The Cell and Its Aqueous Medium

Biochemistry

• Science concerned with chemical components in living organisms and how they interact

• All living organisms use the same types of biomolecules and use energy.

Movement

(Characteristics of Living Organisms)
All living organisms move

Respiration

(Characteristics of Living Organisms)
Chemical reaction within cells, release energy from food

Sensitivity

(Characteristics of Living Organisms)
Ability to detect environmental changes

Growth

(Characteristics of Living Organisms)

All living things grow

Reproduction

(Characteristics of Living Organisms)
Passing genetic information to offspring

Excretion

(Characteristics of Living Organisms)

Getting rid of waste

Nutrition

(Characteristics of Living Organisms)

Intake and use of nutrients

C, O, H, N

Composes 96% of living matter

Ca, P, K, S, Na, Cl, Mg

Composes 4% of living matter

Trace elements

Required in very small amounts

Organic Chemistry

Study of carbon-containing compounds, such as the cellular apparatus of living organisms

Jöns Jacob Berzelius

• Coined the term “Organic Chemistry”

• Believed in vitalism, the idea that organic compounds required "vital force"

vitalism

The idea that organic compounds required "vital force"

Friedrich Wöhler

Synthesized an organic compound from two inorganic compounds

Big Bang Theory

• All matter was originally in a small space

• An explosion occurred, causing rapid expansion and a temperature of ~15 x 109 K

• Average temperature of the universe has been decreasing since its beginning

H, He, and Li

Early elements in the big bang theory

Proteinoids

________ may have aggregated into microspheres

Double-Origin Theory

A coding system and development of catalysis may have occurred independently

C, O, N, H

Most abundant elements in organisms

H, O, N, C

Most abundant elements in the universe

Light from the sun

What is the ultimate source of energy

Spontaneous

If free energy decreases, reaction is ________

not occur (unless energy is provided externally)

If free energy increases, reaction will ______

The system is in a state of equilibrium

If free energy does not change, ________

Cell membrane

• Phospholipid bilayer & carbohydrates

• Selective entry & exit of substances

Nucleus

• Genomic DNA, histone proteins (chromatin); RNA

• Storage of genetic material & DNA replication + transcription

Endoplasmic Reticulum w/ Ribosomes

• Vesicles: Lipids & proteins; Ribosomes: RNA & proteins

• Protein synthesis

Golgi apparatus

• Lipids, proteins, & polysaccharides

• Secretion of waste; protein processing

Mitochondria

• Membrane: Proteins & lipids; Matrix: Enzymes, RNA, & DNA

• Energy metabolism & ATP synthesis

Peroxisomes/ glyoxysomes

• Catalase & other oxidative enzymes

• Oxidative metabolism

Chloroplasts

• Proteins, lipids, chlorophyll, RNA, DNA, & ribosomes

• Photosynthesis

Cytoplasm

• Cytoskeleton

• Single-celled Proteins, small molecules, soluble proteins, enzymes, nutrients, & salts in aqueous solutions

• Provides shape; where metabolic reactions occur

Prokaryotes

• Single-celled

• “Before the nucleus”

• Bacteria & Cyanobacteria

Eukaryotes

• Uni- or multi-cellular

• “True nucleus”

• Paramecium, animals, plants

1. Phosphoric acid + hydroxyl group —> Ester

2. 2 Phosphoric acids —> Anhydride

3. 2 Anhydride linkages + 1 Ester —> ATP

Steps of ATP Formation

Monomers

Living cells include polymers derived from ______

Monomer: Amino Acids

Linkages: Peptide Bonds

Monomer and Linkages of Proteins?

Monomer: Simple Sugars (Monosaccharides)

Linkages: Glycosidic bonds

Monomer and Linkages of Carbohydrates/Polysaccharides?

Monomer: Nucleotides

Linkages: Phosphodiester bonds

Monomer and Linkages of Nucleic Acids?

Monomer: Glycerol and fatty acids

Linkages: Ester Bonds

Monomer and Linkages of Proteins?

True

T/F

Water is a polar solvent

True

T/F

Water can be an H donor and an H acceptor

Polar

______ molecules dissolve easily in water

Nonpolar

______ substances disrupt water-water interactions but cannot establish interactions with water as solutes

Hydrogen bonds

What bonds give water its unusual properties?

104.5^o (Distorted tetrahedron)

The O-H bond angle is _______

O

In water, what is more electronegative? O or H?

False, nonpolar

T/F

Poor solvents are polar

It weakens electrostatic interactions between them and counteracts the lattice network

How does water dissolve salts by hydrating and stabilizing Na⁺ and Cl^- ?

Lattice

Ice has a lower density than water due to the ______ arrangement of molecules

decreases

Gases —> liquid phase (increases/decreases) enthalphy

decreases

Dissolving hydrophobic compounds in water (decreases/increases) entropy

False, poorly soluble

Electrons share equally / opposing dipoles cancel out

T/F

Nonpolar gases are greatly soluble in water. Why?

True

T/F

Water is a good solvent for amino acids, peptides, small alcohols, and carbohydrates.

Micelles

A spherical aggregation of organic molecules in an aqueous solution where the hydrophobic parts are buried inside the sphere, and hydrophilic parts are on the surface.

How close the atom will allow another to approach

Van der Waals radius measures?

1. Attraction forces (London dispersion)

2. Repulsive forces (Steric Repulsion)

2 components of Van der Waals

1. Hydrogen Bonds

2. Ionic Interactions

3. Hydrophobic Interactions

4. Van der Waals forces

What are weak interactions? (4)

Hydrophobic

Binding sites are often (hydrophobic/hydrophilic)

Hypertonic

• When cell shrinks

• Movement of water is outward

Hypotonic

• When cell swells

• Movement of water is inward

Isotonic

• When environment outside and inside of cell is in equilibrium

Unionized

Most water molecules are (ionized/unionized)

High

Cytoplasm has (high/low) protein concentrations

1. Hydrochloric acid (HCl)

2. Sulfuric acid (H₂SO₄)

3. Nitric acid (HNO₃)

Example of acids (3)

1. Sodium hydroxide (NaOH)

2. Potassium hydroxide (KOH)

Examples of bases (2)

proton donors

Acids are proton (donors/acceptors)

proton acceptors

Bases are proton (donors/acceptors)

lower pKa

Stronger tendency for proton dissociation —> stronger acid —> (higher/lower) pKa