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Human Biochemistry. IB Chemistry 3 Robinson High School Andrea Carver. Biochemistry is…. The study of the chemical processes occurring in living organisms. Includes processes involving the flow of both energy and information.

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Human biochemistry

Human Biochemistry

IB Chemistry 3

Robinson High School

Andrea Carver


Biochemistry is
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.


Energy ib objectives
Energy: IB Objectives

  • B.1.1 Calculate the energy value of a food from enthalpy of combustion data.


Energy
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.

O2

Starch

Protein

Rxns of Respiration

CO2 + H2O

Glucose

Glycogen

Fats

Energy


Measuring energy production
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.


Calculation of energy release
Calculation of Energy Release

  • Formula: q=mc∆T

    • q= the energy evolved (J)

    • m= the mass of water (g)

    • c= the specific heat of water (4.18 J/g•K)

    • ∆T= the temperature change of water (K)

  • Example: A 0.78 food sample combusts raising the temperature of 105.10 g water from 15.4°C to 30.6°C. Calculate the energy value of food in kJ/g.


Proteins ib objectives
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.


Proteins function
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


Proteins structure
Proteins: Structure

  • Amino Acids are the building blocks of proteins.


Amino acids
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.


Characteristics of amino acids
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.


Isoelectric point
Isoelectric Point

  • This is the pH at which the amino acid is electrically neutral (typically when the amino acid is a zwitterion).


Condensation of amino acids
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).


Structure of proteins
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.


Primary structure
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?


Secondary structure
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 AA’s apart


Tertiary structure
Tertiary Structure

  • Determines protein’s 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


Quaternary structure
Quaternary Structure

  • The association of more than one chain in proteins.


Analysis of proteins
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


Chromatography
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.


Electrophoresis
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.


Carbohydrates ib objectives
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.






Monosaccharides straight chain forms
Monosaccharides: Straight-Chain Forms


Monosaccharides ring structures
Monosaccharides:Ring Structures








Dietary fibre
Dietary Fibre


Lipids ib objectives
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.



Lipids characteristics
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


Negative effects of lipids
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.


Cholesterol good or bad
Cholesterol: Good or Bad?

  • Cholesterol is insoluble in blood, so it is transported as lipoproteins: HDL and LDL.

  • LDL- “bad cholesterol”

  • HDL- “good cholesterol”


Lipid structure
Lipid Structure

  • Three main types:

    • Triglycerides

    • Phospholipids

    • Steroids



Fatty acids saturation
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.


Essential fatty acids
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)


Iodine number
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.


Digestion of fats
Digestion of Fats

  • Lipases digest fat via hydrolysis reactions.



Micronutrients macronutrients ib objectives
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.


Nutrients
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


Vitamins
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


Vitamins1
Vitamins

  • Vitamin A

  • Vitamin D

  • Vitamin C


Malnutrition
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)


Micronutrient deficiencies
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


Macronutrient deficiencies
Macronutrient Deficiencies

  • Protein Deficiency

    • Marasmus

    • Kwashiorkor


Causes of malnutrition
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.


Possible solutions
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.


Hormones ib objectives
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.


Hormones
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.



Oral contraceptives
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.


Uses and abuses of steroids
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


Enzymes ib objectives
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.



Nucleic acids ib objectives
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.


The role of nucleic acids
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.


Structure of nucleic acids
Structure of Nucleic Acids

  • DNA and RNA are polymers of nucleotides.


Nucleotides
Nucleotides

  • Contain:

    • Pentose sugar (C5H10O5)

    • Phosphate group

    • Nitrogenous base

RNA: A,G,C,U

DNA:

A,G,C,T

Ribose

Forms from condensation reactions between components.


Nitrogenous bases
Nitrogenous Bases

  • Purines

  • Larger

  • Two fused rings

  • Pyrimidines

  • Smaller

  • Single ring


Polynucleotides
Polynucleotides

  • Nucleotides link together via condensation reactions.

  • Linkage occurs between 5’ phosphate and C3 of sugar.


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


Dna replication
DNA Replication

Semi-conservative replication

Occurs during cell division.


Dna profiling
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.


RNA

  • Single stranded poly-nucleotide chain.

  • Less stable than DNA

  • Can cross nuclear membrane

  • Types:

    • Messenger RNA

    • Transfer RNA

    • Ribosomal RNA

tRNA



Respiration ib objectives
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.


Respiration
Respiration

  • Cellular Respiration

  • Oxygen Transport








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