Foundational Concept 2

Foundational Concept 2 nibrown@aamc.org

Content Category 2A: Assemblies of molecules, cells, and groups of cells within multicellular organisms

Content Category 2A: Assemblies of molecules, cells, and groups of cells within multicellular organisms

The processes necessary to maintain life are executed by assemblies of molecules, cells, and groups of cells, all of which are organized into highly-specific structures as determined by the unique properties of their component molecules. The processes necessary to maintain life require that cells create and maintain internal environments within the cytoplasm and within certain organelles that are different from their external environments.  

Cell membranes separate the internal environment of the cell from the external environment. The specialized structure of the membrane, as described in the fluid mosaic model, allows the cell to be selectively permeable and dynamic, with homeostasis maintained by the constant movement of molecules across the membranes through a combination of active and passive processes driven by several forces, including electrochemical gradients.  

Eukaryotic cells also maintain internal membranes that partition the cell into specialized regions. These internal membranes facilitate cellular processes by minimizing conflicting interactions and increasing surface area where chemical reactions can occur. Membrane-bound organelles localize different processes or enzymatic reactions in time and space.  

Through interactions between proteins bound to the membranes of adjacent cells, or between membrane-bound proteins and elements of the extracellular matrix, cells of multicellular organisms organize into tissues, organs, and organ systems. Certain membrane-associated proteins also play key roles in providing identification of tissues or recent events in the cell’s history for purposes of recognition of “self” versus foreign molecules. 

The content in this category covers the composition, structure, and function of cell membranes; the structure and function of the membrane-bound organelles of eukaryotic cells; and the structure and function of the major cytoskeletal elements. It covers the energetics of and mechanisms by which molecules, or groups of molecules, move across cell membranes. It also covers how cell-cell junctions and the extracellular matrix interact to form tissues with specialized functions. Epithelial tissue and connective tissue are covered in this category. 

Topic Biochemistry Biochemistry: A Short Course Biology, 2e Fundamentals of Biochemistry Human Physiology Karp’s Cell and Molecular Biology Organic Chemistry with a Biological Emphasis, Vol. 1
Plasma Membrane (BIO, BC)*
  • General function in cell containment
  • Composition of membranes
    • Lipid components (BIO, BC, OC)
      • Phospholipids (and phosphatids)
      • Steroids
      • Waxes
    • Protein components
    • Fluid mosaic model
  • Membrane dynamics
  • Solute transport across membranes
    • Thermodynamic considerations
    • Osmosis
      • Colligative properties; osmotic pressure (GC)
    • Passive transport
    • Active transport
      • Sodium/potassium pump
  • Membrane channels
  • Membrane potential
  • Membrane receptors
  • Exocytosis and endocytosis
  • Intercellular junctions (BIO)
    • Gap junctions
    • Tight junctions
    • Desmosomes
  • Ch. 12 Lipids and Cell Membranes, pp. 373-398
  • Ch. 13 Membrane Channels and Pumps, pp. 403-431
  • Ch.12 Membrane Structure and Function, pp. 223-239
  • Ch. 9 Lipids and Biological Membranes, pp. 245-292
  • Ch.10 Membrane Transport, pp. 293-321
  • Ch. 3 Cells, pp. 61-64, 91-92
  • Ch. 5 Transport Across the Plasma Membrane
  • Ch. 6 Cell Signaling, pp. 160-161
  • Ch. 4 The Structure and Function of the Plasma Membrane
  • Ch. 7 Interactions Between Cells and Their Environment, pp. 222-253
  • Ch. 8 Cytoplasmic Membrane Systems: Structure, Function, and Membrane Trafficking, pp. 290, 293-300
  • Ch. 1.3A, pp. 35-39
  • Ch. 2.5C, pp. 112-113
Membrane-Bound Organelles and Defining Characteristics of Eukaryotic Cells (BIO)*
  • Defining characteristics of eukaryotic cells: membrane-bound nucleus, presence of organelles, mitotic division
  • Nucleus
    • Compartmentalization, storage of genetic information
    • Nucleolus: location and function
    • Nuclear envelope, nuclear pores
  • Mitochondria
    • Site of ATP production
    • Inner and outer membrane structure (BIO, BC)
    • Self-replication
  • Lysosomes: membrane-bound vesicles containing hydrolytic enzymes
  • Endoplasmic reticulum
    • Rough and smooth components
    • Rough endoplasmic reticulum site of ribosomes
    • Double membrane structure
    • Role in membrane biosynthesis
    • Role in biosynthesis of secreted proteins
  • Golgi apparatus: general structure and role in packaging and secretion
  • Peroxisomes: organelles that collect peroxides
NA
  • Ch. 1 Biochemistry and the Unity of Life, pp. 9-15
  • Ch. 20 The Electron Transport Chain, pp. 400-402
  • Ch. 9 Lipids and Biological Membranes, pp. 245-292
  • Ch.10 Membrane Transport, pp. 293-321
  • Ch. 11 Enzymatic Catalysis, pp. 322-360
  • Ch. 3 Cells, pp. 64-75
  • Ch. 5 Aerobic Respiration and the Mitochondrion, pp. 168-187
  • Ch. 8 Cytoplasmic Membrane Systems: Structure, Function, and Membrane Trafficking, pp. 257-288
  • Ch. 12 Control of Gene Expression, pp. 460-465, 480-483
NA
Cytoskeleton (BIO)
  • General function in cell support and movement
  • Microfilaments: composition and role in cleavage and contractility
  • Microtubules: composition and role in support and transport
  • Intermediate filaments, role in support
  • Composition and function of cilia and flagella
  • Centrioles, microtubule organizing centers
NA NA
  • Ch. 1, Introduction to the Chemistry of Life, pp. 1-22
  • Ch. 3 Cells, pp. 69-71
  • Ch. 9 The Cytoskeleton and Cell Motility
NA
Tissues Formed From Eukaryotic Cells (BIO)
  • Epithelial cells
  • Connective tissue cells
NA NA
  • Ch. 7 Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies: Section 2. Muscle Contraction, pp. 200-201
  • Ch. 3 Cells, pp. 84-92
NA NA
nibrown@aamc.org

Content Category 2B: The structure, growth, physiology, and genetics of prokaryotes and viruses

Content Category 2B: The structure, growth, physiology, and genetics of prokaryotes and viruses

The highly-organized assembly of molecules that is the cell represents the fundamental unit of structure, function, and organization in all living organisms. In the hierarchy of biological organization, the cell is the simplest collection of matter capable of carrying out the processes that distinguish living organisms. As such, cells have the ability to undergo metabolism; maintain homeostasis, including ionic gradients; the capacity to grow; move in response to their local environments; respond to stimuli; reproduce; and adapt to their environment in successive generations.  

Life at cellular levels arises from structural order, and its dynamic modulation. It does so in response to signals, thereby reflecting properties that result from individual and interactive features of molecular assemblies, their compartmentalization, and their interaction with environmental signals at many spatial and temporal scales. 

The content in this category covers the classification, structure, growth, physiology, and genetics of prokaryotes, and the characteristics that distinguish them from eukaryotes. Viruses are also covered here. 

Topic Biology, 2e Fundamentals of Biochemistry Karp’s Cell and Molecular Biology
Cell Theory (BIO)
  • History and development
  • Impact on biology
NA
  • Ch. 1, Introduction to the Chemistry of Life, pp. 1-22
  • Ch. 1 Introduction to the Study of Cell and Molecular Biology, pp. 1-3
Classification and Structure of Prokaryotic Cells (BIO)
  • Prokaryotic domains
    • Archaea
    • Bacteria
  • Major classifications of bacteria by shape
    • Bacilli (rod-shaped)
    • Spirilli (spiral shaped)
    • Cocci (spherical)
  • Lack of nuclear membrane and mitotic apparatus
  • Lack of typical eukaryotic organelles
  • Presence of cell wall in bacteria
  • Flagellar propulsion, mechanism
  • Ch. 1, Introduction to the Chemistry of Life, pp. 1-22
  • Ch. 1 Introduction to the Study of Cell and Molecular Biology, pp. 7-15
Growth and Physiology of Prokaryotic Cells (BIO)
  • Reproduction by fission
  • High degree of genetic adaptability, acquisition of antibiotic resistance
  • Exponential growth
  • Existence of anaerobic and aerobic variants
  • Parasitic and symbiotic
  • Chemotaxis
  • Ch. 22 Mammalian Fuel Metabolism: Integration and Regulation, pp. 773
  • Ch. 1 Introduction to the Study of Cell and Molecular Biology, pp. 7-15
Genetics of Prokaryotic Cells (BIO)
  • Existence of plasmids, extragenomic DNA
  • Transformation: incorporation into bacterial genome of DNA fragments from external medium
  • Conjugation
  • Transposons (also present in eukaryotic cells)
NA
  • Ch. 1, Introduction to the Chemistry of Life, pp. 1-22
  • Ch. 12 Control of Gene Expression, pp. 455-460
Virus Structure (BIO)
  • General structural characteristics (nucleic acid and protein, enveloped and nonenveloped)
  • Lack organelles and nucleus
  • Structural aspects of typical bacteriophage
  • Genomic content: RNA or DNA
  • Size relative to bacteria and eukaryotic cells
NA
  • Ch. 1 Introduction to the Study of Cell and Molecular Biology, pp. 23-25
Viral Life Cycle (BIO)
  • Self-replicating biological units that must reproduce within specific host cell
  • Generalized phage and animal virus life cycles
    • Attachment to host, penetration of cell membrane or cell wall, and entry of viral genetic material
    • Use of host synthetic mechanism to replicate viral components
    • Self-assembly and release of new viral particles
  • Transduction: transfer of genetic material by viruses
  • Retrovirus life cycle: integration into host DNA, reverse transcriptase, HIV
  • Prions and viroids: subviral particles
NA
  • Ch. 13 DNA Replication and Repair, p. 526
nibrown@aamc.org

Content Category 2C: Processes of cell division, differentiation, and specialization

Content Category 2C: Processes of cell division, differentiation, and specialization

The ability of organisms to reproduce their own kind is the characteristic that best distinguishes living things. In sexually reproducing organisms, the continuity of life is based on the processes of cell division and meiosis. 

The process of cell division is an integral part of the cell cycle. The progress of eukaryotic cells through the cell cycle is regulated by a complex molecular control system. Malfunctions in this system can result in unabated cellular division, and ultimately the development of cancer. 

In the embryonic development of multicellular organisms, a fertilized egg gives rise to cells that differentiate into many different types of cells, each with a different structure, corresponding function, and location within the organism. During development, spatial-temporal gradients in the interactions between gene expression and various stimuli result in the structural and functional divergence of cells into specialized structure, organs, and tissues. The interaction of stimuli and genes is also explained by the progression of stem cells to terminal cells. 

The content in this category covers the cell cycle; the causes, genetics, and basic properties of cancer; the processes of meiosis and gametogenesis; and the mechanisms governing cell specialization and differentiation. 

Topic Biochemistry Biochemistry: A Short Course Biology, 2e Fundamentals of Biochemistry Human Physiology Karp’s Cell and Molecular Biology
Mitosis (BIO)
  • Mitotic process: prophase, metaphase, anaphase, telophase, interphase
  • Mitotic structures
    • Centrioles, asters, spindles
    • Chromatids, centromeres, kinetochores
    • Nuclear membrane breakdown and reorganization
    • Mechanisms of chromosome movement
  • Phases of cell cycle: G0, G1, S, G2, M
  • Growth arrest
  • Control of cell cycle
  • Loss of cell-cycle controls in cancer cells
NA NA NA
  • Ch. 3 Cells, pp. 79-83
  • Ch. 14 Cell Division
Biosignalling (BC)
  • Oncogenes, apoptosis
  • Ch. 14 Signal-Transduction Pathways, pp. 455-457
  • Ch. 13 Signal-Transduction Pathways, pp. 245-261
  • Ch. 13 Biochemical Signaling, pp. 402 - 441
  • Ch. 3 Cells, p. 82
  • Ch. 16 Cancer
Reproductive System (BIO)
  • Gametogenesis by meiosis
  • Ovum and sperm
    • Differences in formation
    • Differences in morphology
    • Relative contribution to next generation
  • Reproductive sequence: fertilization, implantation, development, birth
NA NA NA
  • Ch. 23 The Reproductive Systems, pp. 811-816, 823-827
  • Ch. 14 Cell Division, pp. 539-581
Embryogenesis (BIO)
  • Stages of early development (order and general features of each)
    • Fertilization
    • Cleavage
    • Blastula formation
    • Gastrulation
      • First cell movements
      • Formation of primary germ layers (endoderm, mesoderm, ectoderm)
    • Neurulation
  • Major structures arising out of primary germ layers
  • Neural crest
  • Environment-gene interaction in development
NA NA NA
  • Ch. 23 The Reproductive Systems, pp. 840-851
NA
Mechanisms of Development (BIO)
  • Cell specialization
    • Determination
    • Differentiation
    • Tissue types
  • Cell-cell communication in development
  • Cell migration
  • Pluripotency: stem cells
  • Gene regulation in development
  • Programmed cell death
  • Existence of regenerative capacity in various species
  • Senescence and aging
NA NA NA NA
  • Ch. 1 An Introduction to Physiology, pp. 5-6
  • Ch. 23 The Reproductive Systems, p. 839
  • Ch. 7 Interactions Between Cells and Their Environment, pp. 226-234
  • Ch. 15 Cell Signaling and Signal Transduction: Communication Between Cells, pp. 621-625
nibrown@aamc.org