Introduction to Biology: Characteristics of Life, Cells, Viruses, Functional Groups, and Amino Acids

Characteristics of Living Things

Defining Life

Living organisms share a set of fundamental characteristics that distinguish them from non-living entities. These traits are essential for the maintenance, reproduction, and evolution of life.

• Organization: Living things are highly organized, often at the cellular and molecular level.

• Evolution of populations: Populations of organisms evolve over time through genetic changes.

• DNA: All living things use DNA as their genetic material.

• Reproduction: Organisms reproduce to ensure the continuation of their species.

• Growth and development: Living things grow and develop according to specific instructions coded in their DNA.

• Response to environment: Organisms respond to stimuli in their environment.

• Metabolism: Living things carry out chemical reactions to obtain and use energy.

• Homeostasis: Organisms maintain stable internal conditions.

• Contain one or more cells: The cell is the basic unit of life.

Viruses: Are They Alive?

Why Viruses Are Not Considered Living Organisms

Viruses are unique biological entities that challenge the definition of life. They lack several key characteristics of living organisms.

• Structure: Viruses are complexes of protein and nucleic acids.

• Genome: Viral genomes can be made of DNA or RNA, and may be single- or double-stranded.

• Replication: Viruses replicate by hijacking the host cell's machinery, not by independent reproduction.

• Missing Characteristics: Viruses lack cellular organization, metabolism, homeostasis, growth, and independent reproduction.

Size Comparisons

Viruses are much smaller than cells and organelles, which is important for understanding their biology and detection.

Characteristics Lacking in Viruses

• Organization

• Evolution of populations

• DNA (some viruses have RNA genomes)

• Reproduction (use host machinery)

• Growth/development

• Response to environment

• Metabolism

• Homeostasis

• Contain one or more cells

SARS-CoV-2: A Case Study

SARS-CoV-2 is the virus responsible for COVID-19. It is a highly contagious coronavirus with a single-stranded RNA genome. The virus enters human cells by binding to specific cell surface receptors.

Cell Theory and Diversity

What Is a Cell?

The cell is the smallest unit capable of life and reproduction, either independently or as part of a multicellular organism.

• Cell Theory:

  1. The cell is the unit of structure and function in living things.

  2. The cell retains a dual existence as a distinct entity and as part of a larger organism.

  3. All cells arise from pre-existing cells.

Diversity of Cells

Cells are incredibly diverse in form and function, ranging from plant cells, protist cells, human cells, to bacterial cells.

• Plant Cells: Have cell walls, chloroplasts, and large vacuoles.

• Protist Cells: Highly variable, often single-celled eukaryotes.

• Human Cells: Specialized for various functions (e.g., blood cells, neurons).

• Bacterial Cells: Prokaryotic, lack a nucleus and membrane-bound organelles.

Phylogenetic Organization of Life

Domains and Kingdoms

The classification of living organisms has evolved from Aristotle's Scala Naturae to the modern three-domain system.

• Early Classification: Two kingdoms (plants and animals), later five kingdoms (Monera, Protista, Plantae, Fungi, Animalia).

• Current Classification: Three domains—Bacteria, Archaea, and Eukarya—based on molecular evidence, especially rRNA gene sequences.

Protists

Protists are a diverse group of eukaryotic organisms, which can be unicellular (e.g., dinoflagellates) or multicellular (e.g., algae).

Three Domains of Life

• Bacteria: Prokaryotes

• Archaea: Prokaryotes, many are extremophiles

• Eukarya: Eukaryotes, includes protists, plants, fungi, and animals

rRNA Gene Analysis

rRNA gene sequences are highly conserved and used to establish evolutionary relationships.

• All cells contain rRNA genes.

• rRNA sequences evolve slowly, making them ideal for phylogenetic studies.

• Analysis revealed that Archaea and Eukarya are more closely related to each other than to Bacteria.

Origin of Cells

Abiotic Synthesis and Miller-Urey Experiment

The origin of the first cells involved several key phases:

1. Abiotic synthesis of small organic molecules (e.g., amino acids, nitrogenous bases).

2. Abiotic synthesis of macromolecules (e.g., nucleic acids).

3. Evolution of a self-replicating molecule.

4. Formation of a membrane surrounding the information storage molecule.

The Miller-Urey experiment demonstrated that simple organic compounds could be synthesized from reduced atmospheric gases under conditions simulating early Earth.

Prokaryotes vs. Eukaryotes

Cellular Differences

Prokaryotic cells (Bacteria and Archaea) lack a nucleus and membrane-bound organelles, while eukaryotic cells (Eukarya) have these features.

• Prokaryotes:

  • No nucleus

  • Simple internal structure

  • Average size: 1–5 µm diameter

• Eukaryotes:

  • True nucleus

  • Complex internal structure with organelles

  • Average size: 10–100 µm diameter

Measurement Units

• Micrometer (µm): $1 \mu m = 10^{-6} m$

• Nanometer (nm): $1 nm = 10^{-9} m$

• Angstrom (Å): $1 \text{Å} = 0.1 nm = 10^{-10} m$

Functional Groups in Organic Molecules

Definition and Importance

Functional groups are specific groups of atoms within molecules that confer distinct chemical properties. They are crucial for understanding biomolecular structure and function.

• 'R' group: Represents the rest of the molecule, often a hydrocarbon chain.

• Functional group: A group of atoms that imparts specific chemical characteristics to a molecule.

Common Functional Groups

• Carbonyl: Includes aldehyde (terminal) and ketone (internal) groups.

• Acetyl: A specific carbonyl group important in metabolism.

• Carboxyl/Carboxylic Acid: Has acidic properties, can ionize to form carboxylate.

• Hydroxyl: -OH group, not charged in aqueous solution.

• Amine: Acts as a base, can pick up H+.

• Amide: Polar, uncharged, formed from acid and amine.

• Phosphate: Contributes negative charge, involved in energy transfer.

• Sulfhydryl: -SH group, can form disulfide bonds for protein stability.

Functional Group Properties Table

Functional Group	Structure	Example	Properties
Carbonyl (Aldehyde)	R-CHO	Glucose	Polar, found in sugars
Carbonyl (Ketone)	R-CO-R'	Fructose	Polar, found in sugars
Carboxyl	R-COOH	Acetic acid	Acidic, can ionize
Hydroxyl	R-OH	Ethanol	Polar, not charged in aq
Amine	R-NH2	Glycine	Basic, can pick up H+
Amide	R-CONH2	Peptide bond	Polar, uncharged
Phosphate	R-PO4	ATP	Negative charge, energy transfer
Sulfhydryl	R-SH	Cysteine	Can form disulfide bonds

Amino Acids

General Structure

Amino acids are the building blocks of proteins. Each amino acid has a central carbon (alpha carbon) bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique R group.

• Classification: Amino acids are classified as nonpolar, polar uncharged, acidic (negative), or basic (positive).

• In solution: Amino acids can exist in ionized or non-ionized forms depending on pH.

Classes of Amino Acids Table

Class	Examples
Nonpolar	Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline
Polar, uncharged	Asparagine, Glutamine, Serine, Threonine, Cysteine, Tyrosine
Acidic (Negative)	Aspartate, Glutamate
Basic (Positive)	Arginine, Histidine, Lysine

Example: Glycine

Glycine is both an amine and a carboxylic acid, making it an amino acid. It is the simplest amino acid, with a hydrogen as its R group. Additional info: Amino acids are essential for protein structure and function, and their properties determine protein folding and activity. ----------------------------------------