Biochemistry Part 1

Atoms

Smallest particle of an element.

3 subatomic particles:

• electrons

• protons

• neutrons

Isotopes

• Atoms of an element that have the same number of protons but different number of neutrons

• Radioisotope: An unstable isotope that decays over time

  • Emitted particle and energy  

Valence Electrons

• Electrons that occupy the outermost shell of an atom. 

• Participate in chemical bonding 

• Atoms move electrons between their valence shells to achieve a full valence shell

• H, Li, Be are stable with 2 electrons, while most atoms require 8 electrons for a full valence shell

Ion

• Atom or molecule that has become charged due to addition or removal of electrons 

Cation

• Positive charged ion 

  • Lost electrons

Anion

• Negative charged ion 

  • Gained electrons

Ionic Bond

• The electrostatic (positive + negative) force of attraction between two oppositely charged ions 

• Extremely strong

• Often readily readily soluble in polar solvents (water)

Covalent Bonds

• Sharing one or more pairs of electrons between atoms

• Two or more atoms bonded together in this way make a molecule 

Bond Polarity

• Electronegativity (EN)

  • The measure of an atoms attraction to shared electrons

  • Atoms in covalent bonds often don’t share electrons equally 

  • EN values can be compared to determine if a bond is polar or nonpolar

Polar Covalent Bonds

• UNEQUAL SHARING of electrons 

• Difference in EN of atoms bonded is more than of equal to 0.41

Nonpolar Covalent Bonds

• EQUAL SHARING of electrons

• Difference in EN of atoms bonded is less than or equal to 0.40

Molecule Polarity

• Polar bonds have a positive and negative side 

• May cause molecules may also have a positive and negative side 

• Higher EN is the negative side

• Lower EN is the positive side 

• Indicated using dipoles

• If molecules contain only nonpolar bonds, or if their polar bonds are equally distributed, molecules will be nonpolar

Intermolecular Forces

Attraction between two forces

Dipole-Dipole

• Intermolecular force between the negative side dipole of a molecule and the positive dipole of another molecule

London Dispersion Forces

• Help determine the physical properties of substances 

  • Melting point 

  • Boiling point

  • Hardness

• Attractive force between particles caused by attraction of the electron on one particle to the p on the other particle and vice versa. 

  • EXIST BETWEEN ALL PARTICLES

  • Rely on random motion of electrons

  • Temporary & very weak

  • The relative strength increases with the surface area of the molecule and the number of electrons contained within it (more electrons and surface area=more LDF strength)

Dehydration Synthesis Reaction

• Larger molecule is made from smaller molecules via the removal of water

• “Condensation” reaction

• When growing, body dehydrates 

Hydrolysis Reaction

• Water is used to break down larger molecules into smaller

Anabolism

• Biochemical reactions that make larger molecules from smaller ones

Catabolism

• Biochemical reactions that break down larger molecules into smaller ones

Neutralization Reaction

• An acid and a base are combined to make ionic compound (a salt) and water

Water

• All cellular processes occur in an aqueous environment

• Can form four H-bonds with other water molecules

Heat Capacity

• Liquid water only escapes as vapor molecule ONCE enough energy has been provided to break all IMFs surrounding it

• Strong IMFs 

• High melting/boiling point

• While most substances become more dense as they get colder, water molecules become less dense, which makes it float

  • Happens because molecules spread out into a crystalline structure (lattice)

  • Ice insulate aquatic life in cold weather 

Specific Heat Capacity

• Energy required to raise the temperature of 1kg of substance by 1C

Cohesion

•  Attraction of particles within the same substance

  • Ability to stick to itself

Adhesion

• Attraction of particles of different substances

  • Ability to stick to other things 

  • Curve caused by water adhering to glass

Aqueous Solution

• Ion or polar molecule is placed in water and gets surrounded by water molecules in a layer called a Hydration Shell

• Ionic crystals split into smaller pieces in water as the water molecules form dipole-ion IMFs with them and form hydration shells

Hydrophobic

• Nonpolar molecules DO NOT LIKE WATER

Hydrophilic

• Polar molecules LIKE WATER

Ionization and pH

• Autoionization of water

• Water reacts with itself 

  • 2 water molecules can perform the reaction: 

    • H2O + H2O = H3O (hydronium) +OH (hydroxide)

Acids

• Compound that make H3O ions more concentrated than OH ions

• Have an ionization hydrogen (H that can dissociate, break off)

•  Sour

• Watery 

• Red

• Conductor of electricity

• pH of less than 7.0

• H3O

Bases

• Compound that make OH ions more concentrated than H3O ions 

• Bitter

• Slippery 

• Blue
  Conductor of electricity 

• pH or more than 7.0

• 2 ways bases work

  • Have an ionizable hydroxide that can dissociate (break off)

  • May remove an H ion from a water molecule

• OH

pH

• Measurement of concentration of H in a solution 

Functional Groups

• specific combination if atoms that affect the chemical properties of a molecule

• Sites on molecules that reactions take place

• Type of functional group + location determines what the molecule does

• Most are polar 

• Increase solubility within the aqueous cellular environment (organic molecules are mostly nonpolar C-H bonds)

• Carbon is the main element of most biochemical molecules

  • Called organic molecules 

  • Bonded with non-metals

  • Provides 4 possible bonding combinations (4 valence electrons)

  • Carbon forms cyclic structures (ring shaped)

Alkane

• Hydrocarbon carbon-carbon bonds are SINGLE BONDS

Alkene

• Hydrocarbon 1+ carbon-carbon DOUBLE BONDS

Alkyne

• Hydrocarbon 1+ carbon-carbon TRIPLE BONDS

Aromatic Ring

• Cyclic structure with alternating DOUBLE bonds

Aliphatic RIng

• Cyclic structure WITHOUT alternating DOUBLE bonds 

Hydroxyl

• -OH group + C atom

• Defining functional groups in ALCOHOL compounds

Carbonyl

• C=O group + C atom 

Aldehyde

• When attached to a C and a H as well

Ketone

• When attached to 2 Cs

Carboxyl (acid group)

• C atom + COOH group 

• Found in organic acids (amino acids)

Amino

• -NH2 group + C atom

• Compounds classified as amines 

• Found in amino acids

Phosphate

• -PO4 group + C atom 

• Found in biochemical molecules

  • Genetic material 

Sulfhydryl

• -SH group + C atom

• Used give proteins their shape

• Classified as thiols

Carbohydrates (Saccharides)

• Most common biological molecules

• Cx(H2O)y

• High-energy food source (starches, sugars)

• Used fro cellular communication (cells have embedded carbohydrates to communicate with nearby cells)

• ALL HAVE CARBON RINGS WITH O

Monosaccharides

•  Formula: C_nH_2nO_n

• Can be classified by how many carbons they contain

• 5+ Carbons can be folded to make ring shape

• DOUBLE BONDED O NEEDS TO FIND H 

Aldose

• An aldehyde monosaccharide

Ketose

• A ketone monosaccharide

Anomers

• Cyclic isomers with same atomic connectivity, but different 3D arrangements

• C1 carbon is called anomeric carbon (with H and OH, next to O)

Alpha or Beta

• Look at C1 and CH2OH

  • If they are going in the same direction, beta

  • If they are going in opposite directions, alpha 

Isomer

• Molecule with same chemical formula as another molecule, but different arrangement of atoms

• C atoms need to be numbered

Galactosemia

• Genetic inability to metabolize galactose 

• Normal people are able to convert galactose to glucose

• People with galactosemia must avoid dairy (dairy is main source of galactose)

Glycosidic Bonds

• -C-O-C- linkage between monosaccharides

• Results in larger molecule

Naming Glycosidic Bonds

• Take alpha or beta (depending on the format)

• Add the numbers of the carbon atoms 

• Add glycosidic bond to end

Lactose Intolerance

• Person does not have lactase enzyme

Oligosaccharides

• Bonding 2-10 monosaccharides to make a chain 

• Inulin 

  • Indigestible prebiotic for digestive health

• Oligofructose

  • Prebiotic (plant based food)

• In cell membranes act as receptors to help cells communicate

Polysaccharides

• Made from bonding many monosaccharides to make a chain

Complex Carbohydrates

• Very large polysaccharide containing up to thousands of monosaccharides

Polymer

• Large molecule made up of smaller repeating molecules called monomers

• Polysaccharide is a polymer of monosaccharide monomers

Glycogen

• Glucose storage molecule for many organisms including humans 

• Found in liver and muscle cells

Glucose Regulation

• Primary source of energy for body

• Blood-glucose levels controlled by two hormones 

  • Insulin

    • When blood-glucose is too high

  • Glucagon 

    • Blood-glucose is too low 

Hypoglycemia

• Blood-glucose concentration lower than the standard range (less than 60 mg/dL)

• Being on a diet 

Hyperglycemia

• Blood-glucose concentration higher than the standard range (more than 200 mg/dL)

Type 1 Diabetes

• Low insulin

• Glucose is not converted to glycogen 

Type 2 Diabetes

• Insulin resistance 

• Glucose is not converted to glycogen 

Cellulose

• Tough, insoluble, ingestible fiber

• Beta-1,4-glycosidic bonds

• Plant-based food

• Dietary fiber

Chitin

• Beta-1,4-glycosidic bonds

• different

Low Carb Diet

• Initial weight loss is mostly due to glycogen stores in the liver and muscles being depleted

• Less bloating

• Dehydration

• Fatigue

• Loss of muscle tone

Lipids

• Nonpolar organic compound normally consisting of C, H, bit of O

Functions of Lipids

• Long-term energy storage

• Insulation of internal organs

• Membrane structure

• System-wide messenger molecules (hormones)

Fatty Acids

• Hydrocarbon chain with a carboxyl functional group at the end(acidic)

  • Make fatty acids slightly soluble 

• Longer the hydrocarbon chain is the less soluble

Saturated Fatty Acids

• Hydrocarbon chain has only single bonds, results in the maximum amount of H in the molecule

• Long linear carbon chains

Unsaturated Fatty Acids

• Hydrocarbon chain contains double or triple between carbons 

• Bend or linear carbon chains depending in which side of the double bond hydrogen atoms are on 

Polyunsaturated Fatty Acids

• 2 or more double or triple bonds

Cis Fatty Acids

• Unsaturated fatty acids that bend because the H atoms are on the same side of the C=C bond

Trans Fatty Acids

• Unsaturated fatty acids that are linear because the h atoms are on opposite sides of the C=C bond

Hydrogenation

• Additions of H atoms to unsaturated fatty acids 

• Partial hydrogenation can turn a cis fatty acid into a trans fatty acid

• Full hydrogenation will saturate unsaturated fatty acids

Fats

• Lipids made from the dehydration synthesis reaction between glycerol and up to 3 fatty acids 

• Make water 

Ester Linkage

• -COOC- group that connects a fatty acid to a glycerol in a fat molecule 

Monoglyceride

• Fat made with glycerol and 1 fatty acid

Diglyceride

• Fat made with glycerol and 2 fatty acids

Triglyceride

• Fat made with glycerol and 3 fatty acids

Saturated Fats

• Fats that contain only saturated fatty acids

• Often solid at room temperature because their linear fatty acids are packed more closely together

Unsaturated Fats

• Fats that contain one or more unsaturated fatty acids

• Often liquid in room temperature 

• Oils 

• weak IMF

Trans Unsaturated Fats

• Unhealthy fats

• Solids at room temperature because they are linear & densely stack with each other

Essential Fatty Acids

• alpha -linolenic acid (omega--3)

• Linoleic acid (omega-6)

• Effect

  •  Blood clotting

  • Blood pressure

  • Brain growth and function

  • Inflammation

  • Mood

  • Behaviour 

Phospholipids

• A lipid containing a phosphate group

• Used to make cell membranes

• Have a structure similar to phosphattidyl ethanolamine 

Amphipathic

• a molecule that contains both a polar (hydrophilic) and nonpolar (hydrophobic) region

• Bilayer of the cell membrane provides a barrier that is hydrophilic on the exterior with a hydrophobic interior

Steriods

• A lipid with a base framework of 4 carbon rings\

• Bile acid 

  • For lipid absorption in the small intestine

• Campesterol

  • Lowers cholesterol absorption in the small intestine

• Reactants used to from other organic molecules

• Can be hormones 

  • Molecule released into the tissue fluid od an organism that helps regulate its growth or behaviour 

• Testosterone 

  • Regulates body changes during and after puberty 

• Progesterone

  • Regulates the menstrual cycle and pregnancy 

Cholesterol

• helps cell membranes remain fluid and permeable

• Can be converted into vitamin D

2 Forms of Cholesterol

• HDL (High-Density Lipoprotein)

  • Picks up cholesterol around the body and carries it back to the liver for removal from the body 

• LDL (Lower-Density Lipoprotein)

  • Too much LDL in blood may lead to build-up on the artery walls and atherosclerosis

  • Bad cholesterol 

  • Leads to heart attack or stroke 

Effects of Steroids

• effects 

  • Brain

    • Sex drive 

    • Aggression 

  • Skin 

    • Growth of facial and body hair

    • Baldness

  • Male sex organs

    • Sperm production

    • Prostate growth 

    • Erectile function

  • Muscle 

    • Muscle mass and strength

  • Bone marrow

    • Red blood cell production

  • Bone

    • Bone density maintenance

Side Effects of Steroids

• Side effects

  • Hair loss

  •  Irritability

  • Mood swings

  • Ance

  • Gynaecomastia

  • Liver damage

  • Infertility

  • Shrinkage of the testicles

  • Increased cardiovascular risk

  • Impotence

  • Low libido

  • Osteoporosis osteopenia (weak bones)

Waxes

• Large lipid often by the bonding of fatty acids to alcohols or carbon rings

• Extremely hydrophobic (non-polar) 

• Soft solids

• Cutin

  • Is produced by plants t form a waterproof barrier on fruits, stems, leaves

• Birds secrete waxes to keep feathers dry

• Structural component used by bees in their hives

• Earwax traps particles that may cause ear infection

Proteins

• Large, folded polymer molecule made up of amino acids as its monomers 

Structural Proteins

• Provide shape and form to a cell or organism structure

Defensive Proteins

• Helps fight-off infection 

Signal Proteins

• Carry messages around an organism 

• Some hormones