Unit 2 Molecular Biology. Essential Ideas 2.1 - Living organisms control their composition by a...
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Transcript of Unit 2 Molecular Biology. Essential Ideas 2.1 - Living organisms control their composition by a...
Unit 2
Molecular Biology
Essential Ideas
2.1 - Living organisms control their composition by a complex web of chemical reactions
Basic Background
• Organic chemistry = carbon• Biochemistry – attempts to explain the
chemical characteristics of living organism
• 4 categories of organic compounds– Carbohydrates– Lipids– Proteins– Nucleic acids
Basic Background
• Water is the medium of life• Proteins act as enzymes• Genetic information stored in DNA• Compounds of carbon, hydrogen and
oxygen are used to supply and store energy
Section 2.1 Molecules to MetabolismUnderstandings:• Molecular biology explains living processes in terms
of the chemical substances involved.• Carbon atoms can form four covalent bonds, allowing
a diversity of stable compounds to exist.• Life is based on carbon compounds, including
carbohydrates, lipids, proteins, and nucleic acids. • Metabolism is the web of all the enzymes-catalysed
reactions in a cell or organism.
Understandings continued:• Anabolism is the synthesis of complex molecules
from simpler molecules, including the formaion of macromolecules from monomers by condensation reactions.
• Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.
Molecular biology – the chemistry of living organisms
Interactions between organic moleculesExample of Metabolism Insulin (protein hormone)
Facilitates the movement of glucose from the bloodstream into the cell’s interior
Interacts with protein channels to open them Glucose moves high to low
Molecular biology – the chemistry of living organisms
Insulin cont. Why can’t glucose go through the phospholipid
bilayer? Polarity
Insulin and channels are both proteinsCoded by DNA
What category of organic molecule is glucose
Each organic molecule is
represented
Carbon-based life
Are all compounds that contain carbon organic?
Atomic # of carbon is ______Carbon has ___ valence electronsCarbon always forms 4 __________ bonds (share)Covalent bonds are strong bonds.
Carbon dioxide
Challenge yourself
Read through the following example of molecular interactions leading to a physiological response. Try to classify each of the named molecular components as a carbohydrate, lipid, protein or nucleic acid.
Reading
When a predator, such as a snake, catchers and eats a small rodent, one of the main sources of nutrition that the snake is consuming is the muscle of the prey animal. That muscle is primarily composed of two molecules: actin and myosin. When the ingested muscle reaches the intestines of the snake, enzymes (such as trypsin) help the snake digest the actin and myosin into amino acids. Other enzymes (such as lipase) help the snake digest the triglyceride fats within the adipose tissue of the rodent.
Biochemical compounds important to living organisms
• nucleotides• Amino acids
• Glycerol • Fatty acids
• monosaccharides
Carbohydrates(C, H, O)
1:2:1
Lipids(C, H, O)
Nucleic Acids
(C, H, O, N, P)
Proteins(C, H, O, N &Sometimes S)
Common categoriesCategory Subcategory Example molecules
Carbohydrates Monosaccharides Glucose, galactose, fructose, ribose
Disaccharides Maltose, lactose, sucrose
Polysaccharides Starch, cellulose, chitin
Proteins Enzymes, antibodies, peptide hormones
Lipids Triglycerides Fat stored in adipose cells
Phospholipids Bilayer in cell membranes
Steroids Some hormones
Nucleic acids DNA, RNA, ATP
Skill: Drawing Molecules
Glucose:
Skill: Drawing Molecules
• Ribose:
Skill: Drawing Molecules
• Saturated Fatty Acid
Skill: Drawing Molecules• Generalized amino acid:
Skill: Identification of biochemicals as carbohydrates, lipids, proteins and nucleic acids.
Metabolism: reactions controlled by enzymes
• all the reactions within all of the cells (and fluids such as blood or digestion in the small intestines) comprise the metabolism of the organism.
• Catalyzed by enzymes
Factors determining if reactions occur
• Identity of the colliding molecules• Orientation of the colliding molecules
(where they hit each other)• The speed of the molecules when they
collide
Examples of a reaction
• Creating ATP – cellular respiration• Replication of DNA• Synthesis of RNA• Synthesis of proteins• Photosynthesis
Metabolism
Anabolism• Synthesis of complex
molecules• Require energy (ATP)• Condensation/dehydration
synthesis• Examples:
– Protein synthesis– DNA synthesis– Photosynthesis
Catabolism• Breakdown of complex
molecules• Release energy• Hydrolysis• Examples
– Digestion of food– Digestion of dead organic
matter by decomposers
Application:Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.
• Urea (organic) was discovered in urine – 1720’s
• It was widely believed that organic compound could only be made with help of a “vital principle” (vitalism)
• Vitalism = living organism and inanimate things differed fundamentally because living organisms contained a non-physical element.
Application
• Urea is in nitrogenous waste• In humans– Produced in the liver– Enters the bloodstream– Filtered out by the kidneys– A component of urine
Application
• Wohler – German physician & chemist– 1828
• Mixed cyanic acid and ammonium– Crystalline substance formed
• Crystals were urea• Organic molecule synthesized from
inorganic substances
Work is published
Vitalism is questioned as
scientific theory
Click here
Importance
• Scientific theories undergo modifications• Important discoveries are made
accidentally• Scientific discovery is not always
appreciated immediately for its importance
2.2. Water
• Understanding:– Water molecules are polar and
hydrogen bonds form between them.– Hydrogen bonding and dipolarity
explain the cohesive, adhesive, thermal and solvent properties of water.
– Substances can be hydrophilic or hydrophobic
Structure of Water
• Water is the solvent = aqueous• What type of bond is between the oxygen
and the hydrogen atoms of water? – Polar covalent bond
• Because of that bonding, it has – Dipolarity
• And thus short-lived hydrogen bonds
Cohesion
• Same type of molecules• Why– Water forms into droplets when it splits– Water has a surface tension– Water is able to move a water ‘column’ in
the vascular tissues of plants
Adhesion
• Attraction between two unlike molecules• Water is attracted to cellulose• Leads to capillary action
Application • Use of water as a coolant in sweat.
Thermal properties• High specific heat– Water can absorb or give off a lot of
heat without changing temp much– Ocean/beach day vs night
• High heat of vaporization– Water absorbs a lot of heat when it
evaporates
Water evaporates
through stomata – cools plant
Examples
• Basilisk lizards can run on water
Application
• Modes of transport of glucose, amino acids, cholesterol, fats, oxygen, and sodium chloride in blood in relation to their solubility in water.
Solvent properties
• Water is solvent to other polar molecules– Proteins, carbs, nucleic acids
• Excellent medium for transport– Xylem carries water & dissolved minerals– Phloem moves dissolved sugar
• Blood most common transport in animals– Blood plasma– Glucose, amino acids, fibrinogen, hydrogen
carbonate ions
SubstanceHigh or low relative solubility in water
Mode of transport in an aqueous environment
Glucose Polar molecule/high solubility
No special mode of transport needed/dissolves directly in aqueous plasma
Amino acids Varying polarity but all are reasonably soluble
No special mode of transport needed/ dissolves directly in aqueous plasma
Cholesterol Largely non-polar/very low solubility
Transported by blood proteins that have polar amino acids on the outer portion to give water solubility, & non-polar amino acids internally to bind the non-polar cholesterol
Fats Non-polar fatty acid components/very low solubility
Transported by blood proteins that have polar amino acids on the outer portion to give water solubility, & non-polar amino acids internally to bind the non-polar cholesterol
Substance High or low relative solubility in waterMode of transport in an aqueous environment
Oxygen Travels as diatomic O2/low solubility Relatively low solubility in water is exacerbated by the relatively high temperature of warm-blooded animals (oxygen is less soluble in warm aqueous solutions)/haemoglobin is used to bind & transport oxygen molecules reversibly
Sodium chloride Ionizes/high solubility No special mode of transport needed/sodium chloride is an ionic compound, it ionizes into separately charged Na+ and Cl- ions in aqueous plasma
Hydrophobic & hydrophilic• Polar substances = hydrophilic• Non-polar substances = hydrophobic– Organic non-polar = carbon & hydrogen OR large
areas of only hydrogen & carbon (methane)• fatty acids, some proteins depending on the
arrangement of the amino acids• (think integral proteins)
Application
• Comparison of the thermal properties of water with those of methane.
Methane vs WaterFreezing point -183o C 0o C
Boiling point -163o C 100o C
Structure
Phase change No hydrogen bonds influencing phase changes so they escape from each other
Water molecules constantly forming, breaking, and almost instantly reform hydrogen bonds with other water molecules
Liquid to solid No longer has enough molecular motion
Motion low enough, hydrogen bonds lock water molecules into ice crystals
Polar covalent
Non-polar
covalent