biology topic 1 & 2 - notes

Edexcel AS Biology Revision Notes Written by Tim Filtness

Unit 1: Lifestyle, Transport, GenesUnit 1: Lifestyle, Transport, GenesUnit 1: Lifestyle, Transport, GenesUnit 1: Lifestyle, Transport, Genes & & & &

HealthHealthHealthHealth Topic 1: Lifestyle, health & Risk 1.1.2

Water molecules are polar

H = Positively charged (+) O = Negatively charged (-) This allows them to form Hydrogen Bonds with other water molecules. This gives water some useful properties;

Property Explanation

Less dense as a solid Arctic ecosystems float, ice insulates water beneath it etc

High SHC Cells do not heat up or cool down easily, therefore can hold a fairly stable temp. (cf enzymes)

Present naturally in all three states

Allows the water cycle to function

Transparent Allows photosynthesis underwater

Cohesion Generates surface tension, capillary uptake, transpiration etc

Good solvent Essential role in transport in biological systems

Immiscible with hydrophobic molecules

Allows membranes to form and, therefore, control movement in / out of cells

High latent heat of evaporation

Evaporation of water has a strong cooling effect and comparatively little water is required to lose a lot of heat

Buffer Water is capable of accepting and donating protons, therefore acts as a buffer

Edexcel AS Revision


1.1.3 Saccharides are made from sugar molecules, which are made from combinations of the elements Carbon, Hydrogen and Oxygen only

Saccharides are used for;

1. Fuels for respiration (e.g. glucose) 2. Energy storage molecules (e.g. starch and glycogen) 3. Structural molecules (e.g. cellulose)

Monosaccharides one sugar molecule only Disaccharides two sugar molecules joined together Oligosaccharides a few sugar molecules joined together Polysaccharides many sugar molecules joined together You need to know the different structures of glucose. You should be able to draw this out if requested.

Disaccharide Name Component monosaccharides

Maltose Glucose + Glucose

Sucrose Glucose + Fructose

Lactose Glucose + Galactose

Glucose Glucose

H

OH


There are three polysaccharides specifically mentioned on your syllabus (starch, glycogen and cellulose). Cellulose is in Topic 4 (2.4.3) but is included here for reference.

Polysaccharide Structure and Function

Glycogen

1. Made from Poly ( Glucose).

2. Found in muscle and liver cells for energy storage

3. Insoluble, so no osmotic effect in tissues

4. Lots of branches (i.e. 1-6 glycosidic bonds present), which allows quick access to glucose

5. Compact shape, so good for storage

Starch

1. Actually made from two molecules in combination; Amylose and Amylopectin

2. Both are made from Poly ( Glucose).

3. Found in Amyloplasts (starch grains) inside plant cells for energy storage

4. Insoluble, so no osmotic effect in tissues

5. Amylose has no branches (i.e. 1-4 glycosidic bonds only), so access to glucose is slow

6. Amylopectin has some branches (i.e. both 1-4 & 1-6 glycosidic bonds)

Cellulose

1. Made from Poly ( Glucose).

2. Main component of cell walls as it is a very strong structural molecule

3. Insoluble for obvious reasons!

4. Cellulose has no branches (i.e. 1-4 glycosidic bonds only), so adjacent cellulose chains line up close

5. Hydrogen bonds form between adjacent chains, creating very strong cellulose fibrils


Saccharides join together in condensation reactions, which produce water. A glycosidic bond forms between the saccharide molecules. The opposite of a condensation reaction is a hydrolysis. This requires;

1. Heat + HCL 2. OR an enzyme (e.g. Amylase)

1.1.4

Tests for Sacharides:

- Iodine solution turns brown blue/black in the presence of starch

- Benedicts solution turns blue brick red in the presence of a reducing sugar

- Non reducing sugars (most disaccharides and all polysaccharides) will give a positive result to Benedicts if heated in acid first.


1.1.5

Triglycerides are either fats or oils. They are made from the elements C, H & O only.

Triglycerides are used for;

1. Long term energy storage molecules 2. Insulation 3. Protection (e.g. pericardium) 4. Buoyancy 5. Synthesis of specific hormones (e.g. steroids)

The C=C bonds form kinks in the fatty acid chains, which push adjacent triglycerides away from each other. This lowers the effect of intermolecular forces (e.g. van der vaals forces), which lowers the boiling and melting temp.

Triglycerides are formed in condensation reactions between;

1 x glycerol 3 x fatty acid An ester bond forms between the fatty acid and the glycerol

Saturated triglycerides have no C=C bonds in them. They form fats. Unsaturated triglycerides DO have C=C bonds in them. They form oils.

Test for a triglyceride (Emulsion test):

1. Add ethanol (dissolves fat) 2. Add water 3. White precipitate indicates a positive result


1.1.6 Ficks law: Rate of Diffusion = Surface Area x Conc Gradient

Distance If we apply this to a cube, the rate at which O2 reaches the centre of the cube is a product of the ratio of the Surface Area compared to the Volume (i.e. SA:Vol) In humans the mass transport system is the circulatory system and the heart. The specialized exchange organs include the lungs and the digestive system.

Amoeba Large SA:Vol ratio Can rely on diffusion through its surface.

Human Small SA:Vol ratio Diffusion through surface is too slow to supply O2. Therefore require a mass transport system and specialized exchange organs


1.1.7

You need to know;

1. the names of the 4 chambers of the heart

2. the names of the 2 arteries and 2 veins attached to the heart

3. The names of the two sets of valves in the heart

4. The cardiac cycle

5. The initiation and conduction pathways of the heartbeat Contraction in the heart:

Remember, the atria contract first. The L & R atria contract at

the same time. The ventricles contract second. The L & R

Ventricles contract at the same time.

Aorta

Pulmonary Artery

Vena Cava

Vena Cava

Cuspid Valve

Semi-lunar Valve


0 0.2s Atrial Systole The atria contract, atrial pressure rises and blood is pushed from atria ventricles

0.2 0.3s Ventricular Systole

The ventricles contract, ventricular pressure rises above atrial pressure and the cuspid valves shut (1)

Ventricular pressure rises, but no blood leaves the heart yet!

When ventricular pressure rises above pressure in the arteries the semi-lunar valves open (2)

Blood leaves the heart

0.3 0.4s Diastole The ventricles relax. Ventricular pressure falls and when pressure in the arteries > ventricular pressure the semi-lunar valves shut (3).

0.4 0.7s Diastole The entire heart is relaxed. The cuspid valves open (4) and both atria and ventricles fill with blood.


1. SAN sends a wave of electrical activity (depolarization) around the walls of the atria.

2. A ring of insulating tissue blocks the wave from passing into the ventricles.

3. The AVN conducts the wave into the Ventricles slowly, which gives the ventricles time to fill.

4. The Purkinje fibres are fast-conducting and take the wave to the apex of the heart first, so the ventricles contract bottom upwards.

1.1.8

Artery: Arteries carry high pressure blood away from the heart.

Key Points:

collagen & connective tissue

smooth muscle& elastic tissue

lumen (blood)

0.1-10mm

SAN: Sino-Atrial Node AVN: Atro-Ventricular Node Purkinje Fibres (in bundle of His)


1. Thick muscle layer to withstand high pressure blood 2. Elastic tissue allows artery to stretch when blood is forced

into it. The elastic layer recoils during diastole, converting pulsatile into laminar (continuous) blood flow.

3. Protective collagen layer 4. Round shape 5. Relatively small lumen

Vein: Veins carry low pressure blood towards the heart.

Key Points:

1. Thin muscle layer (low pressure blood) 2. Valve to stop backflow 3. Protective collagen layer 4. Not a round shape (wall not thick enough to hold shape) 5. Large lumen (decreases effect of friction)

Capillary: Capillaries are adapted for exchange they are not connected directly to the heart.

basement membrane(collagen)

endothelium cell

red blood cell

8 m

collagen & connective tissue

smooth muscle& elastic tissue

lumen (blood)

semilunar valve

0.1-20mm

Small hole


Key Points:

1. Walls are one cell thick (cells are called endothelial cells) 2. Lumen is the same width as one RBC (therefore more of RBC

in contact with wall, therefore smaller diffusion distance) 3. No muscle or elastic tissue 4. Tiny (compare the scales and remind yourself what a m is)

1.1.9

Dig up your Daphnia Core Practical notes in the Practical Handbook

1.1.10 & 1.1.11 Atherosclerosis is a disease in which the wall of arteries becomes furred up with fatty deposits called plaques or atheromas. The sequence of atherosclerosis is as follows;

1. Endothelial layer on the inside of an artery is damaged

2. Inflammation (an A2 topic) of the artery wall occurs

3. White blood cells move into the artery wall

4. Cholesterol begins to accumulate at the site of damage

5. Atheroma forms

6. Lumen narrows

7. Pressure increases After atherosclerosis has developed there is a chance that a blood clot might form in the damaged area. This makes the problem much worse!

As hypertension speeds atheroma formation these steps are a vicious cycle!


Clot formation:

1. Platelets are activated by substances released by the damaged artery wall

2. Platelets become sticky and form a platelet plug on the surface of the atheroma

3. Platelet plus releases chemicals which activate thromboplastin

4. Thromboplastin initiates the clotting cascade

There is a real danger of the blood clot becoming dislodged from the site of formation. It could be carried around the bloodstream and deposited elsewhere. If this occurs; - in the brain a stroke occurs - in the coronary arteries, CHD or even an infarction might occur - anywhere else, ischaemia and even gangrene are possible

1.1.12 Risk factors for CVD. There are lots, but these 7 are specifically mentioned on your syllabus

Thromboplastin


Risk Factor Explanation

Age Atherosclerosis occurs naturally as our arteries become less elastic with age. Less elastic = higher pressure during systole, hypertension, atherosclerosis bummer.

Gender Girls have less atherosclerosis: fact. Two explanations;

1. Girls make oestrogen, which has a protective effect against atherosclerosis. Evidence to support this theory is that incidence of atherosclerosis in post-menopausal women rises to that of men.

2. Women tend to have less stressful jobs / be at home more less stress less hypertension, etc

Hypertension Speeds up atheroma formation AND causes endothelial damage (which is the 1st step in atherosclerosis)

Smoking Nicotine is very, very good at damaging the endothelium. Remember that next time youre tempted to dally behind the bike shed

Inactivity Allsorts of factors here; - lower BMI = less hypertension - fitter heart = less hypertension - exercise decreases LDL levels - exercise increases metabolic rate lowering BMI - Possibly some indirect contributing factors as well

if you exercise regularly you probably put stock in looking after yourself are you likely to be smoking or drinking as well?

Genetic predisposition Some alleles give you less protection from / greater risk of developing atherosclerosis. To an extent, a higher chance of getting atherosclerosis does run in families

Diet Millions of contributing factors here; - High salt intake causes hypertension - Eating saturated fats decreases HDL level - Eating more calories than you need causes BMI to

increase. High BMI is associated with atherosclerosis

- Alcohol causes hypertension directly


1.1.13

Drug treatments for atherosclerosis and their side effects; Antihypertensives Diuretics The Loop of Henle is the part of the nephron (in the kidney) that regulates water reabsorption. Essentially, it puts Na+ back into the blood by active transport. This lowers the water potential in the blood, so water follows the Na+ by osmosis. Most diuretics block the protein that actively transports the Na+, so less water is returned to the blood, thus reducing the pressure. Three problems with this, however;

1. The blood gets more viscous, which makes the heart beat harder

2. Dehydration can occur 3. Only treating the symptom

Blockers block the adrenaline receptor in the heart. This stops the heart from beating harder in response to stress and, therefore, reduces hypertension. There are some side effects in some cases (e.g. sleep disturbance, depression, vasoconstriction of the extremities) but generally theyre pretty good. One of the main problems is bradycardia, which can become serious if you have CHD. Can you explain why? Ca2+ channel blockers stop the heart muscle from contracting too hard. You dont need to know why, but if youre interested look up Starlings Law of the heart Major side effect is arrhythmia, which can develop into fibrillation and infarction.


ACE Inhibitors are REALLY complicated, but I dont know how much of this youre supposed to know, so here is the full version of things Basically, our kidneys make Angiotensinogen all the time, but it doesnt do anything itself (its not a hormone) it just circulates in the blood. However, when we are hyoptensive (i.e. have low blood pressure) the kidneys start to make Renin enzyme, which turns Antiotensinogen into Angiotensin I. After this, ACE enzymes (found in the endothelial cells lining arteries) quickly turn the Antiotensin I into Angiotensin II, which is a powerful hormone. It has the following effects;

1. General vasoconstriction 2. Causes the hypothalamus to release ADH (look it up from

GCSE, it was in Unit 3), which increases water reabsorption by the kidney

3. Stimulates the brain to release aldosterone, which causes the kidneys to increase salt reabsorption, which in turn increases water reabsorption.

All of these effects increase blood pressure, so ACE inhibitors will, therefore, do the opposite. The major side effect is kidney failure. Vasodilators dilate blood vessels, reducing blood pressure. If this occurs too much you get hypotension, which can cause heart attacks (not enough blood returns to the heart to fill it properly)

Angiotensinogen Angiotensin I Angiotensin II Renin Enzyme ACE Enzyme

A protein made by the kidneys, which circulates in the blood

An intermediate, also circulating in the blood

The important one! This is the hormone that increases blood pressure!


Statins Two effects;

1. Block an enzyme in the liver that makes cholesterol. 2. Remove LDL from the circulation

Associated with liver failure. Anticoagulants As the second stage of atherosclerosis is associated with blood clotting (thrombosis), anticoagulants block the clotting process. There are many, many different ways of doing this. Blood clots slowly. Platelet inhibitory drugs These work in the same way as anticoagulants but target platelets, which are required to activate the clotting process. They, therefore, have the same side-effects.

1.1.14 Cholesterol is the major component in atheromas. High blood cholesterol level is, therefore, a bad thing. We get cholesterol from two sources;

1. Diet 2. It is made by the liver

Lipoproteins (also made by the liver) ferry cholesterol around in the bloodstream and play a role in pushing the liver towards making more cholesterol, or excreting more cholesterol. There are two types of lipoprotein;


High Density Lipoproteins (HDLs) take cholesterol out of the circulation to the liver, where it is converted into bile salts and (ultimately) excreted. HDLs lower cholesterol levels. Low Density Lipoproteins (LDLs) take cholesterol from the liver and put it into the circulation to the liver. LDLs increase cholesterol levels.

Crudely

High HDL = good High LDL = bad High cholesterol = bad

1.1.15 You need to understand that scientists use their scientific knowledge of the effects of diet, exercise and smoking to try and predict risk of CVD and, therefore, to give people advice about how to reduce their risk.

1.1.16

Dig up your Vitamin C Core Practical notes in the Practical Handbook

1.1.17 Body Mass Index = Mass

(Height)2 Your energy budget balances the number of calories you require with those that you consume. Ideally, they ought to be the same.

Energy consumed > Energy expended mass gain Energy consumed < Energy expended mass lost

BMI < 18.5 Underweight BMI between 18.5 and 25 Normal BMI between 25 and 30 Overweight BMI > 40 Obese


1.1.18 & 1.1.19 You need to be able to analyze data on mortality rates to determine health risk. Be careful! If two sets of data follow the same pattern they are correlated

If two sets of data follow the same pattern because one factor directly affects the other they are causal In order to assess whether data is correlated or causal scientists experiment, the idea being to try and falsify the Null Hypothesis that one factor does not affect the other. However, be aware that the design of the experiment often affects the results. Things to watch out for;

1. People selected were not representative of the population (e.g. all students, all female, etc) i.e. not accurate

2. Only a few people were involved in the experiment (i.e. not very reliable)

3. Not all the variables were controlled i.e. a systematic error in the experiment (i.e. smokers included with non-smokers)

If you get a question on this section of the syllabus always

ask yourself WHERE HAS THE DATA COME FROM?

1.1.20 Why might peoples perception of risk be different from the actual risk?

1. They dont understand the risk fully and underestimate it (e.g. if you smoke your risk of CVD is X and if you are obese your risk of CVD is Y. BUT if you are both your risk is not X + Y but XY much greater!)


2. They dont understand the risk fully and overestimate it (e.g. the person who thinks they actually might win the lottery this week)

Broadly speaking, risk factors for CVD tend to be underestimated because people dont realise that risk factors tend to be associated with other i.e. if you smoke and drink and are obese, chances are you also eat a diet high in saturated fat and salt. Quite quickly the risks stack up

Oxygen Dissociation Curve This is not mentioned on the syllabus, but it is in the text book. The prudent man learns it anyway Remember, each Haemoglobin (Hb) can bind up to 4 O2 molecules. The affinity of Hb for O2 changes depending on how many O2 are being carried. A: The haemoglobin is in the lung and is O2 loading. Affinity of Hb is high, therefore it fills up with O2 easily.

A B C


B: The haemoglobin is in the respiring tissues. Initially affinity is high, so Hb does not give O2 away easily to tissues that already have enough. However, when Hb gives up its 1st O2 the affinity suddenly drops, so Hb tends to unload 3 O2 just where it is required! C: With 3 O2 removed the affinity is high again, so the last O2 is kept as an emergency. It is only given up if the Hb passes through tissues with very low PO2 When the line shifts position

1. Foetal Hb has a higher affinity than adult Hb. This is so the foetus will load with O2 from the maternal Hb. Foetal ends with L, therefore shifts to the LEFT

2. Llamas (starts with L) live at altitude and need to have Hb with higher affinity to load O2 in the thin air.

3. Myoglobin (has an L in it) is an O2 store in muscles. It has very, very high affinity for O2 so only gives off O2 when in the emergency section of the graph. Whales and diving mammals have vast quantities of myoglobin in their muscles.

4. Bohr (ends in R) shift occurs when Hb is exposed to acid. The affinity drops and O2 is unloaded more easily. Acids tend to be

- carbonic acid (made from CO2) - lactic acid (made in anaerobic respiration)

Both acids are produced when O2 is in short supply, so it makes sense for Hb to give up more O2 in these circumstances.

End of Topic 1End of Topic 1End of Topic 1End of Topic 1


Unit 1: LifestyleUnit 1: LifestyleUnit 1: LifestyleUnit 1: Lifestyle, Transport, Genes & , Transport, Genes & , Transport, Genes & , Transport, Genes &

HealthHealthHealthHealth

Topic 2: Genes & Health 1.2.2 Cell membranes are made from a double layer (bilayer) of phospholipids, which align heads inwards and tails outward because of their attraction / repulsion from water. Sat in teh membrane are transmembrane proteins. The proteins have a number of roles;

- channels into / out of the cell (see 1.2.4)

- receptors for hormones (tend to be glycoproteins)

- cellular glue joining adjacent cells together (look up desmosomes if youre interested)

- anchors for the cytoskeleton

Edexcel AS Revision

Notes

Charged phosphate head hydrophilic

Uncharged fatty acid tails hydrophobic


1.2.3 Osmosis is the movement of water molecules from high

concentration to low concentration through a partially permeable

membrane.

Water molecules cannot pass through the bilayer itself because they are charged and are repulsed by the fatty acid tails. There are a few theories about how the water actually gets through, but these are the best so far;

1. Passes through special channels called aquaporins 2. Moves through ion channel as ligands on ion complexes (e.g.

with Na+ or Mg2+)

1.2.4 How do molecules move in / out of the membrane?

1. Uncharged hydrophobic molecules (e.g. steroid hormones, cholesterol, ethanol) pass freely between fatty acid tails by diffusion

2. Large hydrophilic molecules (e.g. enzymes) move in by endocytosis and out by exocytosis

3. Small hydrophilic molecules (e.g. glucose, mineral ions, water) move in and out via proteins in the membrane. There are 3 types of these;

Channel Proteins


Movement is governed by molecules diffusing freely through the channel. Sometimes the channel will only open under specific circumstances (i.e. if a certain hormone is present, or under certain environmental conditions e.g. temp, pressure etc). These are gated channel proteins Facilitated Diffusion proteins Protein channel has an active site specific to a particular hydrophilic molecule. It attaches to the molecule, spins around in the membrane and deposits it on the other side. Movement is governed by the concentration gradient. Active Transport proteins As above, but the movement is against the concentration gradient. Energy (in the form of ATP) is required to get movement to occur.

1.2.5

Dig up your Beetroot Core Practical notes in the Practical Handbook

1.2.6 Ficks law: Rate of Diffusion = Surface Area x Conc Gradient

Distance

1111 3333 2222


You should be able to explain breathing in terms of volume and

pressure changes in the Thoracic Cavity (GCSE idea)

Adaptations for rapid gas exchange (all related to Ficks Law)

Remind yourself why humans need lungs in the first place, why

cant we just breathe through our skin like Amoeba do?

Larynx (voicebox)

Bronchiole

Bronchus

Intercostal Muscle

Thoracic Cavity contained within pleural membranes

Diaphragm

Thachea

Ribs

Alveolus

Human Respiratory System

Element of Ficks Law Adaptation

Surface Area Each alveolus has a small SA, but there are millions, which produces a huge total SA

Distance Each alveolus is one cell thick, as are the capillaries which surround them. Therefore, the total diffusion distance is only two cells!

Conc Gradient Ventilation maintains a constantly high PO2 in the alveoli. Additionally, as soon as O2 has been collected by haemoglobin the circulation removes it, therefore maintaining a low PO2 in the blood. This keeps the concentration gradient high!


1.2.7

Amino acids are connected by peptide bonds. They are formed in condensation reactions and broken up in hydrolysis reactions.

Primary Structure a long chain of amino acids connected by peptide bonds. Most proteins do not function in their primary form Secondary Structure the long chain of amino acids is folded into two types of structure;

- Alpha helix - Beta sheet

Both are held together by hydrogen bonds

Test for Protein:

- Biuret solution turns blue purple halo in the presence of protein

Proteins are polymers of amino acids. There are ~20 amino acids, each of which has the same basic structure with a different variable group (R group)


As the shape of a protein determines its function (think about the active site of an enzyme, for example) it is really important that all the bonds holding the shape together form in the right places. The most important bonds are those that hold the 3o and 4o structure together and these all form between R groups of specific amino acids. Therefore;

The specific sequence of specific amino acids determines

the shape of the protein and, therefore, its function.

1.2.8 In the Lock and Key hypothesis, the active site and the substrate are completely complementary.

1. Substrate diffuses into the active site 2. Substrate binds to the active site 3. Bonds in the substrate are broken as a result 4. Products form and unbind from the active site 5. Products diffuse out of the active site

Tertiary Structure sections of secondary structure are folded up further, forming a protein with a 3D shape. The shape is held together by covalent bonds (e.g. disulphide bridges) between R groups of specific amino acids. Quarternary Structure formed when two or more tertiary proteins are combined e.g. haemoglobin is made from 4 x haem proteins


In the Induced Fit hypothesis the mechanism of action is the same except that the active site changes shape to fit the substrate once the substrate has bound. The shape change causes bonds in the substrate to break, forming the products. All enzymes work by reducing the Activation Energy (Ea). This is the energy required to get the reaction to start. Enzymes provide an alternate reaction pathway (i.e. a different way for the reaction to happen in the active site), which requires less energy to start.

1.2.9

Dig up your Enzyme Core Practical notes in the Practical Handbook

1.2.10

DNA is made from many nucleotides joined together. It is, therefore, a polynucleotide Each nucleotide contains 3 things;

(i) Sugar molecule, (ii) Nitrogenous base (iii) Phosphate group (negatively charged)


There are 2 types of nucleotide;

(i) Ribose nucleotides - make RNA (ii) Deoxyribone nucltodies - make DNA

DNA nucleotides have 2H atoms on the C2 carbon atom

RNA nucleotides have an H and an OH on the C2 carbon Other differences: RNA is single stranded, DNA is double stranded RNA has different bases RNA used to make 3 different things (mRNA, tRNA & rRNA),

DNA only used to determine genetic code DNA only found in nucleus, RNA in nucleus & cytoplasm

Polynucleotides are formed by connecting the phosphate group of one nucleotide with the 3rd carbon atom of another, forming the Sugar-Phosphate Backbone

DNA is made from 2 strands of DNA polynucleotides, held together by hydrogen bonds between the bases. Because the strands face in opposite directions DNA is an antiparallel molecule.

H / OH


1.2.11 DNA Synthesis: The proof that DNA Replication is semi-conservative (rather than conservative, or dispersive the other theories) was provided by Meselson & Stahl. Their experiment is shown on the next page (you need to know what they did), but you should be able to interpret their results as follows;

RNA

Adenine (A) pairs with Uracil (T) Guanine (G) pairs with Cytosine (C)

DNA

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

DNA synthesis is semi-conservative (i.e. half of each new strand is old DNA & half is new DNA)

1. Helicase unwinds the DNA forming the replication fork.

2. New nucleotides diffuse into the fork and hydrogen bind with their complementary partners

3. DNA Polymerase joins the nucleotides together forming the new sugar phosphate backbone

You can make this more complicated by looking closely at what happens on the lagging strand, but you dont need to know it (if youre interested look up Okazaki fragments)

Original DNA, all heavy DNA band at bottom of centrifuge

1st generation DNA, old, new DNA band in middle of centrifuge

2nd generation DNA, some and (forms one band at top) & some all new second band in the middle of centrifuge. No other theory predicts formation of TWO BANDS


1.2.12


1.2.12 & 1.1.13 The genetic code is read from the sequence of bases in the DNA. Each of the ~30,000 instructions in the code is a gene and tells the body how to make one specific protein. Genes, therefore, code for proteins. The genetic code is read in sequences of 3 bases, called codons each codon represents one specific amino acid. e.g. in this gene the code is ATG CCA CTA GCA CGC, which corresponds to the following amino acids

1.2.14

Protein Synthesis occurs in two stages;

(i) Transcription

(ii) Translation

A Gene

A Protein


Transcription: Takes place in nucleus A complementary copy of the gene is made using RNA 1. Gene opens up. Hydrogen bonds break between bases

2. RNA nucleotides attracted to complementary bases and form hydrogen bonds.

3. RNA nucleotides joined together by enzyme RNA Polymerase.

4. Complementary RNA copy of gene now made. It is called mRNA (messenger RNA)

5. Single stranded mRNA molecule diffuses out of gene

6. mRNA molecule leaves nucleus through nuclear pore (large holes in nuclear envelope)

7. Many mRNA strands are made before gene closes.

MRNA is complementary, not a copy!

DNA TAC GAA TCT GAG CAC GGC TAT ATC

mRNA. AUG CUU AGA CUC GUG CCG AUA UAG

Translation: Takes place in cytoplasm MRNA code read by ribosome and amino acids assembled in

correct order to make protein 1. mRNA strand binds to cleft in ribosome. Start AUG codon fits

into bottom of P site

2. tRNA diffuses into P site and recognises the mRNA codon using its specific anticodon


3. A second tRNA diffuses into the A site and recognises the

mRNA codon there.

4. The amino acids between the two tRNAs join together forming a peptide bond

5. The tRNA in the P site diffuses into the cytoplasm and binds to another specific amino acid.

6. The ribosome moves one codon down the mRNA chain so that the P site is filled with the tRNA from the A site and the A site is empty

7. When the ribosome reaches the stop codon it releases the mRNA and the amino acid chain.

Most ribosomes translate whilst attached to the rER. The completed primary protein is inserted into the rER, where enzymes fold it into its secondary and tertiary shape. Many ribosomes can translate the same piece of mRNA at the same time. A polysome forms


A Mutation = a change in the genetic code. By changing the genetic code mutations ultimately change the sequence of amino acids in primary proteins. This changes the sequence of R groups in the protein and, therefore, the way in which the protein folds up. This affects on the function of the protein

Any mutation in the CFTR gene that stops / impairs the function of the CFTR protein causes Cystic Fibrosis. To date over 2000 different mutations have been catalogued, each of which causes CF.

Mutation Explanation

Neutral mutations

The function of the protein is unchanged after the mutation (i.e. the protein still does its job as well as it did before the mutation). There are 2 possible causes;

One codon is altered. However, the codon still codes for the same amino acid. Therefore, the protein is the same

A codon is changed, leading to a different amino acid in the primary protein. However, this protein is not in a place crucial for folding, so the protein is still the same shape and functions the same.

Deletion mutations A nucleotide is deleted from the DNA code, which changes all the codons after the deletion. This causes frame-shift.

Insertion mutations A nucleotide is inserted into the DNA code, which changes all the codons after the insertion. This causes frame-shift.

Frame-shift

mutations

All the codons in the sequence are altered, meaning that every amino acid after the addition / deletion is different. Normally, this has a huge impact on the function of the protein.

Non-sense mutations

One of the altered codons in the frame-shifted sequence changes to become a stop codon. Protein synthesis stops half-way through the gene, resulting in only half of the protein being made. Almost always the protein does not function.

1.2.15


1.2.16

Key Definitions:

Gene: a sequence of DNA coding for a specific protein Allele: an alternative version of a gene Genotype: the pair of alleles an individual possesses Phenotype: the physical appearance Recessive: allele does not affect the phenotype in the presence of a Dominant allele Dominant: always affects the phenotype Homozygote: individual possesses two copies of the same allele Heterozygote: individual possesses two different alleles

A Genetic Diagram

Parents Phenotype: Brown eyes Brown eyes

Parents Genotype: B b B b

Gametes: F1 Genotype: B B B b B b b b F1 Phenotype: 3 : 1 Brown eyes : blue eyes

Note the gametes are always put in circles

B b B b

B b

B

b


You also need to interpret inheritance problems involving seed morphology (shape) and plant height.

1.2.17

Goblet cells secrete mucus onto the surface of the epithelium, which lines the lungs. Epithelial cells regulate the water content of mucus. In the alveoli mucus is very watery to allow it to be wafted easily by cilia. However, higher up the lungs water is drawn out of mucus to reduce its volume: one cannot fit the mucus from 6 small bronchioles into one larger one, so water is removed. In Cystic Fibrosis the mechanism controlling the water content of the mucus does not work properly and the water removal process is constantly switched on in all parts of the lung. This means the mucus is too sticky in the alveoli and cannot be wafted.

Disease Heritability Effect

Sickle Cell Anaemia Recessive

A mutation in the haemoglobin genes Cause haemoglobin molecules to stick together inside red blood cells. RBCs become distorted into a sickle shape. They can become stuck inside capillaries leading to clots and stroke. RBCs have limited oxygen carrying capacity.

Thalassaemia

Recessive

A mutation in (usually) the gene coding for alpha haem causes very slow haemoglobin production. This results in anaemia and reduced haemocrit (% RBCs per unit volume of blood). Regular transfusions are required.

Achondroplasia

Dominant

Caused by a mutation in one of genes controlling collagen production in bones. As a result bone growth plates fuse too early, leading to shortening of the long bones. Homozygous dominant genotype is fatal.

Albinism

Recessive

A mutation in the gene coding for melanin protein stops melanocytes from producing melanin. Melanin colours hair, skin etc and provides protection from UV rays.


Normally:

Cystic Fibrosis:

The sticky mucus causes the effects of CF and affects;

a) Lungs, b) Digestive system c) Reproductive system

Cl-

Na+

Mucus

Tissue Fluid

Water

Water

Cl-

Na+

Mucus

Tissue Fluid

Water

Water

X

Cl- moves out of epithelial cells into mucus via the CFTR protein. Na+ is drawn into mucus to balance the charge. Na+ passes between epithelial cells. The combined effect of Na+ and Cl- reduces water concentration making hypertonic mucus. Water is drawn into mucus by osmosis and mucus is dilute.

CFTR is blocked or absent, so Cl- stays inside epithelial cells. Na+ does not move into mucus as there is no charge to balance. Mucus is hypotonic. Water is drawn into epithelial cells by osmosis and mucus is sticky.


1.2.18

The problem with genetic diseases is that they are caused by a mutation that is present in every cell of the body. In order to cure the disease you need to change the DNA in every cell of the body, which is impossible. However, in the case of CF because the CFTR protein is only transcribed by epithelial cells (the cells lining the lungs, digestive system and reproductive tracts) only these cells need to be targeted. So how can you change DNA inside living cells? Answer: use gene therapy, which attempts to add a normal copy of the CFTR gene to the DNA inside epithelial cells. Gene Therapy (in humans no plasmids are used) Step 1: cut out a working copy of the gene from normal DNA using a restriction enzyme. OR use reverse transcriptase enzyme to make a copy of the gene from CFTR mRNA

Step 2: add the gene to a vector, which will insert the new gene into the DNA of the target cell

Step 3: hope the gene is successfully incorporated in the DNA in the nucleus

Tissue Effect of CF

Lungs

Mucus produced is too sticky and blocks the alveoli. This makes the person breathless. The mucus also provides ideal conditions for bacteria, so chest infections are common.

Reproductive system

Mucus blocks the vas deferens in boys and the fallopian tubes in girls, making the individual infertile

Digestion

Mucus blocks the bile duct and the pancreatic duct. Enzymes do not reach the small intestine and food is not digested properly.


Vectors are used to get the working gene into the epithelial cells. Somatic Cells = Body cells. Somatic Cell Gene Therapy therefore only affects the targeted cells

Germ Cells = Gametes. Germ Cell Gene Therapy therefore affects the entire organism that is produced when the gamete is fertilised. NB: Genetic engineering of bacteria is different and involves plasmids and DNA ligase enzyme as well (look it up)

1.2.19

Genetic screening is used to determine whether a person has a genetic disease or not.

Vector Explanation

Liposome

An artificial vesicle. A little bubble of membrane in which the CFTR gene is placed. When the liposome is inhaled the gene can enter the epithelial cell by endocytosis.

Virus

Viruses naturally insert their own DNA into host cells DNA. So, if we remove the viral DNA and replace it with the CFTR gene that ought to be inserted instead.

Method Summary

Amniocentesis

A long needle is inserted through the mothers abdomen into the amniotic fluid of the developing embryo. As this is produced by the embryo it will contain embryionic cells and, therefore, embryo DNA

Chorionic villus

sampling

As above, but cells are taken from the placenta, which is also made by the embryo.

Pre-implantation

genetic diagnosis

(PIGD)

Gametes are fertilized in vitro (outside of the body) and the resultant embryos are then tested. Only embryos known NOT to have the disease are implanted in the uterus.


1.2.20

End of Topic 2End of Topic 2End of Topic 2End of Topic 2

Advantages of genetic testing Can opt for termination Can get counselling Can buy special medical

equipment / care in preparation for birth

Can opt not to have children (if parents are tested)

Utilitarian argument

Disdvantages of genetic testing Abortion is morally wrong Tests can be inaccurate Small chance of test

resulting in miscarriage Unnatural procedure Embryos right to life Embryos cannot give

informed consent

biology topic 1 & 2 - notes

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