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Molecules, Aerobic respiration vs Anaerobic respiration: oxygen required…

- - - - Monosaccharides (simple sugars)
        properties:
        
        low molecular weight
        
        readily soluble in water --> exerts osmotic pressure
        
        able to form crystals
        
        sweet to taste
        
        5-carbon and 6-carbon monosaccharides were most common
        e.g. glucose, fructose, galactose
        
        Ribose:
        
        component of ribonucleic acid (RNA) and used in synthesis of ATP
        
        Glucose:
        
        six-carbon ring with a side chain. 5 carbon atoms are in the ring and 1 forms the side chain
        
        glucose can exist in 2 possible ring forms, known as α and β isomer forms
        
        in α glucose, the hydroxyl group on carbon 1 is below the plane on the ring
        
        in β glucose, the hydroxyl group on carbon 1 is above the plane on the ring
      - Disaccharides (simple sugar)
        created by joining 2 monomers
        e.g. matlose, lactose, sucrose
      - Polysaccharides (complex sugars)
        properties:
        
        high molecular weight
        
        insoluble in water --> does not exert osmotic pressure
        
        does not form crystals
        
        does not taste sweet
        
        e.g. starch, glycogen, cellulose
        
        starch:
        
        major storage carbohydrate of most plants
        
        important energy source in diet of many animals
        
        usefulness lies in compactness and insolubility of its molecule
        
        readily hydrolysed to form sugar when required
        
        mixture of amylose and amylopectin
        
        bonds between glucose residues bring the molecules together as a helix. The whole starch molecule is stabilized by many hydrogen bonds between parts of the component glucose molecules
        
        Glycogen:
        
        polymer of alpha-glucose
        
        chemically similar to amylopectin (larger and more highly branched)
        
        formed by condensation reactions between monomers of alpha-glucose
        
        extensive branching in glycogen means it has a compact structure that allows for more glucose molecules to be stored within a small volume
        
        non-reducing ends due to many branches allows for more rapid enzyme-controlled hydrolysis of glycogen to release stored glucose when there is an increase in energy demand
        
        body's energy reserves and is hydrolysed and respired as needed
        
        Cellulose:
        
        polymer of beta-glucose molecules combined together by glycosidic bonds between carbon-4 and 1 beta-glucose molecule
        
        cellulose molecules are straight an uncoiled
        
        structure is stabilized and strengthened by hydrogen bonds between adjacent glucose units in the same strand
        
        plant cells wall's additional strength comes from cellulose fibres being laid down in layers than run in different directions
    - - Triglycerides:
        
        fats at room temperature contain mainly saturated fatty acid
        
        oils at room temperature contain mainly unsaturated fatty acid
        
        consists of 1 glycerol molecule combines with 3 fatty acid molecules
        
        Saturated fats:
        
        no double carbon bond
      - Phospholipids:
        phospholipids are modified lipids that contain a phosphate group
        
        arrange themselves as bilayers
        
        are major components of cell membranes
      - Steroids:
        hydrophobic compound comprising a complex ring of carbon atoms
        
        essential component of the cell membrane
        
        sex hormones in mammals are produced from steroids
  - - - formation of polypeptides
        
        formed by amino acids
        
        linked by peptide bonds
        
        may consist of 1 or more polypeptides linked together
        
        has specific shapes/folding
        
        shape determines function
      - 9 are essential amino acids which cannot be produced by the body and must be present in the diet
        
        non-essential amino acids can be produced by the body and not required as a part of the diet
- - - - Lock-and-Key hypothesis:
        
        enzyme is the "lock", substrate is the "key" that fits into the active site of the enzyme to form an enzyme-substrate complex
      - Induced-fit model:
        
        binding of the substrate to the active site induces a small conformational change in the enzyme such that the substrate can fit more tightly into the active site
        
        enzyme orientates substrates in the correct position and in close proximity ==> allows the enzyme to catalyst reactions more effectively
    - - temperature:
        
        as temperature increases, rate of reaction increases
        
        substrate and enzyme molecules gain kinetic energy and move more rapidly to collide and react in forming an enzyme-substrate complex
        
        at enzyme's optimum temperature, the rate of reaction reaches maximum
        
        Beyond the optimal temperature, enzymes begin to denature and rate of reaction slows down
        
        excessive heat energy causes atoms within the enzyme to vibrate violently and disrupt the chemical bonds maintaining the secondary and tertiary structure of the globular proteins
        
        active sites will undergo irreversible loss of 3D conformation
      - pH:
        pH of a solution is dependent on the relative number of hydrogen ions (H+) compared to hydroxide ions (OH-)
        
        each enzyme has narrow range of pH which functions effeciently
        
        different enzymes have different values of optimal pH
        
        change in pH from the optimal value gradually alters the 3D shape of an enzyme by disrupting hydrogen and ionic bonds, including the active site
        
        effect is usually reversible provided the change in pH is not too extreme
        
        exposure to extreme acids or alkalis are usually irreversibly denature enzymes
      - substrate concentration:
        
        at low substrate concentrations, all substrates can bind to active sites due to an excess amount of enzymes
        
        as concentration of substrate increases, the rate of reaction will increase as there are more collisions between substrate and enzyme molecules
        
        at higher substrate concentrations, the maximum rate of reactions is reached where there is more substrate than enzymes. All active sites of enzyme are occupied in catalysis
        
        Beyond this point, a further increase in the substrate concentration does not increase the rate of reaction further --> rate of reaction becomes constant as enzyme concentration is now the limiting factor
    - - reasons they are favoured:
        
        enzyme can be recycled and saves long-term costs (as enzymes are expensive)
        
        final product is enzyme-free and free from contamination ==> no need for purification and saves on cost
        
        enzyme is more chemically stable and long lasting, due to the protection by the inert matrix
        
        chemical reaction can be stopped rapidly by removing the enzymes from reaction mixture
      - Application: creating lactose free milk
        lactose intolerant people have their gene for breaking down milk turned off
        
        enzyme lactase acts on lactose
        
        lactose is immobilized to alginate beads
        
        lactose is broken down into monosaccharides
  - - - photosynthesis begins when light energy is absorbed by chlorophyll molecules in the chloroplasts of plant cells
        
        plants absorb water from there environment through roots or surroundings
        
        water molecules are transported to the choroplasts
        
        Photolysis: light energy absorbed by chlorophyll is used to split water molecules into oxygen protons (H+ ions) and electrons
        
        2H2O --> 4H+ + 4e- + O2
        
        electrons produced during photolysis are used to generate ATP and NADPH
    - - oxygen molecules produced during photolysis are released into the atmosphere
  - - - properties of ATP:
        
        soluble in water (so reactions can occur in the cytoplasm)
        
        stable at neutral pH levels (as in cytoplasm)
        
        cannot diffuse out of the cell ==> movement between membrane-bound organelles within cells can be controlled
        
        third phosphate group can easily be removed and reattached by hydrolysis and condensation reactions
        
        hydrolyzing ATP splits it to ADP by removing 1 phosphate group with the help of water. Energy contained in covalent bonds is released.
    - - glucose from food and oxygen is transported via the bloodstream to cells, where it is absorbed into the cytoplasm
        
        glucose is turned into pyruvate during glycolysis --> produces small amount of ATP
        
        pyruvate is transported into the mitochondrion, where it gradually breaks down into carbon dioxide, water and a large amount of ATP
        
        Carbon dioxide is a by-product and diffuses into the bloodstream to be transported to the lungs to be exhaled
    - - glucose is converted into 2 pyruvic acid when 2 ADP + 2P is converted into 2 ATP and water
        
        a) In some bacteria and mammal muscle: 2 lactic acid is produced
        b) in yeast: 2 ethanol + 2 CO2 is produced
        
        useful in high intensity exercise
        
        not enough time to deliver oxygen to cells for aerobic respiration
        
        supply of energy needs to be fast and quickly available so power can be maximized
        
        result: lactate and small amount of ATP is produced
        
        lactate can cause muscle aches and pains
        
        lactate is broken down in the liver in the presence of oxygen
- - - - the + charge ions and - charged ions attract each other to form ionic bonds
        Since water molecules only have partial charges, the ionic attraction is small
        
        attraction between 2 water molecules is called a hydrogen bond
        
        hydrogen bond is a weak intermolecular force but gives water its special properties
    - - water as a habitat
        surface tension: water molecules are more attracted to each other by hydrogen bonding than to air particles
        cohesion between water molecules due to hydrogen bond is greater than attraction between water and floating object ==> energy to break hydrogen bond not available
      - transport of water under tension in plants
        
        when water is sucked from the roots to the leaves, there are continuous columns of water in the xylem vessels
        
        tension in the roots is generated by
        a) attractions between soil particles and water;
        b) tension in the leaves develop as water is lost by evaporation to the atmosphere
        c) attractions between water molecules and cell walls of the leaf cells
        
        cohesion properties of water molecules make the water column remain continuous and pulled upwards
        --> large number of hydrogen bonds between water molecules make it very difficult for them to be broken simultaneously at one point along the xylem vessel ==> can withstand large tensions
    - - metabolism
        Cytoplasm:
        aqueous solution with dissolved solutes such as enzymes
      - Blood:
        transport a diverse range of substances
        
        sodium chloride
        
        amino acids
        
        glucose
        
        oxygen
    - - thermal conductivity:
        helps birds and mammals maintain constant body temperatures
  - - - covalent bonds are formed between the phosphate of 1 nucleotide and the pentose sugar of the next nucleotide
        
        sugar-phosphate backbone comprising of alternating sugar and phosphate groups are formed in both DNA and RNA molecules that help conserve the base sequences
      - bases:
        sequence of bases is how information is stored
        Bases in DNA
        
        adenine (A)
        
        cytosine (C)
        
        guanine (G)
        
        thymine (T)
        
        Bases in RNA
        
        adenine (A)
        
        cytosine (C)
        
        guanine (G)
        
        uracil (U)
      - RNA as a polymer formed by condensation of nucleotide monomers
        RNA is a single, unbranched polymer of nucleotides linked by condensation reactions
        
        Hydroxyl groups (OH) on the phosphate of 1 nucleotide and on the pentose sugar of another nucleotide are used
        
        1 of the OH groups are removed entirely, and is combined with the H atom from the other OH groups producing H2O
      - DNA as a double helix
        
        DNA is composed of strands of nucleotides. Each nucleotide contains a deoxyribose and base
        
        DNA molecule consists of 2 strands of nucleotides linked to each other by bases via hydrogen bonds
        
        the 2 nucleotide strands are antiparallel to each other, where 1 end of the strand ends with the phosphate group of the terminal nucleotide while the other strand ends with a deoxyribose
      - differences between DNA and RNA
        
        DNA is double stranded while RNA is single stranded
        
        DNA has thymine while RNA has uracil
        
        pentose sugar within DNA is deoxyribose while pentose sugar within RNA is ribose
    - - sections of DNA are genes that carry information. when the information has an effect on the cell, it is gene expression
        stages of gene expression:
        
        copying base sequence with the base sequence being made of RNA ==> transcription
        
        1 of 2 DNA strands are used as template
        
        rules of complementary base pairing are followed by adenine is replaced with uracil
        --> RNA produced functions
        
        regulatory or structural role in cell
        
        used in protein synthesis
        
        base sequence of RNA molecules is translated into the amino acid sequence of a protein ==> involved in translation
    - - conservation of the genetic code across all life forms as evidence of universal common ancestry
        
        groups of 3 bases are codons. there are 64 different codons as each base in a codon can be any of the 4 bases
        
        1 codon signals the start of protein synthesis, and 3 codons signal the stop of protein synthesis
        
        genetic code is universal among almost all living organisms and viruses ==> 1 base triplet codes for the same amino acid
- - - - based on a semi-conservative replication theory: each strand of new DNA retains half of the original DNA material before replication
        when DNA replication is completed, there are 2 DNA molecules, each consisting of an original strand and a self-synthesized strand
        complementary base pairing allows for high degree of accuracy in copying base sequences
    - - Polymerase Chain Reacton (PCR)
        
        automated method of DNA replication in a thermocycler
        
        allows for rapid amplification of a small amount of DNA into billion copies of specific fragments of DNA
        
        Method:
        
        Denaturation (melting at 95°): seperation of double-stranded DNA into 2 single strands by breaking hydrogen bonds between complementary bases
        
        Annealing (54°): Forward and reverse primer attach to specific segments of DNA by complementary base pairing to initiate DNA replication
        
        Elongation (72°): Taq DNA polymerase catalyses the formation of new DNA strands using deoxyribonucleotides
      - Gel electrophoresis:
        
        technique to separate DNA fragments by length under the influence of an electrical field
        
        Method:
        
        Agarose forms the gel with pores that allow small molecules to pass through
        
        Negatively charged DNA migrates from negative electrode to the positive electrode when electric current is applied (DNA is negatively charged)
        
        Smaller DNA fragments move faster than the larger DNA fragments
        
        DNA is not visible to the naked eye, fluorescent stains (ethidium bromide) and SYBR Safe are added which binds DNA fragments and fluoresce under illumination of UV light
  - - - as the synthesis of RNA using DNA template
        
        RNA polymerase binds to start of the gene and unwinds the DNA double helix to separate it into 2 strands
        
        RNA polymerase moves along the template strand and adds RNA nucleotides with bases complementary to the template sequence
        
        RNA nucleotides are joined by phosphodiester bonds to form a continuous strand
        
        transcription stops when RNA polymerase reaches the end of the gene
        
        RNA polymerase and the newly synthesized RNA detach from the template strand and DNA double helix reforms
      - template strand (antisense strand) has complementary base sequence with RNA
        
        non-template strand (coding/sense strand) has same sequence as RNA)
    - - mRNA: RNA with information to make a polypeptide, contains codons that determine the order of amino acids in a protein
        
        base sequence of mRNA is translated into amino acid sequence of a polypeptide
        
        tRNA: transfers specific amino acids to ribosome during translation
        rRNA: component of the ribosome
      - ribosome attaches to the mRNA at the location of the start codon
        
        first tRNA with complementary anticodon binds to the codon AUG on mRNA
        
        second tRNA with anticodon pairs with the second codon in the ribosome
        
        peptide bonds forms between first 2 amino acids
        
        first tRNA leaves the ribosome
        
        ribosome moves along the mRNA to the next codon
        
        another tRNA molecules brings its amino acid to add on to the polypeptide
        
        cycle continues and a growing polypeptide is formed until a stop codon is reached
        
        tRNA:
        
        has an anticodon at one end (at the hairpin loop), acts as an attachment point for amino acids corresponding to the anticodon
        
        each type of tRNA molecules has a distinctive shape that is recognized by a dedicated activating enzyme, which attaches the correct amino acid onto the tRNA
    - - Point Mutation: single nucleotide is changed
        
        insert mutation:
        1 or more nucleotide are added to DNA sequences
        frame shift mutation
        
        deletion mutation:
        1 or more nucleotide are removed from DNA sequences
        frame shift mutation
      - substitution mutation: silent mutation
        no change in amino acid sequence of proteins due to degeneracy of genetic sequence
        
        e.g. sickle cell anemia
        converts the 6th codon of gene fro GG to GTG in coding strand or CTC to CAC in non-coding strand
        
        change to chemical property of critical amino acid causes haemoglobin molecules to polymerise into fibres and stick together in tissues with low oxygen concentrations
        
        bundles of mutant haemoglobin molecules are rigid enough to distort the red blood cells into a sickle shape
        
        sickle cells cause damage to tissues by becoming trapped in blood capillaries, blocking them and reducing blood flow