Biochemistry: Molecules and Cells

Biochemistry Defined

• Biochemistry studies chemical substances in living organisms and their interactions.
• New discoveries are constantly revealing how cells synthesize life's molecules and sustain life through chemical reactions.
• Biochemistry explains the structures, mechanisms, and chemical processes common to all organisms ultimately revealing the wonder of life itself.
• Its principles, referred to as the molecular logic of life, have important applications in medicine, agriculture, nutrition, and industry

The Cell Level

• Unity and diversity in organisms can be observed at a cellular level.
• The smallest organisms are single-celled, microscopic entities.
• Larger organisms are multicellular, with diverse cells varying in size, shape, and function, all sharing fundamental properties at the biochemical level.
• Organic substances make up only about one-fourth of the human body's mass.
• Water constitutes over two-thirds of body mass, while inorganic salts contribute another 4-5%.
• The human body is organized from biomolecular building blocks into complex structures and functional body parts
• The major elemental composition of the human body includes 63% oxygen, 25.2% hydrogen, 9.5% carbon, and 1.4% nitrogen.

Major Biomolecules

• Proteins are large polymers of amino acids, comprising most of a cell (excluding water)
• Amino acids, predominantly L-stereoisomers in nature, have a core structure and play roles in energy metabolism and cellular signaling.
• Some act as enzymes, while others serve as structural components or signal receptors.
• They transport specific substances in/out of cells and are highly versatile, with the total proteins in a cell defined as its proteome.
• Carbohydrates are polymers of simple sugars like glucose, present in sugars, starches, & nucleotides.
• Three major functions include energy-rich fuel storage, cell wall structure (in plants/bacteria), and extracellular recognition elements via oligosaccharides.
• Lipids resemble hydrocarbons with limited water solubility so are essential components of membranes, and are significant energy stores for plants and animals.
• Nucleic acids (DNA and RNA) are nucleotide polymers storing/transmitting genetic information, with some RNA molecules having structural and catalytic roles.

Types of Reactions

• Oxidation and reduction reactions involve the interconversion of alcohols and aldehydes.
• Functional groups are transferred within or between molecules, like phosphate groups.
• Water is added or removed, such as during amide hydrolysis into amine and carboxyl groups.
• Carbon-carbon bonds can be broken.
• Life's complexity arises from these simple reactions occurring in diverse situations.
• Water, for example, is added to carbon-carbon double bonds to break down sugars, lipids, and amino acids.

Cell Types

• The cell is the basic unit capable of growth, metabolism, stimulus response, and replication.
• All cells contain DNA, the total of which is called a genome.
• Genes are individual heredity units coding for functional proteins or RNA.

Prokaryotes Facts

• Prokaryotes evolved as the simplest cells with minimal life-process apparatus.
• Bacteria and cyanobacteria (formerly blue-green algae) are the most similar to these early cells.
• They consist of single cells that can form colonies with cellular function differentiation.
• Prokaryotic cells have only a plasma membrane and lack internal membranes, so they have no nucleus or organelles.
• They do possess a nuclear area with a single circular chromosome.
• Some have a mesosome, an internal membranous structure derived from the cell membrane.
• Cellular respiration occurs on these membranes.
• Cyanobacteria form lamellae, sheet-like structures from cell membrane infoldings, which are sites for photosynthesis but are outside of plastids.
• Additionally, they lack a cytoskeleton so the cell wall maintains their structure.
• Some bacteria use flagella to move. While prokaryotes mainly reproduce asexually, sexual exchanges can happen

Prokaryotic Cells

• Cell wall provides support, shape, and protection against swelling, acting as a porous barrier.
• Cell membrane serves as a selective barrier controlling substance entry and housing energy-generating enzymes.
• DNA is the operating instructions for the cell and replicates during cell division.
• Messenger RNA is transcribed from DNA to synthesize proteins.
• Ribosomes are the sites of protein synthesis, with mRNA binding to specify the protein sequence.
• Storage granules store monomeric units for metabolic fuel.
• The cytosol is the site of intermediary metabolism.
• Flagella propel the cell.

Prokaryotes

• Prokaryotes like bacteria and blue-green algae are the most abundant on Earth.
• Prokaryotic cells lack a membrane-bound nucleus with bacteria shaped as cocci, bacilli, or spirilla.
• Cells are divided into eubacteria and archaebacteria, each having a plasma membrane but no subcellular organelles, only mesosomes.
• The DNA, deoxyribonucleic acid, is condensed in the cytosol in a form known as a nucleoid.
• Some prokaryotes possess flagella while others lack them.
• Cell wall contains peptidoglycan, protecting it from pressure.
• Gram-positive bacteria have a thick cell wall surrounding the plasma membrane.
• Gram-negative bacteria have a thinner cell wall and outer membrane enclosing the periplasmic space.

Eukaryotes

• Eukaryotes are more complex than prokaryotes.
• They can be either single-celled or multicellular organisms characterized by a well-defined nucleus and a membrane.
• Eukaryotes evolved from prokaryotes about 1.5 billion years ago.
• Single-celled eukaryotes examples are yeasts and Paramecium.
• Eukaryotes encompass all multicellular organisms such as plants and animals.
• A key difference between eukaryotic and prokaryotic cells is the presence of organelles, especially the nucleus, in eukaryotes.
• Organelles have distinct functions and are surrounded by their own membranes within the cell, which prokaryotic cells lack.
• Both cell types possess a plasma membrane composed of a lipid bilayer with embedded proteins.

Eukaryotes

• Eukaryotic cells have three major organelles that are the nucleus, mitochondrion, and chloroplast.
• Each separated by double membranes.
• The nucleus contains most of the cell's DNA and is the site of RNA synthesis.
• Mitochondria house enzymes for energy-yielding reactions, while chloroplasts (in green plants and algae) are the sites of photosynthesis.
• Both mitochondria and chloroplasts contain DNA & carry out unique transcription and protein synthesis.

Animal Cell Structures

• Extracellular matrix enables cell recognition, adhesion, communication, and protection.
• Plasma membrane separates cell contents from the environment and regulates material exchange through transport systems/receptors.
• The nucleus contains the main genome, which allows for DNA and RNA synthesis
• Endoplasmic reticulum, rough part, which is studded with ribosomes function as the manufacturing sites for proteins involved in secretions
• Golgi apparatus- a flattened membrane series involves protein secretion and sugar linking for macromolecule packaging/processing.
• Mitochondria uses oxidation to produce ATP for energy, contains its own unique DNA, and uses intermembrane for oxidative phosphorylation.
• Lysosomes contain hydrolytic enzymes, that digest intracellular material entering the cell.
• Peroxisomes contain enzymes that metabolize H2O2, later broken into H2O and O2 via enzyme catalase.
• Cytoskeleton determines cell shape, assisting internal movement.

Plant Cells

• Plant cells have walls for protection against mechanical rupture.
• Cell walls interact to cement cells together, forming a plant.
• Plant cells are able to use membrane channels for cell communication
• The plasma membrane transports essential nutrients/ions.
• Nucleus stores chromosomal organization, DNA replication, transcription, and protein synthesis.
• All similar to processes in animal counterparts.
• Chloroplasts use photosynthesis to convert light into the form of ATP: the primary light source for energy.
• Plant mitochondria are the main generators of energy in photosynthetic cells in the dark and in nonphotosynthetic ones under all conditions.
• Vacuoles are able to perform multiple roles in the transport and storage of both the nutrients and the waste products of the cell.