Topic 1 Flashcards
1
Q
Evidence For Evolution
A
- all organisms on earth share common biochemistry.
- all contain same groups of carbon based compounds that interact in similar ways- e.g. all use same nucleic acids as genetic material and same amino acids to build proteins
- These similarities suggest organisms have a common ancestor, which provides indirect evidence for evolution
2
Q
What is a monomer?
A
The smaller units from which larger molecules are made e.g. monosaccharides, amino acids and nucleotides
3
Q
What is a polymer?
A
Molecules made from many monomers joined together
4
Q
Condensation reactions
A
Condensation reactions join monomers together to produce polymers
- Condenstaion reaction joins 2 molecules together with the fomration of a chemical bond and involves the elimination of a water molecule.
5
Q
Hydrolysis reactions
A
- polymers can be broken down into polymers by condensation reactions
- hydrolysis reaction breaks the chemical bond between monomers using a water molecule
6
Q
Carbohydrates
A
- all contain elements C, H and O.
- Monosaccharides are the monomers from which larger carbohydrates are made
- glucose, galactose and fructose are examples of monosaccharides
7
Q
Carbohydrates: Disaccharide formation
A
- A condensation reaction between 2 monosaccharides forms a glycosidic bond and a water molecule is released. This forms a disaccharide.
- maltose is a disaccharide formed from a condensation reaction between 2 glucose molecules
- Lactose is formed from a glucose molecule and a galactose molecule
- sucrose is formed from a glucose molecule and a fructose molecule.
8
Q
Benedict’s test for sugars
A
reducing sugars:
- add benedict’s reagent (blue) to a sample and heat it in a water bath that’s been brought to boil
- positive= coloured precipitate: green-yellow-orange-brick red (further colour change, higher concentration of reducing sugars.
non reducing sugars:
- break down carbohydrates into monosaccharides
- do this by using a new sample of test solution, adding dilute HCl and heat in water bath that’s been brought to boil
- neutralise solution by adding sodium hydrogencarbonate
- add benedict’s reagent
- positive= coloured precipitate forms (green-yellow-orange-brick red
- negative=stays blue
9
Q
Carbohydrates: glucose
A
- hexose sugar (monosaccharide with 6 carbon atoms in each molecule)
- 2 isomers (molecules with same molecular formula but atoms are connected differently): alpha and beta glucose
- the difference between alpha and beta glucose is that the OH and H group are reversed. (‘beat them up’- OH group is at top for beta glucose)
10
Q
Carbohydrates: Polysaccharides
A
- formed from the condensation reaction of many glucose units
- many alpha glucose molecules are joined by glycosidic bonds to form amylose
- polysaccharides can be broken down into their monosaccharides by hydrolysis reactions: for example, amylose is hydrolysed into alpha glucose molecules
- examples: starch, glycogen, cellulose
11
Q
Polysaccharides: Starch
A
- plants get energy from glucose and store excess glucose as starch. It breaks down starch to release glucose when it needs energy. Starch is a mix of 2 polysaccharides of alpha glucose
- amylose= long, unbranched chain of alpha glucose. The angles of the glycosidic bonds make it coiled. This makes it compact so starch is a good storage molecule
- amylopectin= long, branched chain of alpha glucose. Side branches allow enzymes that break down molecule to get to glycosidic bonds more easily, so glucose is released quickly.
- starch is insoluble in water and does not affect water potential, so does not cause water to enter cells by osmosis, making them swell. This makes starch a good storage molecule.
12
Q
Polysaccharides: Glycogen
A
- animal cells get energy from glucose and store excess glucose as glycogen.
- polysaccharide of alpha glucose
- large amount of side branches (more than amylopectin). This means glucose can be released quickly, which is important for energy release in animals.
- compact molecule- good for storage
13
Q
Polysaccharides: Cellulose
A
- made of long, unbranched chains of beta-glucose
- beta glucose molecules bond to form straight cellulose chains
- chains linked by hydrogen bonds to form strong fibres, microfibrils
- microfibrils means cellulose provides cells with structural support for cells, e.g. in plant cell walls.
14
Q
Iodine test for Starch
A
- add iodine dissolved in potassium iodide solution to test sample
- positive= colour change from browny-orange to dark blue/black
15
Q
Lipids
A
- differ from proteins and carbohydrates because they are not polymers formed from long chains of monomers
- all contain hydrocarbons
- all made up of different components which relate to function
- triglycerides and phospholipids
16
Q
Lipids: Triglycerides
A
- formed from the condensation reaction of 1 glycerol molecule and 3 fatty acids
- fatty acids form hydrocarbon tails, which are hydrophobic- make lipids insoluble in water
- all fatty acids have same basic structure, BUT hydrocarbon tail varies (variable ‘R’ group)
- fatty acids can be saturated (no double bonds between carbon atoms- fatty acid is saturated with hydrogen) or unsaturated (do have double bonds between carbon atoms, causing chain to kink). The difference between the two is their R groups
17
Q
Lipids: How are triglycerides formed?
A
- condensation reaction between glycerol molecule and 3 fatty acids
- 3 condensation reactions occur, 1 for each fatty acid molecule
- an ester bond forms between the glycerol and fatty acid (RCOOH), releasing a water molecule
18
Q
Lipids: Phospholipids
A
- lipids found in cell membranes
- one of the fatty acids of a triglyceride is substituted by a phosphate group.
- phosphate group is hydrophilic
- fatty acid tails are hydrophobic
19
Q
properties of triglycerides
A
- energy storage molecules- long hydrocarbon fatty acid tails contain lots of chemical energy that a lot of is released when they are broken down. Due to the tails, lipids contain twice the mount of energy as carbohydrates
- insoluble in water so do not affect water potential of cell and cause water to enter by osmosis- in cells the hydrophobic fatty acid tails face inwards and hydrophilic glycerol heads face outwards.
20
Q
properties of phospholipids
A
- make up phospholipid bilayer of cell membranes. Cell membranes control what enters and leaves a cell
- heads are hydrophilic and tails are hydrophobic, so double layer is formed where heads face out towards water either side
- centre of bilayer is hydrophobic- stops water soluble substances passing through it easily
21
Q
Emulsion test for lipids
A
- shake test sample with ethanol
- pour solution into water
- lipid shows as milky emulsion (more lipid, more noticeable milky colour will be)
22
Q
Proteins
A
monomer of proteins are amino acids
- dipeptide formed from condensation reaction of 2 amino acids
- polypeptide formed from condensation reaction of more than 2 amino acids
- proteins made up of one or more polypeptide
23
Q
What is the structure of an Amino acid?
A
- same general structure- carboxyl group (COOH), an amine/amino group (NH2) and an R group (variable side chain) attached to C atom.
- all living organisms share 20 amino acids that only differ in what makes up the R group.
24
Q
How are dipeptides and polypeptides formed?
A
- A condensation reaction between two amino acids forms a peptide bond.
- molecule of water released in condensation reaction
25
Describe the structure of proteins
- Functional proteins may contain one or more polypeptides
PRIMARY STRUCTURE: sequence of amino acids in the polypeptide chain.
SECONDARY STRUCTURE: hydrogen bonds form between amino acids in cain so it coils into an alpha helix or folds into a beta pleated sheet.
TERTIARY STRUCTURE: chain coils or folds further. Hydrogen bonds, ionic bonds and disulphide bridges form between different parts of polypeptide chain. The tertiary structure is the final 3D structure for proteins made from single polypeptide chain
QUARTERNARY STRUCTURE: The way in which multiple polypeptide chains are assembled together. This forms protein final 3D structure for proteins made from more than one polypeptide (e.g. haemoglobin, insulin, collagen)
26
How does the structure of a protein relate to its function?
- haemoglobin is a compact, soluble protein (easy to transport, so great for transport of O2 around body).
- Enzymes: spherical due to tight folding of polypeptide chains. Soluble, often involved in metabolic processes (e.g. digestive enzymes)
- Antibodies: involved in immune response and found in blood. Made up 2 light (short) polypeptide chains and 2 heavy (long) polypeptide chains bonded together. Have variable regions, where the amino acid sequences vary.
- Transport Proteins: e.g. channel proteins are present in cell membranes and contain hydrophobic and hydrophilic amino acids (cause protein to fold and form a channel). They transport molecules and ions across membranes
- Structural proteins: physically strong. Consist of long polypeptide chains that lie parallel to each other with cross-links between them. Include keratin (hair, nails) and collagen (connective tissue). Collagen has 3 polypeptide chains tightly coiled together (makes it strong, so good supportive tissue in animals).
27
Describe the Biuret test for proteins
1. add a few drops of sodium hydroxide solution to make solution alkaline
2. add copper (II) sulphate solution
positive= solution turns purple
negative= solution stays blue
28
How do enzymes act as biological catalysts?
- enzymes are proteins that speed up the rate of chemical reactions by acting as biological catalysts.
- Catalyse metabolic reactions at a cellular level (e.g. respiration) and for the organism as a whole (mammal digestion)
- Enzymes can affect structures in an organism (e.g. they are involved in collagen production) and they can affect functions (e.g. respiration).
- intracellular (within cells)/ extracellular (outside cells)
- proteins
- have an active site, with specific shape. Substrate molecules bind to active site
- highly specific due to tertiary structure
29
How do enzymes speed up chemical reactions?
- Activation energy needs to be supplied to chemicals before the reaction starts (energy needed for reaction to begin). This is often provided as heat
- Enzymes lower activation energy needed, often causing reactions to occur at a lower temperature than without an enzyme- this speeds up the rate of reaction
- enzyme- substrate complex formed when substrate fits into active site. This lowers the activation energy because:
- if 2 substrate molecules need to be joined, being attached to the enzyme holds them close together, reducing repulsion between the molecules so they bond more easily
- If the enzyme is catalysing a breakdown reaction, fitting into the active site puts a strain on the bonds in the substrate, so the molecule breaks up more easily.
30
How do the models of enzyme action differ from each other?
- The lock and key model: substrate fits into the enzyme like a key in a lock. The active site and substrate have a complementary shape. Enzymes have active sites specific to certain substrates. This model is not accurate, as scientists realised enzyme-substrate complex changed shape slightly to complete the fit.
- The induced fit model helps to explain enzyme specificity and why they only bond to one particular substrate. Substrate has to be the right shape to fit the active site and makes the active site change shape. As the substrate binds to active site, active site changes shape slightly. This model is widely accepted in current day.
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Enzyme Properties
- enzyme properties related to tertiary structure- active site shape determined by tertiary structure, which is determined by the primary structure.
- enzymes are very specific so only usually catalyse one reaction (e.g. maltase only breaks down maltose, sucrase only breaks down sucrose). This is because only one complementary substrate will fit into the active site.
- If substrate shape does not fit active site, enzyme substrate complex will not form, so reaction will not be catalysed
- if tertiary structure of protein is altered (changes in pH or temp), active site shape will change- substrate will not fit into active site and enzyme substrate complex will not form and enzyme will not carry out its function.
- primary structure of protein determined by a gene. If mutation occurs in gene, may change tertiary structure of enzyme produced.
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How is enzyme activity measured?
1. How fast the product is made: . Different molecules present at end of chemical reaction than at start. measure amount of product present at different times during the experiment, reaction rate calculated.
2. How fast substrate is broken down. measure amount of substrate molecules left at different times during experiment, to calculate reaction rate.
33
How does temperature affect enzyme activity?
- increases when temp increases- more heat causes molecules to have more kinetic energy, so they move faster. This means substrate molecules are more likely to collide with enzyme active sites. Energy of collisions increases, meaning each one more likely to result in reaction.
- BUT, if temp too high, then reaction stops. Rise in temp makes molecules vibrate more. If temp goes above certain level, vibration breaks bonds that hold enzyme in shape. Active site changes shape and enzyme and substrate no longer fit. Enzyme is DENATURED, and does not function as catalyst.
- every enzyme has a different optimum temp
34
How does pH affect enzyme activity?
- all enzymes have optimum pH value
- most human enzymes work best at pH7, but exceptions such as pepsin works best at pH 2 (useful as found in stomach)
- Above and below optimum pH, H+ ions and OH- ions in acids and alkalis can disrupt ionic and hydrogen bonds holding enzyme tertiary structure in place- enzyme DENATURES, and active site changes shape.
35
How does substrate concentration affect enzyme activity?
- higher substrate concentration, faster rate of reaction
- more substrate molecules means substrate and enzyme more likely to collide, so more active sites will be occupied.
- This is only the case up to the saturation point- after, there are so many substrate molecules, that all active sites are full, so adding more makes no difference.
36
How does enzyme concentration affect enzyme activity?
- Increasing enzyme concentration increases rate of reaction
- more likely that substrates and enzymes will collide and form an enzyme substrate complex, the more enzyme molecules there are in a solution.
- If all substrate is used up, then adding more enzymes will make no differences, as no more successful collisions can be formed
37
What are competitive inhibitors?
- molecules w/ similar shape to substrate molecules
- compete w/ substrate molecules to bind to active site, but no reaction occurs. They block active site, so no substrate molecules can bind to active site.
- high concentration of inhibitor, little substrate will bind to active sites.
- higher concentration of substrate, will increase rate of reaction (to certain point) as more chance they will bind to active site before inhibitor increase.
38
What are non-competitive inhibitors?
- bind to enzyme away from active site. This causes active site to change shape so substrate molecules can no longer bind to it.
- do not compete with the substrate molecules to bind to active site because they are different shape.
- Increasing substrate concentration will not make any difference- enzyme activity still inhibited.
39
What is the function of DNA and RNA?
DNA (Deoxyribonucleic acid) stored genetic information
RNA (ribonucleic acid) transfers genetic information from DNA to ribosomes. Ribosomes read the RNA to make polypeptides in translation.
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Nucleotide structure
- DNA and RNA molecules are polymers of nucleotides (polynucleotides)
- nucleotide made up of pentose sugar (5 carbon atoms), nitrogenous organic base, phosphate group
41
polynucleotide structure
- strands/chains
- polymer of nucleotides
- nucleotides join up via condensation reaction between phosphate group of one nucleotide and sugar of another- phosphodiester bond formed (phosphate group and 2 ester bonds). Sugar phosphate backbone formed of chain of phosphates and sugars.
42
DNA structure
- double helix- molecule formed from 2 separate polynucleotide strands
- long, tightly coiled (lots of genetic material can fit into small space in cell nucleus)
- DNA nucleotide made of phosphate group, pentose sugar deoxyribose and a nitrogenous organic base.
- sugar and phosphate do not change in nucleotides, but bases vary
- Two DNA polynucleotide strands join together by hydrogen bonds between the bases.
- Complementary base pairing means each base can only join with one particular base. (A-T, G-C)
- always equal amounts of adenine and thymine and equal amounts of guanine and cytosine. There are 2 hydrogen bonds between A and T, 3 between C and G
- 2 polynucleotide strands are antiparallel that twist to form double helix
43
RNA structure
- pentose sugar in nucleotides is a ribose sugar, not deoxyribose
- Uracil (U, a pyrimidine) replaces thymine as a base and pairs with adenine
- nucleotides form single polynucleotide strand
- shorter strands than DNA polynucleotides
44
How did scientists discover DNA carried the genetic code?
- DNA first observed in 1800s but many scientists doubted it could carry the genetic code due to its relatively simple chemical composition.
- argued proteins must carry genetic info, as they are more chemically varied
- double helix structure determines by James Watson and Francis Crick in 1953.
45
Why does DNA replicate?
- copies before cell division so each new cell has the full amount of DNA.
- replicates semi-conservatively (half of the strands in each new DNA molecule are from the original DNA molecule)
- This allows genetic continuity between generations of cells
46
Describe and explain the process of semi-conservatively
1. Enzyme DNA helicase hydrolyses hydrogen bonds between bases on the 2 polynucleotide DNA strands. This makes helix unwind to from 2 single strands
2. Each original single strand acts as a template for a new strand. Complementary base pairing means free floating DNA nucleotides are attracted to their complementary exposed bases on each original template strand. A with T and C with G.
3. DNA polymerase joins the nucleotides via a condensation reaction. Hydrogen bonds form between the bases on the original and new strands. Each new DNA molecule contains one strand from the OG DNA molecule and one new strand.
47
How does DNA polymerase catalyse the condensation that joins DNA nucleotides together with the formation of
- one end of of the DNA strand is the 3' end and one end is the 5' end
- during DNA replication the active site of DNA polymerase is only complementary to the 3' end of the newly forming DNA strand, so the enzyme can only add nucleotides to the new strand at the 3' end. This means the new strand is made in a 5' to 3' direction and DNA polymerase moves down strand in a 3' to 5' direction.
- antiparallel strands mean DNA polymerase on one of template strands moves in opposite direction to DNA polymerase on other template strand
48
Describe Meselson and Stahl's experiment
1. 2 bacteria samples grown for many generations, one in a nutrient broth w/ light nitrogen and one in a nutrient broth w/ heavy nitrogen. Nitrogen taken up from broth to make nucleotides for new DNA, as bacteria reproduced
2. DNA sample taken from each bacteria batch, spun in centrifuge. DNA from heavy nitrogen bacteria settled lower down centrifuge tube than DNA from light nitrogen bacteria (because it's heavier)
3. Bacteria grown in heavy nitrogen broth taken out and put in light nitrogen only broth. Left for 1 round of DNA replication and another DNA sample taken out and spun in centrifuge
4. shows DNA replicates semi conservatively because DNA settled between light and heavy nitrogen DNA settled out, not OG heavy DNA at bottom and new light DNA at the top (would show DNA replication was conservative)
49
Why do plants and animals require energy from ATP?
plants: active transport (e.g. transport solutes from their leaves), DNA replication, cell division and protein synthesis
Animals: active transport, DNA replication, cell division and protein synthesis
50
Describe the structure of ATP
- plant and animal cells release energy from glucose (respiration)
- Energy released form glucose used to make ATP (adenosine triphosphate) as cell cant get energy direct from glucose
- made of nucleotide base adenine, ribose sugar, 3 phosphate groups. ATP is a nucleotide derivative (modified nucleotide)
- After made, ATP diffuses to part of cell requiring energy. Energy in ATP stored in high energy bonds between phosphate groups + released via hydrolysis reactions
51
How is ATP made and used?
- ATP hydrolysed by ADP and Pi
- Phosphate bond broken and energy released
- Catalysed by ATP hydrolase
- energy released can be directly used to make the coupled reaction happen so energy not lost as heat
- released Pi can be added to another compound which often makes the compound more reactive (phosphorylation)
- ATP can be resynthesised in condensation reaction between ADP and Pi. Occurs in both respiration and photosynthesis, catalysed by ATP synthase
52
Why is water important?
- a metabolite in metabolic reactions
- solvent, and most metabolic reactions take place in solution (e.g. cytoplasm of eukaryotic and prokaryotic cells)
- helps temp control due to its high latent heat of vaporisation and high specific heat capacity
- molecules very cohesive, helping water transport in plants and transport in other organisms.
53
Describe the structure of water
- Molecule of H2O is one atom of O joined to 2 atoms of H2 by shared electrons (covalent bonding)
- shared negative hydrogen atom pulled towards oxygen atom, other side of hydrogen atom left w/ slight positive charge
- unshared negative electrons on oxygen atom give it a partial negative charge.
- So water is a polar molecule (partial negative charge on one side and partial positive charge on the other)
- hydrogen bonds form between water molecules because partial negative charged oxygen atoms attract partial positive charged hydrogen atoms of other water molecules.
54
Describe and explain the properties of water
- metabolite: many metabolic reactions involve condensation/hydrolysis reactions, where water molecules are used to break a bond/ a water molecule is released.
- Good solvent: many important substances in bio reactions are ionic (made from 1 positive charged atom and one negatively charged atom). water is polar so the partial positive charged end attracted to negative ion and partial negative charged end attracted to positive ion, so ions surrounded by water molecules (dissolve). This allows living organisms to take up useful substances to transport around body.
- High latent heat of vaporisation: water evaporates (vaporises) when hydrogen bonds holding molecules together broken. Lots of heat energy needed, so water has high latent heat of vaporisation (lots of heated needed to change state). useful for living organisms as evaporation allows them to cool down without losing too much water. water carries heat energy when it evaporates to lower temp, e.g. humans sweat to cool down.
- high specific heat capacity: due to hydrogen bonds. Specific heat capacity is energy needed to raise temp on 1 gram of a substance by 1 degrees centigrade. A lot of energy used to break hydrogen bonds between water molecules, so less heat energy available to increase water temp. Lot of energy needed to heat it up (high specific heat capacity). useful for living organisms as it means water does not have rapid temp changes. Makes water a good habitat as temp of water more stable than land. Water temp inside organisms remains fairly constant temp to help maintain constant internal body temp.
- Very cohesive: due to water molecules being polar. Strong cohesion helps water to flow, so great to transport substances. Strong cohesion means water has a high surface tension when it contacts air, which is why sweat droplets from, which evaporate from the skin to cool down organisms.
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Specialised cells
- cells become specialised to carry out specific functions
- cell structure helps to carry out function
- epithelial cells in small intestine adapted to absorb food efficiently: walls of small intestine have villi to increase SA. Epithelial cells on surface of villi have microvilli to increase SA. Lots of mitochondria to provide energy via ATP for transport of digested food into cell
- Red blood cells are adapted to carry O2 around body. Have no nucleus to make more room for haemoglobin
- Sperm cells have lots of mitochondria to provide lots of energy needed to travel to an egg
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Cell organisation
- specialised cells group together to form tissues (group of cells working together to perform a particular function)
- Different tissues work together to form organs
- Different organs form an organ system
- e.g. epithelial cells make up epithelial tissue. Epithelial tissue, muscular tissue and glandular tissue all form stomach (organ). Stomach is part of the digestive system. This is an organ system made up of all the organs involved in digestion and absorption (small intestine, large intestine and liver).
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