrophil. 

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Exocytosis (k)

Exocytosis

Vesicles within the cytosol of the cell will contain particles or moleucles that need to be expelled from the cell. 

The vesicle moves towards the plasma membrane of the cell and fuses with it. The vesicle then opens up and releases the contents of the cell. The vesicle membrane becomes part of the plasma membrane of the neutrophil. 

The vesicles involved in exocytosis are often derived from the Golgi apparatus. Exocytosis is involved in the expulsion of substances such as hormones, enzymes, antibodies and precursors. 

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Water potential (l)

Water potential  is the measure of the potential energy of water.

If there is a high concentration of water ( low concentration of other solutes such as glucose, proteins and electrolytes) then there is a high water potential.

If there is a low concentration of water (high concentration of solutes) then there is a low water potential.

(http://www.mrothery.co.uk/images/Image72.gif)

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Water potential (m)

water diffuses by osmosis from a high water potential  to a lower water potential.

e.g.

If the concentration of glucose outside a cell increases i.e the water potential decreases, then water inside the cell, will diffuse by osmosis down a conectration gradeint from a high water potential to a low water potential across a partially permeable membrane. 

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Measuring Glucose Concentration (n)

A test strip is placed in the glucose test meter. Skin is then disinfected with alcohol and use a sterile lancet inside the device to ***** your finger to produce a drop of blood. 

biosensor is used to measure blood glucose concentration levels. 

the biosensor contains a test strip with the enzyme glucose oxidase on it. Glucose oxidase converts glucose in the blood into gluconolactone. As this occurs, a small current is produced which is picked up by an electrode and a digital display of the blood glucose concentration reading is given. 

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Structure of Carbohydrates (o), (p)

Below are the structures of a monosaccharide, disaccharide and polysaccharide. These are all types of CARBOHYDRATES.

(http://chemistry2.csudh.edu/rpendarvis/1feb23.gif)

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The role of glucose as a respiratory substrate (n)

Glucose is easily broken down by cells during aerobic respiration

Glucose is a good respiratory substrate becasue it can be easily broken down by cells to produce ATP.

General

Glucose is water soluble so it affects the water potential of cells. It is not lipid soluble as it is a polar molecule, therefore can't pass through the phospholipid bilayer.

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Formation of Glycogen (r)

Glycogen is formed by a condensation reaction between two glucose molecules. A glycosidic bond forms.

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The structure of glycogen (s)

Glycogen is a storage polysaccharide. It is stored in the liver and the muscle cells.

It is ideal as a storage polysaccharide becasue;

1) It is highly branched which means that there are lots of "ends" for enzyme attachemnt so glucose can be rapidly released.

2) It is small and compact so a lot of glycogen can fit into a small space. 

3) It is insoluble in water, therefore the water potential of cells is uneffected. 

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Lipids (t)

There are three main types of lipids. These are triglycerides,phospholipids,cholesterol.

Glycerol

Glycerol is an alcohol. 

(http://www.proprofs.com/quiz-school/user_upload/ckeditor/Glycerol.jpg)

Fatty Acids 

Contain the carboxylic acid group.

(http://study.com/cimages/multimages/16/saturatedfattyacidpicture2.png)

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Formation of Triglycerides (u)

triglyceride is formed by adding 3 fatty acids to one glycerol molecule. The fatty acids are joined by ester bonds to the glycerol molecule. 

Again, it is formed by a condensation reaction. It is broken down by hydrolysis

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Saturated and Unsaturated Fatty Acids (v)

saturated fatty acid only contains single bonds between the carbons. This means it has the maximum number of hydrogens, hence "saturated". Saturated fats have a higher melting point than unsaturated fats. 

An unsaturated fatty acid has double bonds between carbon atoms. Therefore, it does not have as much room for hydrogen atoms as each carbon atom can only have 4 bonds, 2 bonds are taken up by the double bond.

Fatty acids store chemical energy in their hydrocarbon chains. Therefore, triglycerides are another source of stored energy in adipose tissue. Triglycerides are also insoluble in water.

Adipose tissue also acts as an insulator under the skin and around delicate organs. 

Fat soluble vitamins such as Vit A and D, are stored in lipid globules inside the liver cells. 

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Phospholipids (w)

Phospholipids are polar molecules. They form a bilayer which is important in plasma membranes.

A phospholipid molecule is made up of 2 fatty acids and 1 glycerol moleucle. Instead of a third fatty acid chain, a phosphate group is added. It has a polar head and a non-polar hydrocarbon chain.

The kink in phospholipids are due to the carbon-carbon doube bonds in the hydrocarbon chain of the fatty acid chain (unsaturated). This makes decreases the melting point and increases fluidity, a characteristic which is important in the phospholipid bilayer. 

(http://cnx.org/content/m44401/latest/Figure_05_01_03a.jpg)

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Lipids

Cholesterol is also a lipid. It is specifically a steroid. It is also present in the phospholipid bilayer of plasma membranes.  Transport  As lipids are insoluble in water, they can't be trasnported in the blood plasma. Triglycerides in the adipose tissue will break down into the components glycerol and fatty acids. Glycerol can be trasnported in the blood plasma as it is insoluble. Fatty acids will combine with plasma proteins and cna be carried in the blood as small globules. 

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