Unit 1 Biology - Chemistry of Life

Matter

anything that takes up space and has mass

Element

a substance that cannot be broken down into other substances by chemical reactions

Essential elements and trace elements

• Essential elements - elements that are essential to survive and reproduce

• Trace elements - essential elements that are needed in small amounts

  • Iron - transports oxygen as a component of hemoglobin

  • Zinc - immune health

  • Iodine - hormone production

  • Fluoride - teeth

Compound

Two or more elements combined in a fixed ratio

Which elements make up 96% of living matter?

CHONP

Atoms

• Smallest unit of an element that still retains the property of that element.

• Made up of neurons, protons, and electrons

Protons

positively charged particles found in the nucleus of the atom

Neutrons

particles with no charge found in the nucleus of the atom

Isotopes

Isotopes - forms of an element with differing numbers of neutrons

What are isotopes used for

• Radioactive isotopes are widely used in medicine for both diagnosis and treatment

• Radiometric data uses the rate of decay or half-life to determine the ages of fossils and rock strata

Atomic number

Number of protons

Atomic mass

Number of neutrons and proteins averaged over all isotopes

Periodic table

• Elements in the same horizontal row have the same total number of electron shells

• Elements in the same vertical column have the same number of valence electrons (# of electrons in the outermost shell)

Elements want to be stable

• Achieve this by forming chemical bonds with other elementS

Octet Rule

• Octet rule - elements will gain, lose, or share electrons to fill their valence shell and become stable

Valence shell

Valence shell - outermost layer of electrons in an atom

Electronegativity

• Electronegativity - an atoms ability to attack electrons to itself

  • Electronegativity increases horizontally in periodic table

  • Electronegativity decreases vertically in periodic table

Chemical bonds

• Chemical bonds - interactions between the valence electrons of different atoms. Atoms are helped together by chemical bonds to form molecules

Kinds of chemical bonds

• 4 kinds

  • Covalent bonds

  • Ionic bonds

  • Hydrogen bonds

  • Van der Waals interactions

Covalent bonds

• Covalent bonds - when valence electrons are shared by two atoms

• Polar covalent bonds - when valence electrons are shared unevenly (leads to different charges)

• Nonpolar covalent bonds - when valence electrons are shared evenly

Ionic bonds

• Ionic bonds - bonds resulting from the attraction between two oppositely charged atoms (ions)

• Usually between a nonmetal and metal (metal transfers electrons to nonmetal)

• Forms ionic compounds and salt (ex: table salt is formed by ionic bonds between cation sodium and anion chlorine)

• Occurs when there is a transfer of electrons from one atom to another forming ions

  • Cation - positively charged ion

  • Anion - negatively charged ion

Van Der Waals interactions

Very weak connections that are the result of asymmetrical distributions of electrons within a molecule. Contribute to the 3D shape of molecules

Hydrogen bonds

• Hydrogen bonds - weak chemical reactions that form between the partial positive charge of the hydrogen and a strongly electronegative atom of another (oxygen or nitrogen)

  • 4 bonds can be formed in a water molecule (2 with oxygen, 1 with each hydrogen)

  • Is intermolecular - between molecules

  • Play a big role in 3D shape of proteins and nucleic acids

Chemical reaction

• Chemical reaction - shows the reactants with an arrow to indicate their conversion into the products

  • Shows the number of molecules involved (coefficient)

  • Number of molecules same on each side

  • Some chemical reactions are reversible

Structure of water

1 oxygen with 2 hydrogens

Properties of water

1. Polarity

2. Cohesion

3. Adhesion

4. Transpiration

5. High specific heat

6. High heat of vaporization

7. Ice being less dense

8. Universal solvent

Polarity

• Oxygen has a negative charge and hydrogen has a positive charge.

• Formed by polar covalent charges

Cohesion

• Cohesion - linkage of like molecules

  • Allows for the transportation of water and nutrients against gravity in plants

  • Leads to surface tension - surface H2O molecules have a greater inward pull because there are no water molecules to balance the forces

Adhesion

• Adhesion - clinging of one substance to another

• Due to polarity of H2O

• In plants allows water to cling to the cell walls to resists gravity

Capillary action

• Capillary action - he upward movement of water due to combined forces of cohesion, adhesion, and surface tension

  • Happens when adhesion is greater than cohesion

  • Cohesion causes water to stick to each other, adhesion causes water to stick to xylem wall

Transpiration

Process by which water vapor is released from the aerial parts of plants, primarily through small openings called stomata on the leaves

High specific heat

• High specific heat - amount of heat required to raise or lower the temperature of the substance by 1

  • Water resists change in temperature because of hydrogen bonds

  • Because of hydrogen bonds - heat must be absorbed to break hydrogen bonds but heat is released when they form

• Importance

  • Moderates air temperature - large bodies of water can absorb heat during the day and release heat at night

  • Stabilizes ocean temperature - benefits marine life

  • Allows organisms to resist changes in their own internal temperature

High heat of vaporization

• High heat of vaporization - water requires a large amount of energy to evaporate due to hydrogen bonds

• Evaporative cooling - as water molecules evaporate, the surface they evaporate from become cool

• Importance of evaporative cooling

  • Moderates earth’s climate

  • Stabilizes temperature in lake and pods

  • Prevents terrestrial organisms from overheating (humans sweat)

  • Prevents leaves from becoming too warm under the sun

Water is less dense as ice than it is a liquid

• Usually the other way for other molecules

• Due to hydrogen bonds - cause water molecules to form a crystalline structure

• Importance

  • Keeps larger bodies of water from freezing solid, allowing life to exist in ponds, lakes, and oceans

Universal solvent

• Universal solvent - its polar molecules are attracted to ions and other molecules it can form hydrogen bonds with

  • Will form hydrogen bonds with the solute to dissolve it

• Solution - homogeneous mix of 2 or more substances

• Solvent - dissolving agent of a solution

• Solute - substance being dissolved

• Hydrophilic - water soluble. Includes ionic compounds, polar molecules, and some proteins

  • Ionic compounds - partially negative oxygen will interact with a positive atom while the partially positive hydrogen will interact with a negative atom

• Hydrophobic - nonpolar and do not dissolve in water. Oil is an example

pH

• pH - runs between 0 and 14 and measures the relative acidity and alkalinity of aqueous solutions

  • Under 7 is acidic

  • Above 7 is basic

  • At 7 is neutral

Acids and bases

• Acids - releases H and receives OH

• Basic - releases OH and receives H

Buffers

• Buffers - substances that resist changes in pH when acids or bases are added

  • Accepts H from a solution when there is an excess of hydrogen molecules

  • Donates H when there is a lack hydrogen molecules

• Carbonic acid - important buffer in living systems. Moderates pH temperature in blood and the ocean

Major elements of life

• Major elements of life - CHONPS

  • Nitrogen important for building proteins and nucleic acids

  • Phosphorus important for building nucleic acids and some lipids

  • Sulfur is used in building proteins

Organic compounds

Contains carbon and hydrogen

Carbon is unparalleled in its ability to form molecules that are large, complex, and diverse because…

• Has 4 valence electrons which means it can form…

• Up to 4 covalent bonds

• These bonds can be single, double, or triple

• Can form large molecules (macromolecules)

• Molecules can be chains, ring-shaped, or branched

Isomers

• Same molecular formula but different in their arrangements of atoms.

• Results in molecules that are different in their biological activities

What do properties of an organic molecule depends on?

• Arrangement of carbon skeleton and the functional groups attached to it

Variations in carbon skeleton leads to…

• Molecular diversity

  • 4 macromolecules

Functional groups

• Functional groups - chemical groups attached to the carbon skeleton that participate in chemical reactions

  • Hydroxyl - OH

  • Carboxyl - COOH

  • Carbonyl > CO

  • Amino - NH2

  • Phosphate - PO3

  • Sulfhydryl - SH

  • Methyl - CH3

Polymers

chain like macromolecules made out of monomers

Monomers

repeating subunits that make up polymers

Dehydration reactions

• Dehydration reactions - creates polymers from monomers. Two monomers joined by the removal of water

  • H is taken out of one monomer and OH is taken out of the other to form water and bond the monomers

Hydrolysis

• Hydrolysis - breaks apart monomers by adding water

  • H of H2O bonds to one minor and the remaining OH attaches to the other

  • Reverse of dehydration

Polymerization

connection of many polymers

Carbohydrates

• Carbs - simple sugars and polymers of sugars such as starch and cellulose

  • All have a ratio of CH2O

  • CHO

  • Has a carbonyl group and many hydroxyl groups

Monosacarrides

• Monosacarrides - simple sugars

  • Monomers of carbs

  • Multiples of CH2O

  • Most common is glucose

    • Nutrients and fuel for cells

    • Used in cellular respiration

• Can serve as building blocks for amino acids or as monomers for di and polysaccharides

Disaccharides

• Disaccharides - 2 monosaccharides joined by covalent bonds

• Most common is sucrose

  • Monomers are fructose and glucose

Polysaccharides

• Polysaccharides - polymers with many monosaccharides joined by covalent bonds

• Ex: starch, glycogen, and cellulose

Functions of polysaccharides

Energy storage and structural support

Energy storage polysaccharides

• Starch - found in plants

• Glycogen - found in animals

Structural support polysaccharides

• Cellulose - major component of plant cell wall

• Chitin - found in the exoskeletons of arthropods

How are starch and cellulose different?

• Both starch and cellulose are made out of glucose molecules, but the different ring forms and linkages between them result in different functions

• Starch has OH on the top right (beta) while cellulose has it on the bottom right (alpha) which makes starch spread out and branched and cellulose linear and compact

  • If you change the structure you change the function because they’re consistent with each other

Lipids are all?

Hydrophobic

Polymers of lipids

• Don’t have true ponomers because they’re made from a variety of components (not made out of similar monomers)

• “Polymers”

  • Fats

  • Phospholipids

  • Cholesterol

  • Steroids

Monomers of lipids

• Glycerol

• Fatty acids

Fats

• Fats (triglycerides) - made out of a glycerol molecule and 3 fatty acids which are bonded by ester linkage (bonds between hydroxyl -OH and carboxyl - COOH)

• Have hydrocarbon (compounds made out of hydrogen and oxygen) chains of variable lengths which are nonpolar and therefore hydrophobic

Functions of fat

• Provide energy storage - fats store twice as more energy than carbohydrates

• Support cell function

• Provide insulation to keep mammal warm - in mammals fat is stored in adipose cells

Glycerol

Classified as an alcohol (hydroxyl groups)

Fatty acids

long carbon chins (carboxyl at one end)

Saturated fatty acids

• No double C bonds so no kinks

• Solidifies at room temperature

• Linked to cardiovascular tissue (causes blockages in blood)

• Commonly produced by animals

• Ex: butter and lard

Unsaturated fatty acids

Have double C bonds so kinks

Liquid at room temperature

Commonly produced by plants

Ex: corn oil and olive oil

Functions of lipids

• Energy storage - fats store twice as more energy than carbohydrates

• Protection of vital organs and insulation - in mammals fat is stored in adipose cells

Phospholipids

• Phospholipids - major component of cell membranes

  • Hydrophilic head that has a phosphate group and glycerol

  • Two fatty acids tails that are hydrophobic

• Arranged in a bilayer in forming the cell membrane with the hydrophilic heads pointing towards watery cytosol or extracellular environments and hydrophobic tails sandwiched between

Steroids

• Steroids - hormones that support physiological functions like growth and development, energy metabolism, and homeostasis

  • Has 4 rings that are fused together

    • Unique groups attached to the ring determine what type of steroid it is

• Examples

  • Cholesterol - common component of animal cell membranes which provides structural stability

  • Estrogen and testosterone are hormone steroids

Formation of a protein

1. Amino acid

2. Peptide

3. Polypeptide

4. Protein

Proteins

Molecule consisting of polypeptides (polymers of amino acids) folded into a 3D shape

Relationship of shape and function in proteins

Shape (structure) determines function

Amino acids

• Amino acids - molecules that have a central carbon bonded to a carboxyl (COOH) group on one end, an amino group at the other (NH2), a hydrogen atom, and an R group (variable side chain)

  • 20 types of amino acids

R groups

• Each amino acid has a unique side chain (R group)

• Unique aspects of the amino acids are based on the side chains physical and chemical properties

• Side chains can be grouped as

  • Nonpolar (hydrophobic)

  • Polar (hydrophilic

  • Polar/nonpolar

• Side chains interact which determines the shape and function of the protein

Peptide bonds

• Peptide bonds - link amino acids. Formed by dehydration synthesis between amino and carboxyl group of adjacent monomers

• Carboxyl and amino group must be positioned next to each other to form a bond

Polypeptide

• Many amino acids linked by peptide bonds

• Each polypeptide has a unique sequence of amino acids and directionality

• When a polypeptide twists and folds because of R groups it becomes a protein

Directionality in polypeptides

• Each end is chemically unique because of functional groups

• One end is a free amino group (N-terminus)

• One end is a free carboxyl group (C-terminus)

• Sequence of amino acids determine 3D shape

4 levels of protein structure

• Primary - unique sequence in which amino acids are joined. Dictates 2nd and 3rd forms.

• Secondary - refers to one of 2 3D shapes that are the result of hydrogen bonding between members of the polypeptide backbone

• Alpha helix - coiled shape like a slinky

• Beta pleated sheet - accordion shape

• Tertiary - 3D folding due to interactions between R groups. Reinforced by hydrophobic interactions, Van der Waals interactions, hydrogen bonds, and disulfide bridges (covalent bond between sulfur atoms of two cysteine monomers)

  • R groups determine the shape of protein

• Quaternary - association of 2 or more polypeptide chains into one large protein

  • Ex: hemoglobin

Why is protein shape is crucial to protein function

• When a protein does not fold properly its function is changed

• Can result in amino acid substitution which causes diseases

Denaturing

when a protein loses its shape and function due to changes in pH, heat, or other disturbances

Formation of nucleic acids

1. Nucleotides

2. Polynucleotides

3. Nucleic acids

Nucleic acids

polymers made of nucleotide monomers

Function of nucleic acids

Store, transmit, and express genetic information

Directionality of polynucleotides

5’ to 3’

How are polynucleotides formed?

• Polynucleotides - phosphate groups link adjacent nucleotides

• Phosphodiester linkage

Nucleotides are composed of

• Nitrogenous base

• 5 carbon sugar

• Phosphate group

Two types of nitrogenous bases

• Purine - 1 ring with 6 atoms bonded to another with 6 atoms

  • Adenine

  • Guanine

• Pyrimidine - 1 ring with 6 atoms

  • Cytosine

  • Thymine

  • Uracil

Phosphate groups in nucleic acids

• Phosphate group is added to the 5 carbon sugar to form a nucleotide

• Nucleoside - nucleotide without a phosphate group

Two forms of nucleic acids

• RNA

  • 1 polynucleotide

  • Varies in shape

  • A,U, G, C

• DNA - molecule of heredity

  • 2 polynucleotides

  • Double helix

  • Strands are antiparallel - parallel but run in opposite directions

  • Held together by hydrogen bonds

  • C, G, A, T

What does the unique sequence of bases along DNA or mRNA do?

Dictates amino acid sequence so then dictates primary structure of protein and then tertiary structure of protein

Functions of proteins

• Antibodies - help protect the body from disease

• Enzyme - carry out chemical reactions or assist in creating new molecules

• Messenger - transmit signals (hormones)

• Structural - provide structure and support

• Transport/storage - bind to and carry small atoms and molecules throughout the body