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3. Chemistry of Life

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Ruru (Juan Ru) Hoong

on 21 October 2014

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Transcript of 3. Chemistry of Life

glucose + glucose maltose + water
(monos.) (monos.) (disaccharide)
If further monosaccharides are added, a polysaccharide is formed.
3. Chemistry of Life
3.3 DNA Structure
3.4 DNA Replication
3.5 Transcription and Translation
3.6 Enzymes
3.2.1 Distinguish between
organic and inorganic compounds.
Organic compounds are all the complex compounds of carbon found in living organisms (eg. glucose, amino acids), whilst inorganic compounds are not (eg. carbon dioxide, carbonates, hydrogencarbonates)
3.2.2 Identify amino acids, glucose, ribose, and fatty acids.
3.2.5 Outline the role of condensation
and hydrolysis in the relationships between monosaccharides, sucrose, and cellulose in plants.
3.2.6 State the functions of lipids.
3.2.7 Compare the use of carbohydrates and lipids in energy storage.
3.2 Carbohydrates, lipids and proteins
3.2.3 List 3 examples of monosaccharides, disaccharides, and polysaccharides.
Carbohydrates contain C, H, O: most abundant category of molecule in living things & a source of energy.
Monosaccharides: one subunit
In a condensation reaction, two molecules can be joined to form a larger molecule, tied together by strong covalent bonds.
Energy storage (2 times more efficient than carbohydrates)
Thermal insulation (fat in polar bears)
Buoyancy (floating: less dense than water)
Protection (shock absorber)
Nervous function (myelin sheath, nerve impulse insulated)
Phospholipid bilayer/ plasma membranes
Solvent (dissolves some vitamins)
3.3.2 State the names
of the four bases of DNA
3.3.1 Outline DNA
nucleotide structure in terms of sugar, base and phosphate.
3.3.3 Outline how DNA nucleotides are linked together by covalent bonds into a single strand
Nucleotides are linked together to form a DNA molecule
Phosphate group links to sugar of next nucleotide
Links to other nucleotide at C3 by ester bond (covalent)
Within nucleotide: covalent bonds in between phosphate and deoxyribose sugar (C5), between sugar (C1) and base
3.3.4 Explain how a DNA double
helix is formed using complementary base pairing and hydrogen bonds.
Sequence of bases in nucleotide varies, forms genetic code determining the characteristics of an organism
Two strands of nucleotides linked by hydrogen bonds that form between bases
Twisted into a double helix
Complementary base pairing: A--T; G---C by hydrogen bonds
Run in opposite directions: antiparallel
3.3.5 Draw and label a simple diagram of the molecular structure of DNA.
3.4.1 Explain DNA replication in terms of unwinding the double helix and separation of the strands by helicase, followed by formation of the new complementary strands by DNA polymerase.
3.4.2 Explain the significance of complementary base pairing in the conservation of the base sequence of DNA
Complementary base pairing between the template strand and the new strand ensures that an accurate copy of the original DNA is made, as DNA is semi-conservative. New strands are complementary to the old strands, but identical to the other template.
3.4.3 State that DNA replication is semi-conservative
DNA is semi-conservative: no DNA molecule is completely new.
3.5.2 Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by RNA polymerase.
3.5.3 Describe the genetic code in terms of codons composed of triplets of bases
A triplet of bases forms a codon
Each codon codes for a particular amino acid
Amino acids in turn link to form proteins
DNA and RNA regulate protein synthesis
Each of the 20 amino acids involved have 2-3 codons specific to them
There are 'stop' and 'stop' codons
AUG start
UAA stop
3.5.4 Explain the process of translation, leading to polypeptide formation.
3.5.5 Explain the relationship between 'one gene and one polypeptide'.
3.6.2 Explain enzyme-substrate specificity.
3.6.1 Define enzymes and active site.
Enzymes: Globular proteins which act as biological catalysts of chemical reactions, speeding up reactions but remaining unchanged.
3.5.1 Compare the structure of RNA & DNA
One gene codes for a single polypeptide unit
However, there are exceptions:
DNA sequences that act as regulators for the expression of other genes are not transcribed/ translated themselves
Others code for mRNA/ tRNA but not proteins
Variations in modifications made to mRNA strands in cytoplasm leads to production of different polypetides when mRNA is translated
eg. antibodies: lymphocytes splice together sections of RNA in different ways to make range of antibody proteins
Differential expression (eg. insulin-like growth factors in liver)
Some proteins more than one polypetide unit
Arrangement of shape is very precise on active site
Each enzyme catalyzes one specific reaction
Enzyme-substrate specificity
Substrate is a complementary shape
Must fit the active site and be chemically attracted
Lock and key model
Enzyme: lock
Substrate: Key
Catabolic/ Anabolic
Substrates may be bonded together to form new substance
May be broken apart in processes such as digestion/ respiration
3.6.3 Explain the effects of temperature, pH and substrate concentration on enzyme activity.
Temperature
pH
Concentration
Optimum temperature where enzymes work best (eg. 37C in human body)
Below optimum temperature, molecules move more slowly so there is less chance of random collisions, slowing down the production of products
As temperature rises, molecular collisions are more frequent and energetic, therefore rate of enzyme controlled reaction increases
measure of the relative number of H+ and OH- ions in a solution
H+: low pH; OH-: high pH
Pure water neutral, pH 7
Enzyme action is influenced by pH because the amino acids that make up an enzyme molecule contain many +ve and -ve regions
Excess of H+ ions in acidic solution can lead to bonding between H+ ions and negative charges in active site, inhibiting matching process
At extremes of pH, enzyme may lose its shape and become denatured
Not all enzymes have the same optimum pH
Protease in stomach: pH 2; small intestine: pH 8
Concentration of the substrate increases, rate of production increases due to increased chance of collisions
Limit to the rate: if the concentration increases too much, exceed max rate at which enzymes can work
All enzymes occupied, so adding more substrate has no effect as the limit is reached as illustrated by the plateau
3.1 Chemical Elements and Water
3.1.1 State that the most frequently occurring chemical elements in living things are
C, H, O, & N.
C, H, O are found in all the key organic molecules: proteins, carbohydrates, nucleic acids, and lipids.

N is also found in proteins and nucleic acids.
3.1.2 State that a variety of other elements are needed by living organisms, incl. S, Ca, P, Fe & Na.
3.1.4 Draw & label a diagram showing the structure of water molecules to show their polarity and hydrogen bond formation.
3.1.5 Outline the
thermal, cohesive, and
solvent properties of water.
Cohesive Properties (due to hydrogen bonds)
Transport- Water can travel up xylem: continuous column
Surface tension (animals can 'walk on water')
3.1.3 State one role of each.
Calcium
: bones and muscle contraction, co-factor in some enzyme reactions
Sulfur
: needed for synthesis of two amino acids, used to make antibodies
Iron
: component of cytochrome pigments and haemoglobin
Phosphorus
: component of ATP and DNA, energy carriers and nucleic acids
Sodium
: important in membranes & osmosis (changes solute concentration) and nerve impulse transmission
Water is a polar molecule
Dipolar due to difference in electronegativity
Oxygen slightly more negative than hydrogen
Hydrogen bond between +ve & -ve region
Responsible for many properties of water
3.1.6 Explain the relationship between the
properties of water and its uses in living organisms as
a coolant, medium for metabolic reactions, and transport.
Thermal Properties (large amounts of energy needed to break hydrogen bonds)
High Specific Heat Capacity
Stable temperature for metabolic reactions
Homeostasis: keep body temperature constant
Temperature regulator (eg. blood transports heat around body)
High Boiling Points
Liquid at most temperatures in which life exists (useful medium for metabolic reactions)
Acts as a coolant as evaporates
Sweating and transpiration (stream) for heat loss
Solvent (polar molecules interact)
Transport: ions and amino acids
Medium for metabolic reactions
glucose
ribose
fatty acid
amino acid
Carbohydrate
Example
Example of use in plants
Example of use in animals
monosaccharide
disaccharide
glucose, fructose, galactose
sucrose, lactose, maltose
starch, glycogen, cellulose
polysaccharide
fructose: fruits are sweet and attract animals to aid seed dispersal
glucose- energy: cell respiration from the digestion of carbohydrates
sucrose transported in plants as energy source
lactose found in milk, provides energy for young mammals
cellulose: component of cell wall
starch: food store
glycogen: storage carbohydrate of animals; liver and muscles
Condensation
Hydrolysis
glycogen: polysaccharide made of branching chains of glucose
amino acid + amino acid dipeptide + water
If further amino acids are added, a polypeptide chain is formed. Polypeptide chains form protein molecules.
glycerol + 3 fatty acids triglyceride lipid + water
Happens every time food is digested: polysaccharides, polypeptides, and triglycerides broken into smaller units. Water molecules used in hydrolysis reactions (reverse condensation). Enzymes required.
Hydrolysis of starch produces many glucose units
Hydrolysis of water produces fatty acid and glycerol
Hydrolysis of protein produces amino acids
Both lipids and carbohydrates are primary sources of energy for organisms
Stores 2-3x more energy per gram (38 kJ/g)
Lipids
Carbs
Stores less energy per gram (17kJ/g)
Long term storage
Short term storage
Insoluble in water
Soluble in water (easier to transport, more accessible)
Energy not quickly available
Easily and quickly taken out of storage
Deoxyribose nucleic acid molecules make up the genetic material of living organisms
Built up of nucleotides
Sugar (Deoxyribose), Phosphate group, Nitrogenous base
Adenine, Thymine, Guanine, and Cytosine.
Copying DNA precisely so that new molecules are produced with exactly the same sequence of bases as the original strands.
Occurs in S phase of interphase
3. Replication is continuous on the leading strand
DNA Polymerase III
Synthesizes the daughter DNA strand by picking up complementary nucleotides from the free nucleotides pool in the nucleus (A,T; G,C)
Proofreads and ensures correct complementary nucleotides found
1.
Helicase
unzips the 2 parental DNA strands by breaking hydrogen bonds
2.
Single strand binding proteins
provide stability to the 2 separated strands
DNA replication occurs in a 5' - 3' direction.
4. Replication is discontinuous in the lagging strand
RNA primase
makes small RNA primers to initiate replication at various points along lagging strand
DNA polymerase III
uses RNA primers as starting points
DNA replication is discontinuous- short Okazaki fragments
DNA polymerase I
digests the RNA primers and replaces them with DNA nucleotides
DNA ligase
seals the short fragments of DNA on the lagging strand
DNA replication is semi-conservative.
A--T
G---C
Both nucleic acids
DNA
RNA
Both contain sugar, base, and phosphate groups
Deoxyribose as pentose sugar
Double stranded: double helix
Thymine
Ribose as pentose sugar
Uracil
Single strand
3.
RNA polymerase
forms covalent bonds between nucelosides, forming nucleotides
Strand of mRNA is formed (shorter as only one section: gene)
1.
RNA polymerase
binds to promoter region found on sense strand of DNA
DNA unwinds, opens and exposes bases on antisense strand
DNA double helix uncoils.
Transcription occurs in a 5' - 3' direction.
4. Antisense DNA strand is read 3' - 5', mRNA strand runs 5' - 3' (same as sense strand)
2. Free RNA nucleoside triphosphates pair up with the bases on antisense strand
Bound using complementary base pairing (A-U) and (G-C)
Triphosphate: two phosphate groups removed for energy
5. Transcription ends when
RNA polymerase
hits terminator sequence on sense strand.
6. mRNA comes away from the DNA and leaves nucleus via nuclear pore
Associates with ribosome in cytoplasm
7. DNA strands recombine catalyzed by
RNA polymerase
and double helix reforms
3. Peptide linkage forms between the 2 amino acids, forming a dipeptide
1. mRNA binds to the small subunit of the ribosome
4. First tRNA detaches from the ribosome, leaving amino acid behind
2. Only two tRNA molecules can bind to the ribosome at one time
Free tRNA anticodon binds to the first complimentary codon on the mRNA with hydrogen bonds; carrying amino acids
Free tRNA binds to the second complimentary codon on mRNA
5. Ribosome moves along the mRNA strand to the next codon
6. Another tRNA binds over again, peptide bond joins amino acid
7. Process is repeated until complete polypeptide is formed. The final codon is a stop codon that tells ribosome to detach from mRNA
3.6.5 Explain the use of lactase in the production of lactose-free milk.
Milk contains the sugar lactose, digested in intestine by enzyme lactase, producing glucose and galactose which can be absorbed into body
Some people have lactose intolerance: cramps and diarrhea, but children need milk for protein, calcium
Lactase can be commercially obtained from yeast that grows in milk: enzyme used to produce lactase-free milk
Glucose and galactose taste much sweeter than lactose, so manufacturers have to add less sweerner to yogurt
More soluble, so ice cream smoother texture
Fermentation of simple sugars means that there is higher production rate for yogurts and cheeses
Active site: Region on the surface of the enzyme to which substrates bind and which catalyzes a chemical reaction involving the substrates. It is very specific with a precise shape.
If it rises above optimum, enzyme and substrate molecules move faster but atoms within the enzyme molecule move faster so the bonds holding it together break and active site can no longer receive substrate molecules
3D shape lost: substrate permanently destroyed and denatured
Denaturation
is the irreversible changes to the structure of an enzyme or or other protein so that it can no longer function.
3.7 Cell Respiration
3.7.1 Define
'cell respiration'
Cell respiration is the controlled release of energy in the form of ATP from organic compounds in a cell.
3.7.2 State that in cell
respiration, glucose in the cytoplasm is broken down into pyruvate, with a small yield in ATP
In glycolysis, glucose is broken down by a series of enzymes to produce pyruvate with a net production of 2 ATP.
glucose
2 pyruvate +
2 ATP
3.7.3 Explain that, during anaerobic cell respiration, pyruvate can be converted in the cytoplasm into lactate, or ethanol and carbon dioxide, with no further yield of ATP.
Anaerobic respiration occurs w/o energy in the cytoplasm of cells.
In order to generate the small amounts of energy provided by glycolysis, the end product pyruvate must be converted into another substance to replenish the level of hydrogen acceptor for glycolysis to occur and more glucose to be used.
ANIMALS
pyruvate
lactate
eg. during rigorous exercise, build up of lactate in muscle is the sensation of cramps
YEAST
pyruvate
ethanol + carbon dioxide
eg. during alcohol fermentation and making bread
3.7.3 Explain that, during aerobic respiration, pyruvate can be broken down in the mitochondrion into carbon dioxide and water with a large yield of ATP.
Aerobic respiration occurs in the mitochondrion in the presence of oxygen.
glucose + oxygen
carbon dioxide + water
+ 38 ATP
3.8.1 State that photosynthesis involves the conversion of light energy into chemical energy.
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