Structure of the Lungs

The structure of the lungs covers some basic GCSE revision. There is a GCSE review on the SNAB website for you to read through and a short test to see if you're up to date. We won't snoop at the test marks and use them against you. Promise.

The main components of the respiratory system are involved in the movement of gases, either into or out of the lungs.

Useful Links:

GCSE Bite Size Respiration
GCSE Bite Size Respiratory System
SNAB online
Franklin Institute
Inside the human body

Extension:
New Scientist: Stem Cells breathe new life into lung therapy

Activity
Revision Worksheet Available until 24th October 2007

Surface Area to volume ratio

The smaller an object or organism the larger the surface area to volume ratio. The more folds in the surface, the larger the surface area to volume ratio.

the above diagram shows this, the solid block has a smaller surface area to volume ratio than a pile of boxes making up a shape the same size.

Why is this important? If a biological process of benefit to us takes place at the surface of something, then the more surface the more opportunity for the process to take place.

Links:

Exams Tutor
Modelling Activity
Summary Site
Maths revision

Extension:
National Geographic - Different Size Dinosaurs

Sticky Mucus

In normal lungs mucus has a vital role in maintaining normal function. Mucus traps any invading bacteria and with the aid of cilia (fine hair like structures in the lung) move the invading organisms along.

Sufferers of Cystic Fibrosis have a thicker and stickier than normal mucus. Instead of moving bacteria along it traps them in situ and causes an increase in lung infection.

Additionally; Sticky mucus blocks some of the passages in the lungs limiting the area in which gas exchange can take place.

Links
Cystic Fibrosis Trust
BBC Health
Bupa
Wellcome trust

Extension
New Scientist: Drug takes no nonsense from cystic fibrosis

Gas Exchange in the lungs

Gas exchange takes place in the lungs between the alveoli and the capillaries that surround them. Oxygen is breathed in and passed into the circulatory system. The blood containing oxygen is oxygenated. Carbon dioxide is passed from the blood into the lungs. Blood carrying carbon dioxide is deoxygenated.

This process is essential for respiration. Respiration provides the energy vital for all functions in the body. If you look at the structure of the alveoli you will see that these small highly folded structures are well designed for gas exchange.

There are three factors that are important for efficient gas exchange

• Surface area(the more area for exchange, the more exchange can take place)
• Concentration of gas (the more gas, the more gas exchange)
• Thickness of surface (less distance for gas to travel, then more gas exchange)

This can be summarised in Ficks Law:



Links:
Biology Mad

Video:

protein structure

The job of a protein is completely determined by the structure of the protein, from the smallest to the largest part. There are several ordered layers to the structure

1. The primary structure
The primary structure is the sequence of amino acids found in the polypeptide chain. Amino acids are joined together by peptide bonds which are formed in a condensation reaction.

There are three main components to an amino acid:

a. Carboxyl group: COOH
b. Amine group: NH2
c. Residual group: R

It is the residual group that determines the character of the amino acid, and in turn the structure and function of the whole protein!

2. Secondary Structure
There are two forms of secondary structure

a. Alpha Helix: Where the chain twists up to form a spring like structure. Hydrogen bonds forming between the C=O of the carboxyl group and the -NH of the amine group.

b. Beta pleated sheets: Several chains link together with hydrogen bonds to form a pleated motif.

Both of these structures can occur in one protein.

3. Teritary and Quarternary structure
When the chain bends into a three dimensional shape it is reinforced by chemical bonds between the R groups.

Some proteins can be made up of more than one polypeptide chain and this is the quaternary structure. For example, haemoglobin is made up of four polypeptides.

Globular proteins vs. Fibrous proteins Textbook page 59

Links:
SNAB tutorial note: you may need to log in before folowing this link
Unilever tutorial
Protein Data Bank

Extension:
Medical Research Council CF tutorial

Activity:
Revision Worksheet Available Until 24th October 2007

Cell membranes

There are several components to the plasma membrane.

1. Phospholipid.
The phospholipid has a hydrophillic head and a hydrophobic tail. The heads will point towards water while the tails will turn away. The membrane is a bilayer so two layers of phospholipids.

2. Transmembrane proteins
These are usually channel proteins involved in transport that span across the membrane. Trans means across so Transmembrane - across membrane. These proteins are usually involved in transport.

3. Glycoproteins and Glycolipids
These are proteins or lipids with a polysaccharide tail attached. Poly meaning many and Saccharide as in sugar, so a tail of many sugars. Glycolipids are lipids with polysaccharides attached and Glycoproteins are proteins with sugar tails.

The fluid Mosaic Model.
The components of the cell membrane are not fixed - they are fluid and move around, and it is called a mosaic model because it is made up of so many different parts.

Links:
Cell Membranes Tutorial

Activity:
Revision Worksheet Available until 24th October

Transport across a cell membrane

Diffusion: Movement of molecules from a high concentration gradient to a low concentration gradient. This is a passive process.

Osmosis: Movement of water from low water potential to high water potential. This is a passive process.

Facilitated Diffusion: Process where molecules that are too large to diffuse across the membrane are aided by channel proteins that provide them with a route to travel. From a high concentration gradient to a low concentration gradient, this is a passive process.

Active Transport: Transport of molecules against the concentration gradient. Molecules are forced through a channel/carrier protein with the aid of energy in the fom of ATP. This is an active process as it requires energy.

Endocytosis: Movement of material in bulk into the cell. In the form of a discrete package that fuses with the plasma membrane releasing matter into the cell.

Exocytosis: Movement of material in bulk out of the cell. A discrete package fuses with the plasma membrane releasing matter out of the cell.

Links:
GCSE Bitesize
Extension:
Revision PDF

CFTR

CFTR - Cystic Fibrosis Transmembrane Receptor Protein

In the cell membrane of the epithelial cells that line the lungs there is a transmembrane protein called CFTR. This helps regulate the consistency of mucus in the lungs.

If the mucus is too watery Chloride and Sodium ions are pumped away from the mucus, this creates a change in water potential and water leaves the mucus.

If mucus has too little water, chloride and sodium ions pump in and water follows, hydrating the mucus.

In CF the CFTR which regulates the transport of Chloride ions into the mucus is defective, so it is not possible to hydrate the mucus.

Links:
CFTR gene
CFTR review page

DNA base pairing

DNA is made up of three units.

1. Phosphate group
2. Deoxyribose sugar
3. Nucleotide or Nitrogenous Base

There are four different bases found in DNA.

Adenine (A)
Thymine (T)
Guanine (G)
Cytosine (C)

They bind very specifically; so A only binds to T and G only binds to C

Links
Base pairing
Biochem site
Genome talking glossary
Genetics home reference

Extension
National Centre for Biotechnology Educatioan

Transcription

Transcription is the process of transcribing DNA so that a copy can be taken away and used as a template for making proteins.

The hydrogen bonds between the two lengths of DNA are forced apart and a length of ribonucleic acid, or RNA, is formed.

In RNA there is no T (thymine), instead there is a different nucleotide, Uracil (U), which pairs with A.

Each set of 3 RNA base units forms a codon.

Codons are
1. Non overlapping
2. Degenerate
3. Triplet code
4. Codes for one amino acid

This first type of RNA is messenger RNA or mRNA

Links
Gene Expression- Transcription
Interactive tutorial
Molecular Biology Notebook

extension
New Scientist - Biology's Master Chefs

Translation

Translation is the process where the copied stretch of mRNA is translated into proteins.

This occurs in ribosomes, either free floating in cells or bound to the endoplasmic reticulum.

An enzyme called RNA polymerase catalyses the reaction. A tRNA triplet code lines up alongside the single stranded mRNA molecule. tRNA has an amino acid binding site attached, and the amino acid that binds is dependent on the codon of the tRNA molecule.

When two amino acids are next to each other on the tRNA then a peptide bond forms between them and the first amino acid breaks free of the tRNA.

Links:
Ultranet
Translation animation
Thinkquest notes

Activity:
Thinkquest Quiz

DNA replication

DNA replication involves the separation of the two strands. The hydrogen onds break and the DNA helix opens. Nucleotides that are free within the nucleus then come and bind with the open DNA. Because the nucleotides are specific you end up with one old strand of DNA bound to a complementary new strand of DNA.

This was discovered by Meselston and Stahl in various experiments outlined on the SNAB website.

This is called a semi-conservative method of replication because half of the DNA is conserved or kept.

Links:
DNA replication animation
Essential Biochemistry
Another animation

Monohybrid Inheritance

Cystic Fibrosis is affected by only one gene and because of this it is inherited by a process called monohybrid inheritance. This simply means that only one gene is involved.

Cystic Fibrosis is a recessive condition, which means only if an individual is homozygous for for the disorder they will show it.

If an individual is heterozygous and has the condition then they are a carrier of cystic fibrosis.

Links:
Genomics Website
CF website
Bitesize

Gene therapy

Gene therapy is a treatment type that means changing a defective gene that causes a disease. This can mean replacing the gene that doesn't work with a functioning gene, or even 'knocking out' the gene all together.

There are two methods of delivering the new gene to the affected DNA

1. Liposome
2. Viral

In CF this isn't especially effective, but it has cured a rare immunodeficiency disease. Gene therapy affects somatic cells only, it is not a germ line therapy.

Links
Human Genome Project

Extension:
Guardian Special Report

Electrophoresis

Agarose Gel Electrophoresis is a technique used in genetic screening to determine whether a gene is present or not.

First the DNA is cut using a restriction enzyme. These recognise specific sequences of DNA and make an incision if they find it. If the sequence isn't present, the enzyme will not cut.

The electrophoresis chamber runs from negative to positive and because DNA has a slight negative charge it will be drawn to the positive end.

DNA is separated on the basis of size, smaller fragments running faster.

If a gene is present a probe is inserted that recognises and binds to the sequence. This is how CF is screened for.

Note: The electrophoresis practical (activity 2.19) is a core practical and all questions must be answered.

Links:
University of Utah virtual lab
Colorado state university
Gene almanac animation

Genetic Screening

An ethical dilema??

Ethics:The rules or standards governing the conduct of a person or the members of a profession.

We have the ability to screen individuals for potential transmitance of a disease, we can also screen embryos. But what does this achieve?

Some helpful sites relating to your half term assignment: