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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.
  • 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.




Rxns of Respiration

CO2 + H2O





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

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.


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.
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 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 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
  • Vitamin A
  • Vitamin D
  • Vitamin C
  • 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.
  • 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.
  • Contain:
    • Pentose sugar (C5H10O5)
    • Phosphate group
    • Nitrogenous base





Forms from condensation reactions between components.

nitrogenous bases
Nitrogenous Bases
  • Purines
  • Larger
  • Two fused rings
  • Pyrimidines
  • Smaller
  • Single ring
  • Nucleotides link together via condensation reactions.
  • Linkage occurs between 5’ phosphate and C3 of sugar.
  • 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.
  • Single stranded poly-nucleotide chain.
  • Less stable than DNA
  • Can cross nuclear membrane
  • Types:
    • Messenger RNA
    • Transfer RNA
    • Ribosomal RNA


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.
  • Cellular Respiration
  • Oxygen Transport