Topic 2

2.1 ii Ficks law of diffusion

Ficks law = rate of dissusion is proportional to (surface area x difference in concentration)/ lenght of diffusion pathway (membrane thickness)

• If there is a large surface area there is more area for diffusion to occur over
• if there is a steep concentration gradient, diffusion occurs at a faster rate
• If the membrane thickness is thin then there is a shorter diffusion pathwas so it can diffuse at a faster rate

2.1 iii - alveoli adaptations

• There is a steep concentration gradient between the capillaries and the alveoli - the levels of carbon dioxide in the alveoli are low and high in the blood, whereas the oxygen levels are low in the blood and high in the alveoli, providing a steep conc gradient for each gas to travel up

• The alvoli are one cell thick, as are the capillaries and so there is a short diffusion pathway 

•  The shape of the alveoli is a wrinkly bulb, giving it a larger surface area than if it was smooth, there is also lots of them, which means there is a larger surface area for diffusion to occur over.

2.2 - cell membrane stucture

phospholipds = allows passage of lipid soluble substances / prevents passage of water soluble substances 

Cholesterol = regulates fluidity and stability and restricts movement

Glycolipids = antigens for cell recognition

Channel proteins = allows small charged, molecules through the membrane

Carier proteins = transports large molecules across the membrane

Glycoproteins = antigens for cell recognition and binding sites for hormones and antibodies/ transfort proteins/ cell adhesion

2.2 - cell membrane properties

Phospholipids:

• Hydrophylic head = meakes protein structure water soluble (polar)
• Hydrophobic tail = non-polar and wont interact with water
• The phospholipids make up the majorit of the fluid mosaic model

Intrinsic proteins = inside / all the way through

Extrinsic proteins = outside / on the surface

2.3 - osmosis

Osmosis is the movement of water molecules from an area of of low concentration of solute molecules to and area of high concentration of solute molecules  through a partially permeable membrane

There is no energy required for osmosis 

2.4 i - passive active and bulk tarsnport

Passive Transport:

• Facilitated Diffusion - goes doen concentration grandient - doesnt require ATP - it moves larger and polar molecules - requires a carrier / channel protein.

• Diffusion - gows down concentration gradient - doesnt require ATP - it moves small and non polar molecules

Active Transport :

• Requires energy in the form of ATP (adenosine triphosphate)
• it goes against the concentration gradient
• it uses a carrier protein

Endocytosis = Bulk transport into cell via vesicle - requires lots of ATP

Exocytosis = Bulk transport out of cell via vesicle - requires lots of ATP

2.4 ii - Carrier and channel proteins

Carrier protein:

• transports large and charged molecules across the membrane
• Are used in facilitated diffusion and Active transport

Channel protein:

• transports small and polar molecules across the membrane
• Are used in facilitated diffusion 

2.5 i - mononucleotides

• A nucleotide is a Phosphate group, a pentose sugar and a nitrogen containing base all bonded together
• In DNA the pentose sugar is deoxyribose
• In RNA the pentose sugar is ribose

The bases:

• A = adenine - Purine Base        }      has two nitrogen containing rings
• G = guanine - Purine Base        } 

• T = thymine - pryimidine base       }
• C = cytosine - pyrimidine base       }         has one nitrogen containing rings  - a purine base always pairs 
• U = uracil - pyrimidine base            }      with a corresponding pyrimidine base

Each nucleotide bonds via a phosphodiester bonds between the phosphate and pentose sugar - ligase catalyses this reaction.

Each chain of nucleotides has a 5 prime and three prime end ( where carbon 5 is at one end and carbon 3 at the other) DNA has two chains running antiparallel.

2.6 i Transcription

• RNA polymerase carries out transcription
• Helicase unwinds the section / gene being transcribed
• Compliamentry base pairing between the DNA template (antisense) strand and nucleotides occurs
• mRNA leaves the nucleus and attackes to the ribosome

key words:

• polypeptide = chain of amino acids
• mRNA = messenger ribonucleic acid
• tRNA = transfer ribonucleic acid
• RNA polymerase = joins the nucleotides together during complimentary baseparing
• Helicase = breaks hydrogen bonds between DNA bases

2.6 i translation

• Codons on the sense strand (copy of DNA/mRNA) pair with anticodons on the tRNA
• the ribosome acts as framwork holding the mRNA and tRNA amino acid complex together
• tRNA are attached to amino acids
• The sequence of bases determines the sequence of amino acids, these join together via a peptide bond
• the ribosome continues along the mRNA untill it reaches a stop codon, at which point the tRNA no longer attaches to its codons, and the peptide chain is cast off

2.7 - nature of the genetic code:

• triplet code = a sequence of three nucleotides on a DNA or RNA strand, which codes for a specfic amino acid in protein sysnthesis
• the genetic code is degenerate because there are a number of amino acids which can be coded for by different codons
• non-overlapping = no single base on a condon can code for more than one amino acid, as the triplet code is read once only

2.8 - Genes 

• A gene is a sequence of bases on a DNA molecule that codes for a sequence of amino acids in a polypeptide chain
• A gene has a locus, which is its specific place on a chromosome
• A gene can code for phenotypic features, such as hair colour and eyecolour

2.9 i - amino acid structure

• All amino acids have an amine group and a carboxylic group, the variable group is R, there are 20 different types of R group.

                                                          H           H           O      

                                                N --- C --- C  

                                          H            R           OH

2.9 ii - Peptide bonds + primary structures 

• Amino acids join together via a peptide bond
• this is a condensation reaction
• peptide bonds can be broken via hydrolysis
• the peptide bond forms between the OH group on one amino acid and the H group on the other by displacing these groups and producing water 
• Amino acids joined together is called a polypeptide

Significance of the primary structure 

• the primary structure is important in determining the three dimentional structure of a protein has the order of amino acids will determine where the hydrogen bonds will form once the protein starts to fold
• If the order of amino acids is wrong and there is a mutation, the protein will potentially fold in the wrong places or not at all, making the protein ineffective at its role

2.10 i - 3D structures of enzymes

• Primary structure = polypeptide chain
• Secondary structure = hydrogen bonds interact with the R groups of amino acids to make alpha helix's or beta pleated sheets
• Tertiary structure = The alpha helix's and beta pleated sheets then fold again into a 3D shape due to disulphide bridges (between sulphur elements), ionic bonds (between positive and negative carboxyl groups), and hydrophobic bonds (between two non polar R groups) forming 

For enzymes they must fold correctly for their active site to fit it's substrate

2.10 ii - Enzymes as catalysts

• Enzymes are biological catalysts as they reduce the activation everygy 
• they reduce activation energy by breaking apart their substrate into smaller peices, giving a larger surface area for digestion and therefore reducing the amount of energy needed to break the substrate down.

Intracellular enzymes = catalyse reactions inside the cells

Extracellular enzymes = catalyse reactions out side of the cells 

2.11 - DNA replication

Semi-conservative model

• each cell starts with a full set of DNA in a double helix
• DNA replication starts with the DNA helicase breaking the hydrogen bonds between the base pairs in order to unzip the helix
• free nucleotides from the nucleoplasm are attracted to the exposed bases
• the free nucleotides base pair to the old strands and form new hydrogen bonds
• DNA polymerase binds the free nucleotides together to form a sugar phosphate backbone on the new leading strand
• The lagging strand is sythesised in okazaki fragments which get joined together by DNA ligase
• The DNA then rewinds back into 2 double helix's each containing 1 new and one old strand

2.11 ii - Meselson and Stahl

• Meselson and Stahl used heavy and light DNA in their experiment, they did this by using DNA from E.cloi that had been grown in a medium of the heavy isotope of nitrogen

• All the bacteria at the start of the experiment contained heavy nitrogen
• They then moved the bacteria into a medium containing only the light isotope of nitrogen
• This meant any new nucleotides replicated in the DNA were light and the old ones were heavy
• They then centrifuged the DNA, the heavy nitrogen sank to the bottom and the light collects in a band near the top
• And a band of medium DNA is in the middle, so the medium density DNA must contain both heavy and light DNA
• They then repeated and after two rounds of replication, two bamds were present - one medium and one light

• The presence of both medium and light bands confirmed the semi-conservative model

2.12 i - Mutations

• Insertion = A base gets added in, which moves the whole code down changing the composition of all the triplet codes
• Substiution = One base gets swapped out, this only effects the triplet codon with the mutation in
• Deletion = A base gets deleted from the code, moving the whole code back a base, changing the composition of the triplet codes

These mutations occur when innacuracies with complimentry base pairing occurs and an incorrect base slips into place 

Some mutations have no effect on the organism as some parts of the DNA dont code for anything or the same amino acids is produced by the mutated triplet codon.

2.12 ii - Cystic fibrosis causes

• The CF gene is a section of DNA carrying the code to make CFTR protein
• The CFTR protein contains 1480 amino acids which fold into a channel
• In the CF gene hundreds of mutations have been identified which can give rise to cystic fibrosis
• The muations affect the CFTR protein in different ways:

--> In some cases ATP is unable to bind and open the ion channel

--> In other cases the channel is open but changes in protein structure lead to reduced movement of chloride ions trhough the channel

--> the most common muation is known as the DF508 muation, which is the deletion of three nucleotides causing the loss of phenlalanine, which results in th misfolding of the protein

2.13 i - key word definitons

Gene = A section of DNA that codes for a certain characteristic

allele = alternative forms of a gene found at the same locus

genotype = the genetic makeup that gives rise to the phenotype

phenotype = an organisms visible traits - so its physical structure and behavior

recessive = an allele whose effects can he hidden by the presense of a dominant allele and which only comes into effect when two ressesive alleles are present

dominant = An allele whose effects over power that of a ressesive allele and only one dominant allele is needed for its traits to be present, although it can have two dominant alleles with the same effect as one

incomplete dominance = When a dominant allele doesnt prevail over another characteristic trait and so therefore there is a midway characteristic expressed

homozygote = two of the same alleles for a certain trait

heterozygote = two different alleles for a certain trait

2.14 - effects of CF

Gaseous exchange 

• mucus plugs the bronchioli and reduces surface area of the lungs
• hyperinflation causes trapped air in the alveoli which reduces the steepness of the concentration gradient
• mucus around the alveoli blocks the diffusion pathway

digestive system

• the mutated CFTR gene mostly effects the pancreas
• the pancreas secretes substances which help with digestion
• CF causes the secretions to become thick blocking the pancreatic ducts so the digestive system doesnt get enough digestive enzymes

reproductive system

• in children, thickening of mucus can cause obstruction of the hormones needed, causing a lack of development of reproductive organs

2.15 i genetic screening

• identification of carriers - 
• pre-implatation genetic diagnosis - is the genetic profiling of embyos prior to implantation via IVF
• prenatal testing - a set of procedures used to check the genetic health of a baby before its birth, it can diagnose genetic disorders and diseases
• aminocentesis - looks for genetic disorders in unborn babies
• chronic villus sampling - looks for genetic disorders by analysing a small peice of placenta.

Ethical issues - if there is a genetic disorder with the child that is potentialy life inhibiting, then there is a decision to be made about if the baby is born, which poses the question is it ethical to abort a child because they have a genetic disorder.

implications - there is a risk of infection or misscarridge with may of the prenatal testing methods, there is also the rist of termination if there is a disorder with the baby in prenatal genetic screeing.