Cell Structure and Function

Foundations of Biochemistry

• Biochemistry is the chemistry of living matter.
• Key themes include the distinguishing features of living organisms, cell structure and function, the roles of biomolecules, energy transformation, regulation of metabolism and catalysis, DNA coding, and evolution.

Characteristics of Living Matter

• Living matter has complexity, organization, and uses energy to create and maintain structures.
• It involves dynamic, coordinated interactions between individual components.
• It adapts to the environment.
• It self-replicates with enough alterations allowing for evolution.

Complexity and Organization

• Cells contain a nucleus, chromatin, and large secretory vesicles.

Intake and Transformation of Nutrients

• Living organisms must take in and transform nutrients as a source of energy.

Reproduction

• Living organisms must accurately reproduce.

Domains of Life

• Life is divided into three domains: Prokaryotes, Eukarya, and Archaea.
• Six kingdoms classify life by organism, cellular, and molecular differences.
• Archaea and Bacteria consist of unicellular prokaryotes, while Protista consists of unicellular eukaryotes.
• Fungi can be either uni- or multicellular eukaryotes.
• Plantae and Animalia include multicellular eukaryotes.

The Cell

• The cell is the universal building block of life.
• Living organisms are made up of cells.
• The simplest organisms are unicellular.
• Larger organisms have multicellular functions that vary for different purposes.
• Cells share common features but can have distinct components.

Cell Structure

• All cells have cytoplasm, a plasma membrane, and ribosomes.
• Eukaryotic cells have a membrane-bound nucleus and organelles, while bacterial cells have a nucleoid, but no organelles.
• Eukaryotic cells are more complex than prokaryotic ones.
• Segregation of energy-yielding and energy-consuming processes helps to keep the cell at equilibrium.

Bacterial Cell Components

• The cell wall provides mechanical support, and the cell membrane acts as a permeability barrier.
• The DNA carries genetic information.
• Ribosomes are responsible for protein synthesis.
• Pili mediate adhesion and conjugation.
• Flagella provides cell motility.
• Cytoplasm is the site of metabolism.
• Peptidoglycans are glycan strands cross-linked by short peptides.

Eukaryotic Cells' Complexity

• Eukaryotic cells have membrane-bound nuclei.
• Nuclei provide protection for DNA and acts as site for DNA metabolism.
• The nuclear membrane pores allow for selective import and export.
• Membrane-enclosed organelles, such as mitochondria, chloroplasts, and lysosomes, are present.
• Mitochondria are sites for energy production in animals, plants and fungi.
• Chloroplasts are sites for energy in plants.
• Lysosomes digest unneeded molecules.
• Compartmentalization maintains homeostasis and separation from equilibrium.

Unique Animal/Plant Cell Components

• Animal cells contain ribosomes to synthesize proteins, and peroxisomes which oxidize fatty acids.
• The cytoskeleton supports the cell and aids in organelle movement.
• Lysosomes degrade intracellular debris.
• Transport vesicles move lipids and proteins between the endoplasmic reticulum, Golgi apparatus, and plasma membrane.
• The Golgi complex processes, packages, and targets proteins to other organelles or for export.
• The smooth endoplasmic reticulum creates lipids and metabolizes drugs.
• The nucleus houses the genetic information.
• The rough endoplasmic reticulum is the site of protein synthesis.
• Mitochondria oxidize fuels to produce ATP.
• Plant cells contain cell walls, chloroplasts, thylakoids, and glyoxysomes.
• Thylakoids drive ATP synthesis through light.
• Glyoxysomes use enzymes for the glyoxylate cycle.

Cytoplasm / Cytoskeleton

• The viscous cytoplasm is the location of many reactions.
• The cytoskeleton consists of microtubules, actin filaments, and intermediate filaments.
• Cytoskeleton controls cellular shape, division, organization, mobility, and intracellular transport

Basic Chemistry

• Life’s processes are chemical reactions occurring within cells.
• Chemistry is the basis for complexity, energy extraction and use, dynamic interactions, environmental response, and self-replication.

Classification of Organisms

• Organisms are classified by energy source and carbon source.
• Chemolithotrophs/chemoorganotrophs use chemical sources, unlike photolithotrophs/photoorganotrophs, who use light..
• Chemoautotrophs use CO2 as opposed to chemoheterotrophs (organic compounds).
• Photoautotrophs convert H2O to CO2, as opposed to photoheterotrophs who use organic compounds.
• Chemoorganoheterotrophs such animals and fungi break down chemical energy sources.

The Molecular Logic of Life

• Biochemistry explains initiation and acceleration of reactions as well organization and specificity of metabolism, plus storage and transfer of information.

Molecular Hierarchy

• Cells' organization goes from simple chemical units to complex organelles .
• Monomeric units form macromolecules which assemble as supramolecular complexes.
• Examples include nucleotides forming DNA, amino acids forming proteins, and sugars forming cell walls,.

Biochemistry and Carbon

• Carbon's capacity to form stable covalent bonds accounts for life's diversity.
• Carbon binds with H, O, and N for many molecular structures.

Essential Elements

• Six elements including H, O, N, P, and S are common.
• Metal ions play a role in metabolism.

Functional Groups

• Common functional groups in biomolecules include hydroxyl, carbonyl, carboxyl, amino, and phosphoryl groups.

Biological Molecules

• Biological molecules typically have several functional groups.
• The function of molecules depends on stereospecific 3-D structure.
• Stereoisomers are molecules with the same chemical formula and bonding but differ in spatial arrangement.
• Geometric isomers, such as cis and trans isomers, have different physical/ chemical properties based on substituent arrangement around a double bond or ring structure.
• Enantiomers are mirror images with identical physical properties.
• Enantiomers react identically with achiral reagents but differ in reaction with polarized light.
• Diastereomers have different physical and chemical properties.
• Enantiomers are labeled as L and D forms.
• Thalidomide can be prescribed as an immunomodulatory, anti-angiogenic, and anti-inflammatory treatment.
  • The binding of chiral biomolecules is stereospecific.

Biochemical Interactions

• Macromolecules fold into 3D shapes which have distinct binding pockets.
• Specific molecules can bind in these pockets.

Energy and Work

• Organisms maintain a dynamic steady state to remain alive.
• Living organisms must stay away from equilibrium.
• They can transform matter, coupling energy to do work.
• The entropy of the universe drives the need for work and energy to support life.
• Biological catalysts reduce the energy requirements.

Energy Transductions

• Metabolic processes either break down compounds simpler than initial fuel molecules (catabolism) or use simple compounds to form macromolecules (anabolism).
• Reactions are accelerated by raising temperature or concentration, coupling it to faster reactions but also catalysis can be used to lower these requirements.
• Enzymes lower activation energy by catalysis.

Equilibrium

• Equilibrium and free energy change (ΔG°) measure the spontaneity of a reaction.
• For a reaction aA + bB ↔ cC + dD, the equilibrium constant (Keq) indicates the ratio of products to reactants at equilibrium.
• A negative ΔG° indicates a spontaneous reaction, while a positive ΔG° means the reaction requires energy.

Favorable / Unfavorable Reactions

• Synthesis of complex molecules often requires energy (endergonic).
• Metabolites, such as ATP, NADH, and NADPH, can be synthesized using sunlight and fuels.

Energy Coupling

• Chemical coupling of exergonic (energy-releasing) and endergonic (energy-requiring) reactions makes unfavorable reactions happen.
• ATP reacts directly with an initial metabolite as activation energy.

Catalysis

• Catalysts increase reaction rates.
• Catalysts lower the activation energy.
• Enzyme catalysis performs in mild conditions, with high specificity, as well as regulatory ability.

Enzymes

• Enzymes lower the activation energy to increase the reaction rate.

Reaction Series

• A connected series of enzymatically catalyzed reactions forms pathways.
• These pathways can either involve the metabolism function or the signal transduction pathway.
• Metabolic pathways make energy or valuable materials while signal transduction pathways transmit information.
• Pathways are controlled for metabolite level regulation, often through feedback inhibition where products inhibit early steps.

Origins of Life

• Life began on Earth 3.5-3.8 billion years ago.
• A key emergence of self-replicating molecules occurred.
• The RNA World theory posits that RNA could have been the first genetic material.
• Early genetic material may have consisted of short strands undergoing replication/catalysis evolving from RNA/protein components.
• Complementarity in DNA allows for replication with near-perfect fidelity.

Biochemistry Central Dogma

• Genetic information flows from DNA to RNA to protein via translation and complimentary mRNA through transcription.

Natural Selection

• Mutations occur randomly through DNA and RNA.
• Mutated polynucleotides may synthesize into proteins.
• Natural selection propagates mutations which give a species a unique advantage in a given environment.

This quiz covers cell structures, their functions, and differences between cell types. It addresses cell components like ribosomes and cytoskeletal elements. It also touches on the domains of life and characteristics of living matter.