Biology: Chemistry of Life & H₂O

Bio Exam Review

Chapter 1: Principles of Life

• Introduces the fundamental principles of life but contains no specific details

Chapter 2: Life's Chemistry & H₂O Importance

• All matter comprises atoms
• An element is a substance consisting of only one type of atom.
• Atomic mass is measured in Daltons, 1.7 x 10^-24 grams
• Usually disregard electron weight
• Atomic number equals the number of protons, identifies the element.
• Mass number is the total count of protons and neutrons in the nucleus.
• Each electron shell has one spherical orbital
• Second and subsequent shells have three p orbitals.
• Lower electron shells possess more energy
• S-orbitals store more energy than p-orbitals
• Atoms with at least two electron shells become stable when their outermost shell contains eight electrons (Octet Rule).
• Electronegativity describes an atom's tendency to attract electrons from another atom.
• Amount of electrons in the outer shell affects electronegativity
• The more electrons it has the higher electronegativity it has
• Closer electrons are to nucleus affects electronegativity
• The closer it is to the nucleus, the higher electronegativity is
• Chemical bonds are the attractive forces linking atoms to form molecules

Types of Chemical Bonds

• Ionic Bonds: Highly electronegative atoms pull one or more electrons from atoms with low electronegativity.
• Cations: Positively charged, thus are attracted to Anions
• Anions: Negatively charged, thus are attracted to Cations
• Results in Molecules & salts
• Covalent Bonds: Form when two atoms share one or more pairs of electrons to achieve a stable electron configuration
• Each atom contributes one member of the electron pair
• Atoms share two electron pairs in Double Bonds
• Electronegativities must be similar for covalent bonds to happen

Covalent Bonds, Characteristics and Behaviour

• Orientation, including length, angle, and direction, is constant for covalent bonds
• Strength and stability: Covalent bonds are very strong
• Unequal sharing typically occurs when two atoms are different.
• Nonpolar Bonds: Electrons are shared equally.
• Polar Bonds: Electrons are pulled closer to the nucleus of the more electronegative atom.
• More electronegative atoms are slightly negative (-).
• Less electronegative atoms are slightly positive (+).
• Dipole: Separation of opposite electric charges, also known as polar covalent bond.
• Dipole-dipole interactions: Slightly charged atoms can interact with other atoms; categorized as weak interactions.
• Hydrogen Bond: Attraction between a slightly positive charged covalently bonded hydrogen and highly negative charged covalently bonded nitrogen or oxygen.
• Van der Waals Interactions: Movement of electrons results in small temporary dipoles.
• These attractions are very weak but many tiny interactions can lead to a significant force.

Chemical Transformations and Energy

• Energy enables change
• Kinetic energy is energy of movement € Includes thermal sound, and electromagnetism
• Potential energy is stored energy 　 Includes gravitational, elastic, chemical, and nuclear energy.
• Thermodynamics Laws: Govern changes in energy
• First Law: Energy cannot be created or destroyed
• Second Law: Energy increases when energy transforms
• After-energy transformation some energy becomes unavailable to work.
• Entropy can only decrease if energy is added to the system.
• Chemical Reaction: When atoms combine or change their bonding partners
• Gibbs Free Energy (G): Total energy change, calculated from the difference between bond energies
• Includes change In entropy
• A negative G signifies reactions are exergonic and release energy
• A positive G signifies reactions are endergonic and require energy.
• Activation Energy (Ea): Energy required to initiate a reaction, required in both endergonic and exergonic reactions
• Chemical Bonds and Energy Relationships: Energy is required to break chemical bonds.
• Energy is released when chemical bonds form
• Stronger bonds require more energy to break
• More energy is released when strong bonds form.

Functional Groups

• Organic molecules hold carbon
• Their chemistry is largely determined by functional groups
• These are small groups of atoms with specific chemical properties that, when attached to a larger molecule, give those properties to it
• Biological molecules can have many functional groups
• Methyl Functional Group (-CH3)
• Classified as Alkyl
• Non-polar
• Important modification of proteins and cytosine nucleotide
• Hydroxyl Functional Group (-OH)
• Classified as Alcohol
• Polar
• Involved in hydrogen bonding
• Often involved in condensation reactions
• Required on sidechain for phosphorylation of proteins
• Sulfhydryl Functional Group (-SH)
• Classified as Thiols
• Polar
• Can form disulfide bridges to stabilize protein structure

Functional Groups Continued

• Aldehyde Functional Group (-COH)
  • Classified as Aldehydes
  • Polar
  • Reactive
  • Important in energy releasing functions
• Keto Functional Group (OH)
  • Classified as Ketones
  • Polar
  • Important in Carbs and Energy Reactions
• Carboxyl Functional Group (ate = 0)
  • Classified as Carboxylic Acids
  • Charged
  • Acidic
  • Ionizes in Living Tissues To form -COO-(H+)
  • Reacts with amino group to form peptide bond
• Amino Functional Group (H-N-H) 　 - Classified as Amines
  • Charged
  • Basic
  • Accepts H+ in Living Tissues To form -NH3
  • Reacts with Carboxyl group to form peptide bond
• Phosphate Functional Group (8 P in middle)
  • Classified as Organic phosphates
  • Charged
  • Acidic
  • Ionizes in living tissue to form -O-P-O3² (H+)
  • Enters into condensation reactions
  • When bonded to another phosphate, hydrolysis is strongly exergonic

Chapter 3: Macromolecules

• Macromolecules are large molecules formed by covalent linkages of smaller molecules
• Consist of proteins, carbohydrates, nucleic Acids, and lipids.
• Polymers exist outside of lipids
• Polymers: Many units
• created by covalent linkage of smaller molecules (called monomers)
• formed and broken apart in reactions involving H₂O
• Condensation: Removal of water
• creates a covalent bond between monomers.
• Hydrolysis: Addition of water breaks
• covalent bond between monomers.

Lipids

• Hydrocarbons consist of C and H atoms
• Insoluble In H₂O due to nonpolar covalent bonds
• Weak additive Van der Waals interactions hold molecules tightly
• Store energy in C-C and C-H bonds
• Play a structural role in cell membranes as well as thermal insulation
• Triglycerides (Simple Lipids):
  • Solid at room temp as fats
  • Liquid at room temp as oils
• Low polarity and are extremely hydrophobic
• Structure:
  • Three fatty acids: Non-polar hydrocarbon chain attached
  • to polar carboxyl group (COOH)
  • One glycerol: An alcohol with a hydroxyl group (-OH).
• Synthesis involves three condensation reactions.
• Fatty Acids:
  • Chains can vary in length and structure.
  • Amphipathic: They have a hydrophilic end and a hydrophobic tail. -Saturated Fatty Acids: - All bonds between carbon atoms are single, therefore creating a saturated solution with hydrogens. -Unsaturated Fatty Acids: - Hydrocarbon chains have one or more double bonds, causing kinks in the chain and preventing molecules from packing tightly.
• Phospholipids:
  • Two fatty acids and a phosphate compound bound to glycerol.
  • The phosphate has a negative charge making that part of the molecule hydrophilic.
  • Forms a bilayer in aqueous environments.
  • Hydrophobic tails pack together
  • Hydrophilic heads face outward.
  • The component is good for biomembranes.

Carbohydrates

• Roles are as a source of stared energy
• Transports stared energy within the cell (Complex organisms)
• Structural Molecules - give many organisms their shapes
• Recognition or Signaling Molecules - can trigger specific bio responses
• Large group of MoleculesThat have Similar composition, but differ in several Important properties
• Composition: Cn(H₂O)n
• Fires: -Simple Sugars-Small Carbs -Some large polymers of the simple sugars
• Types:
  • Simple Sugars-Carbs with 12 or fewer Carbons
  • Monosaccharides-5 or 6 Carbons, Usually in a ring (Pentose - 5, Hexoses - 6)
  • Disaccharides: 2 monosaccharides Linked 2 glycolic Bond
  • Oligosaccharides: 3 to 10 Monosaccharides Joind by glycolic Bonds
    • Have additional functional groups
    • Bonded to proteins & lipids on cell surfaces, recognition signals
  • Polysaccharides: Large polymers
  • Monosaccharides can be branched
  • Starches - family of polysaccharides of glucose
  • Glycogen- highly Branched polymer of mammal glucose & Main energy storage Molecule in

Carbohydrates Continued

• Polysaccharides
  • Cellulose is the earth's most abundant carbon-containing (AKA Organic) biological compound.
  • Very stable and a good structural material.

Nucleic Acids

• Polymers specialized for strorage, transmission and use of genetic information
• Consist of:
• DNA (deoxyribonucleic acid)
• RNA (ribonucleic acid)
• Monomers of Nucleic Acids are Nucleotides
• Nucleotide
• Pentose(5 Carbon) sugar
• Nitrogen Containing base+phosphate group
• Nucleosides Pentose Sugar
• +N-containing base
• Bases of Nucleic acids
• Primidines- Single rings
• purines-double rings Sugars of Nucleic Acids
• deoxyribose in DNA
• ribose in RNA
• Nucleotide formation
• Occurs in condensation reactions to form phosphodiester linkages
• Hs cabon of one ribose
• Hs cabon of Next Ribose
• Forms chain of alternating sugar 3 phosphate molecules AKA phosphate backbone
• Grow 5 to 3 directions
• Oligonucleotides
• 20 Monomecs of Neccleotides 3 Include small RNA molecules

Nucleic Acids Continued

• Important for DNA replications 3 gene expression
• Polynucleotides longest polymers in living world
• That DNA

DNA Double Strands

• Held together by complementary Base Pairing using H Bonds

• Bases:

• DNA

• Adenine with thymine (A-T)

• 3 form hydrogen

• Cytosine with guanine (G-G)

• Bonds in RNA & DNA strong but not stronger than Covalent

• Base pairs separate with small ammount of energy

• DNA stand characteristics

• Anti-parallel and in opposite directions (s'ends oppiste sides)

• Ladder wists into double helix

• Sugar phophate groups-sides of ladder

• hydrogen bonded bases rungs

• RNA Structure is

• Single Stranded

• Often Folds on itself to form short double stranded regions and its complimentary base pairing

• Structure is dtermined by order of Bares