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A Level Biology

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Sophie Baxter

on 1 May 2014

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Transcript of A Level Biology

A Level Biology
AS Biology

Functions of Water:

- Water is liquid and a solvent and cohesive and can transport substances
-Vital for chemical reactions
-High specific latent heat capacity and high latent heat of evaporation
-Water is a good habitat for many organisms
Structure of Water:

- Water is a polar molecule and
consists of one oxygen atom
joined to two hydrogen
-The shared hydrogen electrons are
pulled towards the oxygen atom, making the hydrogen atoms slightly positive and the oxygen atom slightly negative
-There can be hydrogen
bonding between water
-Hydrogen bonds form
between slightly negative oxygen atoms and slightly positive hydrogen atoms
Properties of Water:

-Hydrogen bonding means that water has a high specific heat capacity (energy needed to raise 1 gram of a substance by 1 degrees Celcius). When water is heated a lot of the heat energy is used to break the hydrogen bonds between the molecules and there is less energy to increase the temperature of the water - this is useful for living organisms as it stops rapid fluctuations of temperature
-Water evaporates when the hydrogen bonds holding the molecules together are broken and molecules escape as gas. Lots of energy needed which means water is good for cooling things - carries away heat energy when it evaporates from the surface
-Water is very cohesive - water is polar so molecules are attracted to each other and this helps water to flow, making it great for transporting substances
- Water has a lower density when solid as in ice water molecules are held further apart which makes ice less dense than liquid water and can float on top of water. Insulating layer on top of water ensuring that the water below doesn't freeze - useful for organisms
-Water is a good solvent as it is polar -
slightly negative end attracted to the
positive ion and vice versa. Ions will be surrounded by water molecules and organisms can transport dissolved substances around body
What Proteins are made from-

-Proteins are polymers made of monomers, or amino acids
-A dipeptide is formed when two amino acids join together
-A polypeptide is formed when more than two amino acids join together
-Proteins are made up of one or more polypeptides

Amino Acid Structure:

-All amino acids have an amine
group and carboxyl group
-The difference between amino
acids is the variable groups
attached to the carbon, the
simplest being a hydrogen, making Glycine
Polypeptide Formation:

-Peptides are joined by
condensation reactions
(the removal of water)
and form peptide bonds
-The reverse reaction is
hydrolysis which splits
the dipeptide by adding water
Protein Structure:

-Protein Structure can be described in four levels
-Primary, Secondary, Tertiary and Quaternary
-The different levels have different types of bonds
Primary Structure:

-The sequence of amino acids in
the polypeptide chain
-Held together by peptide bonds

Secondary Structure:

-Hydrogen bonds form between the -NH and -CO groups of the amino acids
-Will either coil into an alpha helix or fold into beta pleated sheets
Tertiary Structure:

-The amino acid are then coiled and folded further and more bonds are formed such as ionic attractions - between positively and negatively charged
R groups on different parts of the molecule
which are weak.
-Disulfide bridges or bonds
can be formed between
two sulfurs
(in the amino acid cysteine)
-There are hydrophobic and hydrophilic R groups leading to different interactions affecting the final structure. Hydrophobic R groups tend to stick closely to each other so hydrophilic R groups are pushed to the outside
-There are additionally weak hydrogen bonds between slightly positive hydrogen atoms and slightly negative atoms in R groups
-For proteins made up of one polypeptide chain, tertiary structure is the final 3D structure
Quaternary Structure:

-Final 3D Structure of proteins with more than one polypeptide chain
-Haemoglobin is a protein made up of four polypeptide chains
(two a, two b) with a prosthetic haem group, which contains an
iron Fe 2+ ion
Fibrous and Globular Proteins:

-Fibrous - Tough, rope shaped and tend to be found in connective tissue
-Collagen has 3 polypeptides, triple helix with covalent bonds
-Globular Proteins are round and compact and soluble, so easily transported in fluids
-Haemoglobin transports oxygen around the body, hydrophobic side faces inwards and hydrophilic outwards so soluble in water - good for transport in the blood
What Carbohydrate are made from:

-Monosaccharides are the monomers of Polysaccharides
-Alpha Glucose has the H at the top as opposed to the bottom
-It is soluble and easily transported
-Its chemical bonds contain lots of energy and is the main energy source in animals and plants
Polysaccharide Formation:

-Condensation reactions can join monosaccharides together with glycosidic bonds, with the reverse hydrolysis reactions splitting them up again
-Disaccharides are formed when two monosaccharides join together and polysaccharides are formed when more than two monosaccharides join together
Functions of the Carbohydrates:

-Starch is the main energy storage material in plants - cells get energy from glucose and plants store excess glucose as starch, which can be broken down into glucose when needed
-Starch is insoluble in water, and stops water entering cells by osmosis and causing swelling, making it good for storage. It is a mixture of two polysaccharides of alpha glucose
-Amylose is a long, unbranched chain of alpha glucose
-The angles (1,4) of the glycosidic bonds are different between two
alpha glucose molecules than two beta glucose molecules,
leading to a coiled, helical structure which is very compact and makes it good for storage as more can be fitted into a small space
-Amylopectin is a long, branched chain of alpha glucose and has side branches which allows enzymes that break down the molecule to get at the glycosidic bonds easily meaning the glucose can be released easily
-Glycogen is the main energy store in animals, who store excess glucose as glycogen.
It is branched much like amylopectin, except that is has a lot more side branches,
meaning stored glucose can be released quickly. It is a compact molecule which
makes it easier to store
-Cellulose is the main component of cell walls in plants and is made of long, unbranched chains of beta
glucose with straight bonds between the sugars, making the cellulose chains straight.
The chains are linked together with hydrogen bonds to form microfibrils which are
strong fibres that provide structural support for cells in plant walls
Cellular Control
How DNA codes for Proteins
-Genes are sequences of bases that code for one or more polypeptides
-Most genes are in the nucleus in the chromosomes, though a few are in the mitochondria
-Each gene occupies a locus on the chromosome
-1 chromosome = 1 molecule of DNA
-3 bases = amino acid
-Degenerate code - all amino acids except methionine have more than one code
-Some codes indicate 'stop' at the end of the polypeptide
-There are some variations
-The first stage of Protein Synthesis is transcription where free nucleotides are activated - DNA unzips and unwinds into the nucleolus, hydrogen bonds break
-Two extra phosphoryl groups released to give energy for bonding adjacent nucleotides
-mRNA complementary to the template strand, so equivalent to coding strand
-mRNA leaves nucleus to go to ribosomes
-Sequence dictated by codons (three bases)
-Ribosomal RNA and proteins form ribosomes in the nucleus with a groove for the mRNA
-tRNA molecules have exposed bases where the amino acid can bind and three unpaired nucleotides which are anticodons, complementary to the relevant codon
-The amino acid is relevant to the codon
-mRNA binds to the ribosome
-Using ATP and an enzyme, a tRNA with the correct amino acid and its complementary anticodon form hydrogen bonds with the codon (mRNA bonds with tRNA temporarily)
-A second tRNA comes with a different amino acid and binds to the second exposed codon with its complementary anticodon
-Peptide bonds form between the two amino acids, catalysed by enzymes
-Ribosome moves along mRNA, reading the next codon, tRNA with anticodon brings correct amino acid, chain of amino acids forms
-tRNAs can leave and return with more amino acids
-Polypeptide chain grows until stop codon is reached
- Mutation is a random change to genetic material and may occur in DNA Replication in both Mitosis and Meiosis
-Mutagens such as tar, UV light, X Rays and Gamma Rays can also cause mutations
-Mutations during meiosis can be inherited
-Point mutations are effectively substitutions
-Insertion and Deletion mutations cause frameshifts
-Cystic Fibrosis - Deletion of triplet
-Sickle Cell Anaemia - point mutation on codon 6 of the gene for the beta polypeptide chains of haemoglobin
-Point mutations can result in cancer
-Huntingdon Disease - Expanded triple nucleotide repeat
-Mutations can be neutral or effective
-Sometimes can be positive or negative depending on the environment
The Lac Operon
-E Coli ordinarily only have small amounts of Beta galactosidase and lactose permease to metabolise lactose, but the presence of lactose can induce the production of the enzymes through the lac operon
-Z - BG
-Y - LP
-O - Operator region
-P - Promoter region
-I - Regulatory gene
-Lactose absent - I synthesises repressor protein which binds to O and covers part of P so RNA Polymerase can't attach
-Structural genes cannot be transcribed into mRNA or translated into proteins
-Lactose present - lactose binds to repressor protein, changing its shape so it can't bind to O and breaks awya from the O region
-P unblocked, RNA Polymerase binds to P, enables synthesis of Z and Y
-Bacteria can break down the lactose into glucose and galactose and be used in respiration
Homeobox Genes
- When cells are dividing in the fruit fly, at first no new cell membranes form, but by the 11th mitotic division, the 256 nuclei have formed an outer layer around a central yolk filled core
-The nuclear genes start transcribing and the plasma membrane folds inwards around the now 6000 nuclei and a new outer layer is formed
- After several hours there are segments which correspond to the body plan - thoracic, head and abdominal segments
-Some genes refer to which end is anterior and posterior (maternal genes, polarity)
- Segmentation genes determine the polarity of each segment
-Homeotic selector genes specify the identity of each segment and the development of each segment - complexes that regulate head and thorax, and thorax and abdominal segments
- Homeobox genes can initiate transcription, so regulating the expression of other genes
-Arranged in Hox Clusters
-Worms - 1 cluster, Fruit Fly, 2 clusters, Vertebrates - 4 clusters
-Homeobox genes expressed in specific patterns in certain stages during the development of the embryo in invertebrates and vertebrates
- Apopstosis is programed cell death that avoids the release of harmful hydrolytic enzymes after around 50 mitotic divisions
-Enzymes break down the cytoskeleton with organelles becoming tightly packed
-Membrane changes as blebs form, and the chromatin condenses and the nuclear envelope breaks, releasing DNA fragments
-Breaks into vesicles that are engulfed by phagocytosis and is a quick process
-Controlled by cytokines and hormones, growth factors, nitric oxide which makes the inner mitochondrial membrane more permeable tyo protons
-Very important fro getting rid of excess cells and can destroy ineffective T Lymphocytes, cause the digits to seperate from each other
-Not enough Apoptosis leads to tumours but too much leads to cell loss and degeneration
What Lipids are made from-

-Lipids are not polymers
-Made up always of hydrocarbons and other components depending on the lipid's function

-Made up of one molecule of glycerol and three fatty acids joined by ester bonds
-Fatty acids are a carboxylic acid group with long hydrocarbon tails which are hydrophobic making fatty acids insoluble in water
-Saturated fatty acids have no double bonds whereas unsaturated fatty acids have one or more double bonds

-Phospholipids are found in membranes and are very similar to triglycerides except one of the fatty acids is replaced by a phosphate group
-Phosphate group is ionised and attracts water
-The phosphate part is hydrophilic and the rest is hydrophobic

-Type of lipid that can be used to make steroids and can be found in membranes
-Hydrocarbon ring and tail with hydroxyl group making it soluble in water but not blood, meaning its carried around by lipoproteins
Functions of Lipids-

-Triglycerides can be used for energy storage - when broken down, the hydrocarbon tails release a lot of energy
-Insoluble and bundle together as insoluble droplets
-Phospholipids form the bilayer of cell membranes, with the membrane being hydrophobic in the middle
-Cholesterol helps to strengthen the membrane and can fit in between the phospholipid molecules in the membrane and binding to the hydrophobic tails, packing them closer together to increase rigidity of the membrane
Biochemical Tests for Molecules
Biuret Test for Proteins-

-First add sodium hydroxide to the sample to ensure conditions are alkaline
-Copper(II) Sulfate solution added
-If protein is present, the solution will turn purple
Benedict's Test for Sugars-

-Benedict's Reagent added to sample which is heated
-If Reducing Sugars are present, a brick red precipitate will form, otherwise it will stay blue
-To test for non-reducing sugars the sample is boiled with dilute hydrochloric acid then add sodium hydrogencarbonate and add Benedict's, which will go brick red if non-reducing sugar is present
Quantitative version of the Benedict's Test-

-A colorimeter can be used which measures the strength of the solution based on the amount of light that passes through it - more concentrated, more absorbed
-Need to measure the Benedict's solution after the test, and make a calibration curve
-Several glucose solutions with different concentrations and do a Benedict's test
-Remove precipitate by leaving the test tubes for 24 hours or centrifuge them then use a colorimeter with a red filter on the test tubes and make a calibration curve
-Use the graph to find unknown glucose concentrations
Iodine Test for Starch-

-Add iodine dissolved in potassium iodide solution to the test sample
-If starch is present there will be a colour change from browny-orange to a very dark blue black colour
The Emulsion Test for Lipids-

-Shake test substance with
ethanol then pour into water
-Lipids will show up as a
milky emulsion
Nucleic Acids
DNA Function-

-DNA stands for deoxyribonucleic acid
-Contains your genetic information

DNA Structure-

-Has a double helix structure
-The strands are polynucleotides and are made up of many nucleotides in a long chain
-DNA molecules are really long and are also coiled up really tightly so that a lot of genetic information can fit into a very small space in the cell nucleus
-Each nucleotide is made up of a phosphate group, a pentose sugar (deoxyribose) and a nitrogenous base
-There are four bases - Adenine and Guanine (Purines) and Thymine and Cytosine (Pyrimidines)
-The nucleotides form polynucleotide strands with the bases joining between the phosphate and sugar groups, forming a sugar phosphate backbone
-There are hydrogen bonds holding the two strands together between complementary base pairs - one purine and one pyrimidine in each pair - A pairs with T and has two hydrogen bonds whereas C pairs with G and has three hydrogen bonds
-the strands are also antiparallel which forms the DNA double helix
RNA Function-

-RNA stands for ribonucleic acid
-There are different types of RNA, the main one being mRNA

RNA Structure-

-RNA is also made up of bases like DNA
-It also has polynucleotide strands with a sugar phosphate backbone
-There are differences though, as the sugar in RNA nucleotides is ribose sugar, not deoxyribose although like deoxyribose, it is still a pentose sugar
-The nucleotides form a single polynucleotide strand not a double one
-Uracil, U, a pyrimidine replaces Thymine as a base, and will always pair with adenine in RNA
DNA Replication
Why DNA replicates-

-DNA copies itself before cell division so that each new cell has the full amount of DNA
-This is important for making new cells and passing genetic information from generation to generation

How DNA is replicated-

Protein Synthesis

-DNA contains genes which is a sequence of DNA nucleotides that codes for a polypeptide or protein
-Proteins are made from amino acids - the order of bases in a gene determines the order of amino acids in a protein
-Three bases = 1 amino acid - different sequences of bases code for different amino acids

Gene Mutations-

-Mutations are changes in the base sequence of DNA - may also change the sequence of amino acids and thus the overall protein
-This may affect the protein's overall shape so a different or non-functional protein may be produced

DNA, RNA and Protein Synthesis-

-DNA is found in the nucleus of the cell
-Ribosomes assemble proteins and are found in the cytoplasm
-The gene is copied onto mRNA as DNA is too large to leave the nucleus and joins with the ribosome in the cytoplasm to make the protein
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