AS Biology, topic 1

Atoms can combine using:

• Covalent bonding-atoms share electrons to fill both outer shells-more stable
• Ionic bonding-positive and negatively charged ions attract to form ionic bonds (weaker than covalent)
• Hydrogen bonding-neg and pos regions of different molecules attract forming an electrostatic bond. Individually, weak, but collectively these bonds form important forces, especially with water

• Made up of carbon and water, so all contain elements C, H and O
• Most are polymers, as carbon atoms readily form bonds with each othe, allowing sequences that other atoms can attach to, to build. So, they're made of monomers, e.g. monosaccharides, nucleotides and amino acids
• The basic monomer in carbs is a sugar (a saccharide); a single momomer in a carbohydrate is called a monosaccharide- 2 can combine to form a disaccharide, then polysaccharides
• Monosaccharides have the general fromula (CH2O)n. Examples inc glucose. fructose and galactose. Glucose is a hexose sugar; monosaccharide with 6 carbon atoms per molecule. There are two types of glucose, which are isomers: alpha and beta
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Condensation reactions

They join 2 monosaccharides together to from a disaccharide; forms a glycosidic) and releases a water molecule. E.g.

• Glucose + glusose= maltose
• Glucose + fructose= sucrose
• Glucose + galactose= lactose

Hydrolysis reactions

Break polymers down into monomers by breaking the chemical bond between them with a water molecule. This can break carbohydrates down into thei constituent monosaccharides

'Sugar' is a general term for mono/dissacharides; all sugars are either reducing or non- reducing:

Reducing sugars:

• This inc all monosaccharides and some disaccharides (e.g. maltose and lactose)
• Add an excess (to ensure all sugar reacts) of (blue) Benedicts reagent to the sample, heat in a water bath until it is boiling
• If test is positive, a coloured precipitate will from (blue, green, yellow, orange, brick red). The higher the colour change, the higher the concentration of reducing sugar. This is a semi-quantitative test that can be used to compare amounts in different solutions; a more accurate way would be filter and weigh solutions

Non-reducing sugars:

• Have to break the disaccahride down into monosaccharides through hyrolysis. Do this by adding dilute HCI acid then heating the sample up in a water bath until it's brought to boil. Neutralise with sodium hydorocarbonate, then carry out Benedict's test as before; if positive, it'll form a coloured precipitate

They're formed when more than 2 monosaccharides are joined by condensation recations. 3 examples are starch, glycogen and cellulose:

Starch:

• Plants store excess glucose as starch (only found in plant cells, animal cells have glycogen), breaking it down when they need the energy. It's a mixture of 2 alpha-glucose polysaccharodies: amylose and amylopectin.
• Amylose- long, unbranched a-glucose chain with a coiled strcture, making it compact so good for storage
• Amylopectin- long, branched chainn of a-glucose. Side branches allow enzymes to quickly break down the moleclue as they can get to the glycosidic bonds easily. So quick release of glucose
• Starch is insoluble in water (can't dissolve), so doesn't impact water potential, meaning water can't enter cells via osmosis, which would make them swell. Makes it good for storage

Use the Iodine test for starch

Add idoine dissolved in potassium iodide solutionn; if starch, the sample changes from browny-orange to a dark, blue-black colour

Glycogen:

• Found in animal and bacteria, never plant cells. Animal cells store excess glucose as glycogen
• A polysaccharide of a-glucose
• Strucurally similar yo amylopectin, but has lots more side branches coming off, meaning energy can be released very quickly-importsnt as animals are more active and higher metabolisms
• Very compact, so good for stprgae. And is insoluble- doesn't draw water in cells via osmosis or diffuse out

Cellulose:

• Major component in plants' cell walls; made of long, unbranched monomers of b-glucose. When they bond, they form straight cellulose chains that're linked by H2 bonds to form strong fibres microfibrils that provide structural support for the cell.
• Prevents cell walls bursting as water enters by exterting an inward pressure that stops any more from coming in. Esp important in maintaing stems

They're a kind of lipid and are made of one molecule of glycerol and three molecules of fatty acid. (Glycerol in blue, fatty acid structure in red and the hydrocarbon tail in black) The hydrocarbon tail is hydrophobic, so makes lipids insoluble in water. Whilst all fatty acids have the same basic structure, the hyrocarbon tail varies. It's the carbon atom that links the fatty acid to glycerol. The hydrocarbon tail can be saturated or unstaturated (this determines whether or not the fatty acid is saturated). Saturated= no double bonds between carbon atoms (first two), unsaturated= at least one double bond between carbons (last one)

They're formed by condensation reactions. When the ester bond between the two (-O-) is formed, the H from the glycerol and the HO from the fattu acid form a molecule of water that is released to allow the fatty acid to bond at the carbon molecule and form the condensation reaction. This process happen twice more (at each of the 3 strands of the glycerol) to form a triglyceride

 The lipids found in cell membranes are 'phospholipids'. Similar to triglycerides; one of the fatty acids is replaced with a hydrophillic phosphate group, whilst the fatty acid tails remain hydrophobic

Triglycerides- mainly used as energy storage molecules:

• long hydrocarbon tails contain lots of chemical energy that's released when broken down. 
• Insoluble- don't impact cell's water potential + prevent water entering via osmosis (no swelling). They clump together as insoluble droplets in cells, as the hydrophobic tails face inwards, sheilding themselves from water with glycerol heads

Phospholipids-make up the bilayer of cell membranes (controls what enters/exits cells):

• Hydrophobic tails and hyrophilic heads- forms a double layer with heads facing out towards the water on either side. The centre of the bilayer is hydrophobic, preventing water-soluble substances from easily passing through, as the membrane acts as a barrier to this

Tells you if there's a fat in a particular food:

• Shake test substance with ethanol until it dissolves, then pour solution into water
• If there's a lipid present. it'll show up as a milky emulsion; this will be more noticable the more lipid there is

• Their monomers are amino acids; dipeptides form when 2 amino acids join amd polypeptides when more than 2 join. So proteins are made of 1 or more polypeptides
• Whilst each amino acid has a different variable group, they all have the same general structure; a carboxyl group (the acidic group that gives the amino acid its name), an amine/amino group and an R (variable side group). It is the R group that diffirentiates living things, as they are all otherwise made up of a bank of 20 amino acids

Polypeptodes are formed using condensation reactions that link the amino acids; because of this, a molecule of water is released during the reaction and peptide bonds are formed between the amino acids (the opposite occurs during digestion). Through a series of many condensation reactions, many amino acids join (polymerisation), resulting in a polypeptide being formed. (R=variable group)

There are 4 structural levels to a protein-

Primary structure- the sequence of amino aicds in the polypeptide chain- this determines the ultimate shape/function- changes in this can prevent it carrying out its function

Secondary structure- the straight, flat chain coils into an alpha helix or folds into a beta pleated sheet as the H2 bonds readily form between the amino acids

Tertiary structure- Usually, the chain folds/coils further as more bonds form on different parts of the chain, inc hydrogen and ionic bonds (which are both easily broken). Disulfide bridges also form when 2 molecules of amino acid cysteine come close, as the sulfur atoms bond. For proteins made from a single polypeptide, this is their final 3D structure

Quaternary structure- This is for proteins made with multiple chains held together by bonds and concerns how they're assembled together. This is their final 3D structure. 3D structures are important to how the protein functions as it's what makes each one distingushable to other molecules, impacting how they interact with each other. But it's the amino acid sequence that determines this final structure

All proteins have different shapes and sizes, making them specialised to carry out their function:

Enzymes- ususally spherical due to tightly folded polypeptide chains. Soluble, often involved in metabolism, e.g. digestive enzymes break down large food molecules and others help to synthesize molecules

Antibodies- Immune response, mafe of 2 short chains and 2 long ones that're bonded. They have variable regions- the amino acid sequences in these vary greatly- highly specific

Transport proteins- e.g. channel proteins- in cell memberanes, contain hydrophobic and hydrophillic amino acids that cause the protein to fold up and form a channel that transports molecules and ions across cell membranes]

Structural proteins- physically strong, made of long polypeptode chains that lie parallel with cross-links between them

1. The test solution needs to be alkaline so add sodium hydroxide solution

2. Then add Copper (II) Sulfate solution:

• Positive- if a protein is present, the solution will turn purple
• Negative- if there's no protein, the solution will remain blue

• proteins that catalyse metabolic reactions at a cellular level and for the organism as a whole
• can impact structures and functions (e.g. respiration) in an organism, with their action occuring both inside and outside of cells
• have an active site-specific shape that binds to a specific substrate
• highly specific due to their tertiary structure
• Enzymes speed up the rate of reaction by allowing chemical reactions to occur at a lower activation energy, often meaning they can occur at a lower temperature. This is the result of the enzyme-substrate complex being formed because attaching sustrate molecules to an enzyme refuces any repulsion between them as they are being held so close together, meaning they can join more easily if needed. Also, byr fitting into the enzyme's active site, a strain is put on the substrate's bonds, meaning they the substrate breaks up more easily, speeding up the reaction.
• Initially the 'lock and key' model was accepted to explain how the enzyme and substrate fit together. Now, the 'Induced fit' model explains why enzymes are so specific, only bonding to one substrate; the substrate has to be the right shape to fit the active site and causes it change shape slightly when the enzyme-substrate complex is created

• As only one complementary substrate fits into the active site, enzymes usually only catalyse one reaction. 
• The active site is unique to each enzyme as it's determined by their unique tertiary structure
• If this structure is altered, the active site will change shape, preventing the complex being formed and the enzyme fulfilling its function. It can be altered by changes in pH or temperature
• The enzyme's primary structure (amino acid sequence) is determined by a gene- if a mutation occurs in the gene, it can change the subsequent tertiary structure

Temperature

Higher temp, enzyme molecules vibrate more, more frequent collisions, faster rate of reaction. But if the temp is too high, the vibration breaks some of the bonds that hold the enzyme's shape, changing (denaturing) the active sAite's shape so it can no longer be a catalyst

pH

All enzymes have an optimum pH value- most human enzymes are pH 7. Above/below this. the H+ and OH- bonds in the acids/alkalis can mess up the ionic and hydrogen bonds holding the tertiary structure, breaking them and denaturing the enzyme

Enzyme/substrate concentration impact rate of reaction

Enzyme-more molecules, more likely substrates will collide and form a complex, increases rate, but only as long as there is enough substrate, after this adding more enzymes has no further effect. Substrate-more likely to be a collision, but only up to a saturation point- once all the active sites are full, there's no further effect. Also, substrate concentration decreases over time unless more is added, so this will also slow down the rate of reaction as it progresses

Activity can be prevented by enzyme inhibitors, which bind to the enzyme they inhibit:

Competitive inhibition (CI):

CI molecules are a similar shape to substrate, so block active site so substrates can't fit. Inhibition depends on the relative concentrations of the inhibitor and substrate; if the inhibitor has a high concentration then it'll take up most of the active sites, leaving few for the enzyme, and vice versa. Therefore. increasing substrate concentration will increase reaction rate (up until a point)

Non-competetive inhibition (NCI):

NCI molecules bind to the enzyme away from the active site, changing its shape so that substrate molecules can't bind to this. They don't compete to bind to the active site, as they're a different shape. Because of this, increasing the substrate concentration doesn't impact rate of reaction; enzyme activity will still be inhibited

They're both tpes of nucleic acid; DNA is used to store genetic info, inc all the instructions a organism needs to grow from a fertilised egg to adult. RNA transfers genetic info from DNA to the ribosomes, which help to make proteins- they read the RNA to make polypeptides during 'translation' (Protein synthesis). Ribosomes are made from RNA and proteins.

DNA and RNA are made up of monomers called nucleotides, which are a type of biological molecule containing a pentose sugar (a sugar with 5 carbon atoms), a nitrogen containing organic base and a phosphate group

• DNA: the pentose sugar in a DNA nucleotide is deoxyribose; each one has the same sugar and a phosphate group, but a variation of the bases adenine, thymine, cytosine and guanine
• RNA: the pentose sugar is ribose, each nucleotide has a phosphate group and one of four different bases- uracil replaces thymine as a base in RNA

Polynucleotides= a polymer of nucleotides which is formed by both DNA and RNA nucleotides. The nucleotides join in a condensation reaction between the phosphate group of one nucleotide and the sugar of anothe, forming a phosphodiester bond (made up of the phosphate group and two ester bonds). The chain of sugars and phosphates is called the sugar-phosphate backbone

DNA is made of two polynucleotide chains that're joined via H2 bonds between the bases (complementary base pairings, A-T, C-G: this means there's always an equal amount of A/T and C/G). Two H2 bonds connect A and T and 3 connect C and G. The two strands run antiparallel to each other (in opposte directions) and twist to form DNA's double-helix. 

DNA is a stable molecule as the phosphodiester backbone protects the bases (which are more reactive) inside the double helix. Also, the H2 bonds that link the bases form bridges; as there are more bonds between C/G, the higher the proportion of these pairings, the more stable the DNA is.

Initially, it was believed that DNA's chemical composition was too simplistic to carry the genetic code, but by 1953, experiments determined this was the case and Watson and Crick confirmed its double-helix structure.

RNA is made from a single polynucleotode chain, and is much shorter than most DNA polynucleotides

DNA needs to replicate before it divides in mitosis/meiosis to ensure that each new cell has a full amount of DNA. This is considered 'semi-conservative', as half of the strands in each new DNA molecule are from the original one, producing genetic continuity between generations of cells

• DNA helicase (enzyme) unwinds the double-helix by breaking the H2 bonds betweeb the bases on the two polynucleotide DNA strands
• Each strand is a template for a new strand- free floating DNA nucleotides are attarcted to their complementary exposed bases on each template strand
• Condensation reactions catalysed by DNA polymerase join the nucleotides of the new strands together, with H2 bons forming between the bases on both the new and original strands
• Now there are two molecules of DNA, each one containing one orginal DNA strand and one new one

The DNA helix strands run in opposite directions; each end of the strand is slightly different, one is a 3' (3 prime) end and the other a 5' (5 prime) end. DNA polymerase's active site is only complementary to the 3' end, so can only add nucleotides to the new strand at this end. As they're antiparralel, the polymerase moves in opposite directions along each strand

Their experiment validated Watson and Crick's theory about DNA replication being semi-conservative by using two isotopes of nitrogen (which DNA contains)- heavy (15N) and light (14N)

• Grew 2 bacteria in nutrients- one containing 15N, the other 14N, so it can part of the bacteria's DNA as it reproduced
• Samples of DNA taken from ech and spun in a centrifuge- 15N settled lower down the tube than 14N
• Bacteria grown with 15N was put in with a broth containing 14N and left for 1 round of DNA replication, then another sample taken from this and spun again
• The semi-conservative nature of this reaction was confirmed by the new DNA molecule settling in between the heavy and light nirogen, showing that it contained a strand of each nitrogen

• Adenosine triphosphate is found in all living cells; it acts as the main energy source to carry out processes within cells. It is produced from the energy released in respiration from glucose (which cells need to release energy), as cell's aren't able to get their energy directly from glucose.
• ATP is made from the nucleotide base adenine, a ribose sugar and 3 phosphate groups. It's called a 'nucleotide derivative' as it is a modified form of a nucleotide.
• Once made, ATP diffuses to the part of the cell needing energy, where energy stored in the bonds between ATP's phosphate groups is released during a hydrolysis reaction. These bonds are unstable and have a low activation energy, meaning they're easily broken and release lots of energy when they do so. 

• ATP is broken down into ADP (adenosine diphosphate) and Pi when energy is needed in a cell via a hydrolysis reaction catalysed by the enzyme ATP hydrolase. During this, a phosphate bond is broken and energy is released to be used by cells
• If needed, ATP hydrolysis can join with other energy-requiring reactions, meaning that the energy produced in the hydrolysis will be used directly to make this other reaction happen, rather than be lost as heat
• The Pi that is produced can be added to another compound (phosphorylation), often making it more reactive
• The conversion of ATP to ADP is a reversible reaction; if Pi is added to ADP, it can reform into ATP during a condensation reaction (which uses up energy from respiration or photosynthesis)
• Cells don't store lots of ATP, but it can be formed very quickly (far more quickly than glucose- making it suited as an immediate source of energy)
• ATP must be continuously made in the mitochondria of the cells that need it, as it can't be stored

• Makes up around 80% of cell's contents: it's a metabolite (substance involved in metabolic reactions) in many important metabolic reactions (keep organisms alive), inc hydrolysis and condensation reactions
• It's a solvent, which is important as most metabolic reactions take place in solution, e.g. in the cytoplasm
• Helps temperature control- high latent heat of vapourisatiob and high specific heat capacity
• Water molecules are cohesive (stick together), helping transport in plants and other organisms
• Simple structure: one atom of O2 and two of H2, joined by shared electrons- the shared H2 electrobs are pulled towards the O2 atom, leaving the other side of each H2 atom with a slight positive charge. O2's unshared electrons give it a slight negative charge.
• The above makes water a polar molecule- partial positive charge on one side and a partial negative on the other
• This allows hydrogen bonding, as the negative oxygen atoms attract the postive hydrogen atoms of other water molecules- helps give water some of its useful properties

• It's an important metabolite- as many metabolic reactions involve a condensation (releases water as new bond is formed) or hydrolysis (needs water to break a bond) reaction
• It has a high latent heat of vapourisation- so takes lots of energy (heat) to break water's H2 bonds, meaning lots of energy is used up when water evaporates- lets animals use water loss through evaporation to cool down without using too much water
• It can buffer (resist) changes in temp- the H2 bonds between molecules can absorb lots of energy, giving water a high SHC as it takes lots of energy to heat up. Useful for organisms as it means water doesn't have rapid temp changes- both internal water (body temp) and external (good habitat)
• It's a good solvent- due to water's polarity it can dissolve ions (substances made by one pos and one neg charged atom/molecule- many important substances in metabolic reactions are ionic). This is because water's pos end is attacted to the negative ion, and the neg end is attarcted to the pos ion- so completely surrounds (dissolves) it
• Strong cohesion between water molecules-this is because water is polar. It's cohesion helps water to flow, so is good for transporting substances, e.g. cohesion-tension theory-xylem. Strong cohesion also gives water a high surface tension when it comes into contact with air

• Ions have an electric charge- positive= cation, negative= anion. Generally, inorganic ions don't contain carbon and are found, in solution, in the cytoplasms of cells and in the body fluids of organisms. Each ion has a specific role, dependent on its properties. Its role determines whether it's found in high or low concentration
• Iron ions are an important part of haemoglobin- it's made of 4 different polypeptide chais. each with an iron ion in the centre that binds the O2 to the haemoglobin. When the O2 is bound, the Fe2+ temporarily becomes Fe3+ until the O2 is released
• Hydrogen Ions (H+) determine pH- the more H+ present in an environment, the lower the pH, so more acidic it is
• Sodium ions (Na+) help transport glucose and amino acids across membranes- via co-transport
• Phosphate ions are an essential part of ATP and DNA- when phosphate ions are attached to another molecule, there known as phosphate groups- contained in DNA, RNA and ATP. ATP stores its energy in the bonds between these groups. In DNA and RNA, the phosphate griups allow nucleotides to join up and form polynucleotides