Biology 1 The chemistry of living things

Properties of biological molecules depend on?

• The types of atoms they contain

• The bonds between atoms

• Their three-dimensional structure

• Their interactions with water and other molecules

most important elements in living organisms are

C H O N P S

Mnemonic:

Carbon

Hydrogen

Oxygen

Nitrogen

Phosphorus

Sulfur

= make up most biological molecules

Difference between atoms and elements

atom is a single, fundamental particle of matter made of protons, neutrons, and electrons.

→ smallest unit of an element that maintains its chemical properties.

consists of:

1 Nucleus

Contains:

• Protons (+ charge)

• Neutrons (no charge)

2 Electron shells

Contain:

• Electrons (- charge)

! number of electrons in the outer shell determines chemical behavior

element is a pure chemical substance that consists entirely of one specific type of atom.

→ not done more information follows!

Why is carbon so important?

basis of organic chemistry

four valence electrons

→ means can form 4 covalent bonds!

Allows carbon: long chains, branches, rings, complex three-dimensional structures, example: carbs, lipids, proteins, nucleic acids

(Almost all biological molecules are carbon-based molecules)

What are chemical bonds?

Atoms join together through chemical bonds.

What are covalent bonds + examples

Covalent bonds form when atoms share electrons. They are strong bonds.

Examples:

• C–C bonds in organic molecules

• Peptide bonds in proteins

• Glycosidic bonds in carbohydrates

• Phosphodiester bonds in DNA

What are ionic bonds?

Ionic bonds form between atoms with opposite charges. They are formed through the transfer of electrons.

Example: Na⁺ + Cl⁻ → NaCl

Ionic interactions occur between charged groups, such as during protein folding and interactions between enzymes and substrates.

What are hydrogen bonds? And common atoms involved? Examples of hydrogen bonds?

Hydrogen bonds are weak attractions between a hydrogen atom attached to an electronegative atom and another electronegative atom.

common atoms:

• Oxygen

• Nitrogen

Examples hydrogen bonds:

• Water molecules

• DNA base pairing

• Protein structure

Why are weak interactions and not only covalent and so on important as well?

Together, thousands of them create stable biological structures

Weak interaction: hydrogen bonds

Between water molecules create: cohesion, surface tension, high boiling point

Hold complementary DNA bases together: adenine - thymine (2 hydrogen bonds), guanine - cytosine (3 hydrogen bonds)

For protein structure: stability for alpha-helices & beta-sheets

Weak bonds: hydrophobic interactions

→ water fearing!

Nonpolar molecules avoid contact with water

Example: fatty acids tails of phospholipids → causes formation of cell membranes, protein folding

Weak bonds: Van der Waals forces

caused by temporary changes in electron distribution

Important for: molecular recognition, protein interactions

Weak bonds: Ionic interactions

Attraction between charged molecules

Important for: protein structure, enzyme-substrate interactions

Water H2O

WATER:

60-70% of human body

Properties due to: polarity (oxygen: slightly negative, hydrogen: slightly positive), hydrogen bonding

→ water a polar molecule

water as solvent: dissolves many substances (these substances are hydrophilic): salt, sugar, amino acdis, substances that not dissolve (hydrophobic): oils, lipids = fats

Cohesion: attraction between water molecules (due to hydrogen bonds)

Adhesion: attraction between water and other surfaces

Temperature: water has high specific heat capacity → requires high energy to change temp. (for remaining body temperature)

Acids

ACIDS:

substance that releases hydrogen ions: H+

Example: HCl → H⁺ + Cl⁻

Base

BASE:

A substance that accepts hydrogen ions or releases hydroxide ions (hydroxide is a negatively charged diatomic ion with the chemical formula OH⁻, consisting of one oxygen atom covalently bonded to one hydrogen atom):

OH⁻

Example:

NaOH → Na⁺ + OH⁻

pH scale

PH SCALE:

Ranges from:

0 → 14

• pH < 7 = acidic

• pH = 7 = neutral

• pH > 7 = basic

Biological importance of pH

Proteins and enzymes require specific pH conditions.

Changes in pH can alter protein shape.

Example:

Stomach enzymes work in acidic conditions.

Buffers

A buffer prevents large changes in pH.

Important biological buffer:

Bicarbonate buffer system

Maintains blood pH around:

7.35–7.45

four major groups of biological macromolecules are

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids

CARBOHYDRATES

Carbohydrates are organic molecules made mainly of:

• Carbon (C)

• Hydrogen (H)

• Oxygen (O)

important for:

• Energy production

• Energy storage

• Structural support

Forms of carbohydrates:

1 Monosaccharides: simplest carbs, can’t be broken down into smaller carbs, examples: glucose (main cellular energy source), fructose (sugar in fruits), galactose (in lactose)

2 Disaccharides: = monosaccharide + monosaccharide, chemical bond: glycosidic bond due to condensation reaction (2 molecules joined, water removed), examples: sucrose (glucose+fructose), lactose (glucose+galactose), maltose (glucose+glucose)

3 Polysaccharide: long chains of monosaccharide, 2 main functions: 1) energy storage → starch (in plants) & glycogen (in animals) liver, skeletal muscle 2) structural support → cellulose (in plants) for strength&rigidity and chitin (in fungal)

LIPIDS

Lipids are a diverse group of molecules that are mostly:

• Carbon

• Hydrogen

• Oxygen

They are generally:

* Nonpolar (molecules where electrons are shared equally between atoms, resulting in a balanced distribution of electrical charge) means they have molecules with the same or similar electronegatvity?)

* Hydrophobic

* Insoluble in water

Functions:

1. energy storage: 1 gram of fat stored twice as much energy as carbs

2. cell membrane: phospholipids

3. Insulation: fat beneath skin for heat loss & organ protection

4. Hormone production: some hormones derived from lipids: steroid hormones: cortisol, estrogen, testosterone

Fatty acids (building blocks of lipids): consist of: carboxyl group (-COOH), hydrocarbon chain → can be:

• saturated fatty acids: no double bonds, straight chains, pack tightly, solid at room temp. (z.B. butter fat)

• unsaturated fatty acids: one or more double bonds, bent structure, less tightly packed, usually liquid at room temp. (z.B. olive oil)

Triglycerides: most common type of fat made of 1 glycerol molecule (sugar alcohol) + 3 fatty acids → of ester bonds & is for long term energy storage

Phospholipids: main components of cell membranes made of glycerol, two fatty acid tails, phosphate group, are amphipatic (have both hydrophilic head + hydrophobic tails)

PROTEINS

most important biological molecule

They are polymers made of amino acids

Functions: enzymes, structural support, transport, movement, defense, signal

All amino acids contain:

• Amino group (-NH₂)

• Carboxyl group (-COOH)

• Hydrogen atom

• Variable side chain (R group)

The R group determines the properties of the amino acid.

amino acids join through peptide bonds formed by condensation reaction (amino acid + amino acid → dipeptide + water)

Many amino acids form polypeptide chains

Protein structure: has 4 levels:

1 primary structure

2 secondary structure

3 Tertiary structure

4 Quaternary structure

Protein Denaturation: loss of normal protein shape (not breaking peptide bonds, just changing shape) caused by: high temperature, extreme pH, chemical changes → protein loses function (example: egg whites solid when cooked)

IMAT PROTEIN FUNCTIONS

Function	Example
Enzyme	Amylase
Transport	Hemoglobin
Defense	Antibodies
Structure	Collagen
Movement	Actin and myosin
Hormone	Insulin

NUCLEIC ACIDS

Nucleic acids store and transmit genetic information

2 types: DNA, RNA

their monomer: Nucleotide → each contains: sugar, phosphate group, nitrogenous base

DNA: Deoxyribonucleic acid (stores genetic information, double helix, 2 antiparallel strands) Sugar (Deoxyribose), Bases (Adenine - Thymine, Cytosine - Guanine)

RNA: Ribonucleic acid, producing proteins, single stranded, Sugar (Ribose), Bases (Adenine - Uracil, Cytosine - Guanine)

Activation energy (Ea)

every chemical reaction requires an initial energy to start (activation energy)

Without enzyme: high activation energy needed, reaction slow

With an enzyme: lower activation energy needed, reaction fast

→ means enzymes lower the activation energy for chemical reactions

ENZYMES

Enzymes are special proteins that act as biological catalysts to speed up chemical reactions

Enzyme have active site (specific pocket where substrate binds) enzyme + substrate create a final product (which got broken down or build up) after that enzyme repeats :)

Example: breaking things down (digestion): Substrate: Lactose (sugar in milk)

Enzyme: Lactase

End product: Glucose & galactose (smaller sugars your body can use for energy)

Enzyme + substrate → enzyme-substrate complex → enzyme + product

Why are enzymes highly specific?

One enzyme usually catalyzes one reaction or one type of substrate

Examples:

Lactase breaks down lactose

Amylase → starch

Lipase → lipids

Pepsin → proteins

Depends on shape & chemical properties of active site

Models of enzyme action

1. Lock-&-Key Model: older model suggests actor site has fixed shape, only correct substrate fits, like key fits lock

   pro: explains specificity con: assumes enzyme is rigid (starr)

2. Induced fit Model: currently accepted model, when substrate approaches, enzyme changes slightly, active site fits substrate closely

   pro: improves binding and catalysis

→ 2nd Model considered more accurate cause enzymes flexible molecules!

Which factors are affecting enzyme activity?

1) Temperature: molecules faster when temp. high, collisions between enzyme & substrate increase → reaction rate increases (optional temp. for most enzymes: 37 Grad Celsius)

2) pH: each enzyme has optimum pH (z.B. Pepsin: 1-2, salivary amylase: 7, Trypsin: 8)

3) Substrate concentration: explanation will follow, once I understood this

4) Enzyme concentration: Increased enzyme con. increases the reaction rate cause more active site available

Enzyme inhibition

reduces or prevents enzyme activity

2 types:

1) competitive inhibition: inhibitor competes with substrate for active site (only one can bind at once!) example: Methotrexate competes with folic acid metabolism

2) non-competitive inhibition: inhibitor binds to different site on enzyme (allosteric site), changes shape of active site → substrate can’t bind anymore

Allosteric Regulation

Molecules binding on a site other then the active site → allosteric site

Increases enzyme activity

Decreases enzyme activity

→ for regulation of cell metabolism

Cofactors & Coenzymes

many enzymes can’t function alone → require helper molecules

Cofactors: inorganic ions (stabilize enzymes or participate in the reactions), example:

• Mg²⁺

• Zn²⁺

• Fe²⁺

• Cu²⁺

Coenzymes: organic helper molecules (many derived from vitamins, carry e- or chemical groups between reactions), example:

• NAD⁺

• FAD

• Coenzyme A

Metabolic pathway

= cell reactions in sequences

product of 1 reaction → substrate for next

Example:

Glucose → Intermediate → Intermediate→ ATP

(each step catalyzed by different enzyme for precise regulation of metabolism)

IMAT HIGH-YIELD SUMMARY TABLE

Concept	Must Know
Enzyme	Biological catalyst
Substrate	Molecule acted upon
Active site	Region where substrate binds
Activation energy	Energy required to start a reaction
Effect of enzyme	Lowers activation energy
Competitive inhibitor	Binds active site
Non-competitive inhibitor	Binds allosteric site
Cofactor	Usually inorganic ion
Coenzyme	Organic molecule, often vitamin-derived
Denaturation	Loss of protein structure and function

Enzyme names

most names end with -ase

What they digest:

Enzyme	Substrate	Product
Amylase	Starch	Maltose
Maltase	Maltose	Glucose
Lactase	Lactose	Glucose + Galactose
Sucrase	Sucrose	Glucose + Fructose
Lipase	Triglycerides	Fatty acids + Glycerol
Pepsin	Proteins	Peptides
Trypsin	Peptides	Smaller peptides
DNA Polymerase	DNA nucleotides	DNA