Biochemistry is The study of the chemical processes occurring
in living organisms. Includes processes involving the flow of both
energy and information. Deals with biomolecules such as proteins,
carbohydrates, lipids, and nucleic acids.
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Energy: IB Objectives B.1.1 Calculate the energy value of a
food from enthalpy of combustion data.
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Energy Every living cell contains thousands of biological
molecules each of which is involved in the interlinked processes of
metabolism. Cellular respiration is the oxidative process by which
energy stored in food is made available for use by the cell.
Glucose Glycogen Starch Fats Protein Rxns of Respiration Energy CO2
+ H2O O2
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Measuring Energy Production Combustion analysis is used to
determine the amount of energy produced from a unit of a particular
food. A bomb calorimeter measures the heat of combustion of a
reaction. Food is burned within the calorimeter, and heat released
raises the temperature of a known quantity of water.
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Calculation of Energy Release Formula: q=mcT q= the energy
evolved (J) m= the mass of water (g) c= the specific heat of water
(4.18 J/gK) T= the temperature change of water (K) Example: A 0.78
food sample combusts raising the temperature of 105.10 g water from
15.4C to 30.6C. Calculate the energy value of food in kJ/g.
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Proteins: IB Objectives B.2.1 Draw the general formula of
2-amino acids. B.2.2 Describe the characteristic properties of
2-amino acids. B.2.3 Describe the condensation reaction of 2-amino
acids to form polypeptides. B.2.4 Describe and explain the primary,
secondary (alpha helix and beta pleated sheets), tertiary, and
quaternary structure of proteins. B.2.5 Explain how proteins can be
analyzed by chromatography and electrophoresis. B.2.6 List the
major functions of proteins in the body.
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Proteins: Function Structure- Proteins make up many diverse
protective, contractile, and supporting structures in the body.
Examples: keratin, collagen, myosin, immunoproteins, hemoglobin,
casein, mucoproteins Tools- Proteins are valuable operators on the
molecular level such as enzymes and hormones. Examples: lactase,
insulin
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Proteins: Structure Amino Acids are the building blocks of
proteins.
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Amino Acids 2-amino acids- Numbering begins with carbonyl
carbon and R group is bound to carbon 2. Carbon 2 is also bound to
H, NH2, and COOH. R group- defines the amino acid. Amino acids can
be classified by the chemical nature of this group (non- polar,
polar, basic, acidic). 20 amino acids occur naturally.
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Characteristics of Amino Acids Crystalline, high melting
points, greater solubility in water than in non-polar solvents.
Exist as dipolar ions- contain both positive and negative charges-
zwitterions. Amphoteric- can react as both an acid and a base.
Amino acids can act as buffers.
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Isoelectric Point This is the pH at which the amino acid is
electrically neutral (typically when the amino acid is a
zwitterion).
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Condensation of Amino Acids Amino acids link together through
condensation reactions to form proteins. Condensation reaction- H2O
is eliminated as a new bond is formed. Forms a peptide bond. Two
amino acids combine to form a dipeptide. Three amino acids combine
to form a tripeptide. More amino acids combine to form a poly
peptide. The sequence of linked amino acids will determine the
nature of the polypeptide=> variety of proteins (millions of
possibilities).
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Structure of Proteins Primary Structure-Number and sequence of
amino acids in polypeptide chain. Secondary Structure- Folding of
polypeptide chain due to hydrogen bonding between peptide groups.
Tertiary Structure- Further twisting, folding of the chain due to
interactions between R-groups (side chains). Quaternary Structure-
Association between more than one polypeptide subunit.
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Primary Structure Forms covalent backbone of molecule. Held
together by peptide bonds. All other levels of structure determined
by primary structure. What determines primary structure of a
protein?
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Secondary Structure Two main types: Beta pleated sheets side by
side polypeptides Pleated sheets cross-linked Inter-chain H-bonds
Flexible, but inelastic Alpha helix Regular, coiled Flexible and
elastic Intra-chain H-bonds H-bonds four AAs apart
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Tertiary Structure Determines proteins conformation. Important
for function of enzymes, hormones, etc. Most stable arrangement
accounting for all possible interactions between side chains.
Possible Interactions: Hydrophobic Interactions Hydrogen Bonding
Ionic Bonding Disulfide Bridges
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Quaternary Structure The association of more than one chain in
proteins.
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Analysis of Proteins First, amino acid composition can be
determined by hydrolyzing the peptide bonds which link together
amino acids in the polypeptide chain. Specific linkages can be
hydrolyzed using certain enzymes. Then peptides can be separated
based on differences in size and charge using the following
techniques. Chromatography Electrophoresis
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Chromatography Amino acids are treated with a locating reagent
to colorize them. A small amount of the mixture is placed at the
origin. Stationary Phase- does not move (paper) Mobile Phase-
travels taking some sample with it (solvent) Movement of peptide
fragments determined by size. Rf= distance traveled by amino acid
distance traveled by solvent Specific amino acids have
characteristic Rf values.
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Electrophoresis Separates amino acids based on movement of
charged particles. A charge gradient is established on a gel.
Proteins migrate based upon charge of side chains present. Proteins
settle near their isoelectric points.
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Carbohydrates: IB Objectives B.3.1 Describe the structural
features of monosaccharides. B.3.2 Draw the straight chain and ring
structural formulas of glucose and fructose. B.3.3 Describe the
condensation of monosaccharides to form disaccharides and
polysaccharides. B.3.4 List the major functions of carbohydrates in
the human body. B.3.5 Compare the structural properties of starch
and cellulose, and explain why humans can digest starch but not
cellulose. B.3.6 State what is meant by the term dietary fiber.
B.3.7 Describe the importance of a diet high in dietary fiber.
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Carbohydrates
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Carbohydrates: Functions
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Carbohydrate Structure
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Monosaccharides
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Monosaccharides: Straight-Chain Forms
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Monosaccharides: Ring Structures
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Disaccharides
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Polysaccharides
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Starch
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Glycogen
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Cellulose
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Digestion of Polysaccharides
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Dietary Fibre
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Lipids: IB Objectives B.4.1 Compare the composition of the
three types of lipids found in the human body. B.4.2 Outline the
difference between HDL and LDL cholesterol and outline its
importance. B.4.3 Describe the difference in structure between
saturated and unsaturated fatty acids. B.4.4 Compare the structures
of the two essential fatty acids, linoleic (omega-6 fatty acid) and
linolenic (omega-3 fatty acid) and state their importance. B.4.5
Define the term iodine number and calculate the number of C=C
double bonds in an unsaturated fat/oil using addition reactions.
B.4.6 Describe the condensation of glycerol and three fatty acid
molecules to make a triglyceride. B.4.7 Describe the enzyme
catalyzed hydrolysis of triglycerides during digestion. B.4.8
Explain the higher energy value of fats compared to carbohydrates.
B.4.9 Describe the important roles of lipids in the body and the
negative effects that they can have on health.
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Lipids
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Lipids: Characteristics Hydrophobic, insoluble in water Soluble
in non-polar solvents Contain Carbon, Hydrogen, and Oxygen Less
oxidized than carbohydrates (more H, less O) Include fats, oils,
steroids, and phospholipids Functions: Energy Storage Insulation
Protection of Organs Absorption of Fat Soluble Vitamins (A,D,E,K)
Structural-Membrane Component Myelin Sheaths of Axons
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Negative Effects of Lipids Excess lipids are stored in the body
as adipose tissue. Sometimes excess lipids are deposited into the
walls of arteries- Atherosclerosis. Atherosclerosis (aka hardening
of the arteries) can lead to hypertension, stroke, and myocardial
infarction. The image shows the aorta of an individual with
atherosclerosis.
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Cholesterol: Good or Bad? Cholesterol is insoluble in blood, so
it is transported as lipoproteins: HDL and LDL. LDL- bad
cholesterol HDL- good cholesterol
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Lipid Structure Three main types: Triglycerides Phospholipids
Steroids
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Triglycerides
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Fatty Acids: Saturation Saturated fatty acids have no double
bonds. Mono-unsaturated fatty acids have one double bond.
Polyunsaturated fatty acids have more than one double bond.
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Essential Fatty Acids Some fatty acids cannot be synthesized by
the body and must be obtained from the diet. These are essential
fatty acids. Linoleic acid (omega-6) Linolenic acid (omega-3)
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Iodine Number Determination of the number of double bonds in a
fatty acid based upon its reactivity with iodine. Iodine can add to
formerly double bonded carbons (addition reaction). The iodine
number is the number of grams of iodine which can react with 100
grams of fat.
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Digestion of Fats Lipases digest fat via hydrolysis
reactions.
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Structure: Steroids
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Micronutrients & Macronutrients: IB Objectives B.5.1
Outline the difference between micronutrients and macronutrients.
B.5.2 Compare the structures of retinol (vitamin A), calciferol
(vitamin D), and ascorbic acid (vitamin C). B.5.3 Deduce whether a
vitamin is water or fat soluble from its structure. B.5.4 Discuss
the causes and effects of nutrient deficiencies in different
countries and suggest solutions.
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Nutrients Nutrients are necessary for the body and must be
obtained from the diet. Recommended Daily Intake is the amount of a
given nutrient which must be consumed each day. Macronutrients-
nutrients required in large amounts Micronutrients- nutrients
required in extremely small amounts
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Vitamins Vitamins are organic compounds required in small
amounts by the body. These compounds must be obtained from the
diet. Categorized by solubility: Fat Soluble Vitamins A, D, E,
& K Non-polar molecules, hydrocarbon chains or rings Slower
absorption Excess can be stored in fat which can be pathological
Water Soluble Vitamins C Polar bonds, can hydrogen bond Transported
directly in blood Excess can be removed by the kidney
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Vitamins Vitamin A Vitamin D Vitamin C
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Malnutrition Results from deficiencies or imbalances in the
diet. Broad spectrum of conditions which compromise health. Refers
to both nutrient-deficiency diseases and diseases associated with
consumption of micro- nutrient poor, energy dense foods (i.e.
diabetes, obesity)
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Micronutrient Deficiencies Iodine Deficiency Necessary for
thyroxine synthesis Goitre Mental retardation Vitamin A Deficiency
Necessary for healthy skin and vision Yellow and orange fruits and
veggies, spinach, egg yolks Xerophthalmia Possible solution:
vitamin A fortification of margarine or rice Iron Deficiency Most
prevalent micronutrient deficiency in the world Essential component
of hemoglobin Anemia
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Macronutrient Deficiencies Protein Deficiency Marasmus
Kwashiorkor
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Causes of Malnutrition Lack of distribution of global
resources. Depletion of nutrients in the soil due to erosion or
misuse. Lack of nutrition education. Over-processing of food
products. Use of chemical treatments such as herbicides.
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Possible Solutions Fortification of staple foods with
micronutrients. Availability of nutritional supplements. Genetic
modification of food to improve nutrient content. Food labels
include content information. Education emphasizing importance of
balanced diet and personal responsibility in diet choices.
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Hormones: IB Objectives B.6.1 Outline the production and
function of hormones in the body. B.6.2 Compare the structures of
cholesterol and the sex hormones. B.6.3 Describe the mode of action
of oral contraceptives. B.6.4 Outline the use and abuse of
steroids.
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Hormones Used for communication within the body by the
endocrine system. May be proteins, steroids, modified amino acids,
or fatty acids. Produced and secreted into the bloodstream by
endocrine glands. Bind to receptors on target cells to produce
response.
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Steroid Hormones
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Oral Contraceptives The Pill typically consists of one or both
of the sex hormones, estrogen and progesterone. This provides
negative feedback to the pituitary to prevent the production of FSH
and LH which normally trigger ovulation. No ovulation = no
pregnancy. Typically taken daily, but morning after versions are
available for emergency use.
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Uses and Abuses of Steroids Uses: Oral Contraceptives Hormone
Replacement Therapy (HRT)- Medications prescribed to replace
hormones lost during menopause. Anabolic Steroids (Androgens such
as Testosterone)- Promote muscle tissue growth following
debilitating diseases. Can be abused by athletes. Side effects-
Changes in secondary sex characteristics, liver
toxicity-cancer
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Enzymes: IB Objectives B.7.1 Describe the characteristics of
biological catalysts (enzymes). B.7.2 Compare inorganic catalysts
and biological catalysts (enzymes). B.7.3 Describe the relationship
between substrate concentration and enzyme activity. B.7.4
Determine Vmax and the value of Michaelis constant (Km) by
graphical means and explain its significance. B.7.5 Describe the
mechanism of enzyme action, including enzyme substrate complex,
active site, and induced fit model. B.7.6 Compare competitive
inhibition and non-competitive inhibition. B.7.7 State and explain
the effects of heavy-metal ions, temperature changes, and pH
changes on enzyme activity.
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Enzymes
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Nucleic Acids: IB Objectives B.8.1 Describe the structure of
nucleotides and their condensation polymers (nucleic acids or
polynucleotides). B.8.2 Distinguish between the structures of DNA
and RNA. B.8.3 Explain the double helical structure of DNA. B.8.4
Describe the role of DNA as the repository of genetic information,
and explain its role in protein synthesis. B.8.5 Outline the steps
involved in DNA profiling and state its use.
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The Role of Nucleic Acids Includes deoxyribonucleic acid and
ribonucleic acid. DNA stores genetic information. stable structure,
contains a code, able to replicate Double helix structure RNA
enables expression of genetic information stored in DNA.
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Structure of Nucleic Acids DNA and RNA are polymers of
nucleotides.
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Nucleotides Contain: Pentose sugar (C5H10O5) Phosphate group
Nitrogenous base Ribose Forms from condensation reactions between
components. RNA: A,G,C,U DNA: A,G,C,T
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Nitrogenous Bases Purines Larger Two fused rings Pyrimidines
Smaller Single ring
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Polynucleotides Nucleotides link together via condensation
reactions. Linkage occurs between 5 phosphate and C3 of sugar.
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DNA Double helix of two poly- nucleotides held together by
hydrogen bonds between bases. 10 bp/turn Turn=3.4nm Base pairing:
A-T G-C Sugar phosphate backbone Stability Code Replicable
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DNA Replication Semi-conservative replication Occurs during
cell division.
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DNA Profiling Every person has a unique genome. A person can be
identified by DNA Profiling. Applications Identify crime victims
Identify suspects Confirm biological relationships Determine
relationships between populations to study evolution, etc.
Procedure: DNA is extracted and cut using restriction enzymes. DNA
is amplified using PCR. Fragments are separated and detected using
gel electrophoresis. Autoradiogram is produced.
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RNA Single stranded poly-nucleotide chain. Less stable than DNA
Can cross nuclear membrane Types: Messenger RNA Transfer RNA
Ribosomal RNA tRNA
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The Central Dogma
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Respiration: IB Objectives B.9.1 Compare aerobic and anaerobic
respiration of glucose in terms of oxidation/reduction and energy
released. B.9.2 Outline the role of copper ions in electron
transport and iron ions in oxygen transport.
