Biological and Biochemical Foundations of Living Systems

What Will the Biological and Biochemical Foundations of Living Systems Section Test?
The Biological and Biochemical Foundations of Living Systems section asks you to solve problems by
combining your knowledge of biological and biochemical concepts with your scientific inquiry and
reasoning skills. This section tests processes that are unique to living organisms, such as growing and
reproducing, maintaining a constant internal environment, acquiring materials and energy, sensing and
responding to environmental changes, and adapting. It also tests how cells and organ systems within an
organism act independently and in concert to accomplish these processes, and it asks you to reason
about these processes at various levels of biological organization within a living system.

This section is designed to:

▪ Test introductory-level biology, organic chemistry, and inorganic chemistry concepts.

▪ Test biochemistry concepts at the level taught in many colleges and universities in first-semester
biochemistry courses.
▪ Test cellular and molecular biology topics at the level taught in many colleges and universities in
introductory biology sequences and first-semester biochemistry courses.
▪ Test basic research methods and statistics concepts described by many baccalaureate faculty as
important to success in introductory science courses.
▪ Require you to demonstrate your scientific inquiry and reasoning, research methods, and
statistics skills as applied to the natural sciences.

Test Section Number of Questions Time

Biological and Biochemical 59 95 minutes

Foundations of Living Systems
(note that questions are a
combination of passage-based
and discrete questions)

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 Scientific Inquiry and Reasoning Skills
As a reminder, the scientific inquiry and reasoning skills you will be asked to demonstrate on this section
of the exam are:

Knowledge of Scientific Concepts and Principles

▪ Demonstrating understanding of scientific concepts and principles.

▪ Identifying the relationships between closely related concepts.

Scientific Reasoning and Problem-Solving

▪ Reasoning about scientific principles, theories, and models.

▪ Analyzing and evaluating scientific explanations and predictions.

Reasoning About the Design and Execution of Research

▪ Demonstrating understanding of important components of scientific research.

▪ Reasoning about ethical issues in research.

Data-Based and Statistical Reasoning

▪ Interpreting patterns in data presented in tables, figures, and graphs.

▪ Reasoning about data and drawing conclusions from them.

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 General Mathematical Concepts and Techniques
It’s important for you to know that questions on the natural, behavioral, and social sciences sections will ask
you to use certain mathematical concepts and techniques. As the descriptions of the scientific inquiry and
reasoning skills suggest, some questions will ask you to analyze and manipulate scientific data to show you
can:

▪ Recognize and interpret linear, semilog, and log-log scales and calculate slopes from data found in
figures, graphs, and tables.
▪ Demonstrate a general understanding of significant digits and the use of reasonable numerical
estimates in performing measurements and calculations.
▪ Use metric units, including converting units within the metric system and between metric and English
units (conversion factors will be provided when needed), and dimensional analysis (using units to
balance equations).
▪ Perform arithmetic calculations involving the following: probability, proportion, ratio, percentage, and
square-root estimations.
▪ Demonstrate a general understanding (Algebra II-level) of exponentials and logarithms (natural and
base 10), scientific notation, and solving simultaneous equations.
▪ Demonstrate a general understanding of the following trigonometric concepts: definitions of basic
(sine, cosine, tangent) and inverse (sin‒1, cos‒1, tan‒1) functions; sin and cos values of 0°, 90°, and
180°; relationships between the lengths of sides of right triangles containing angles of 30°, 45°, and
60°.
▪ Demonstrate a general understanding of vector addition and subtraction and the right-hand rule
(knowledge of dot and cross products is not required).

Note also that an understanding of calculus is not required, and a periodic table will be provided during the
exam.

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 Resource
You will have access to the periodic table shown while answering questions in this section of the exam.

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 Biological and Biochemical Foundations of Living Systems Distribution of Questions by
Discipline, Foundational Concept, and Scientific Inquiry and Reasoning Skill
You may wonder how much biochemistry you’ll see on this section of the MCAT exam, how many
questions you’ll get about a particular foundational concept, or how the scientific inquiry and reasoning
skills will be distributed on your exam. The questions you see are likely to be distributed in the ways
described below. These are the approximate percentages of questions you’ll see for each discipline,
foundational concept, and scientific inquiry and reasoning skill. (These percentages have been
approximated to the nearest 5% and will vary from one test to another for a variety of reasons,
including, but not limited to, controlling for question difficulty, using groups of questions that depend on
a single passage, and using unscored field-test questions on each test form.)

Discipline:

▪ First-semester biochemistry, 25%

▪ Introductory biology, 65%
▪ General chemistry, 5%
▪ Organic chemistry, 5%

Foundational Concept:

▪ Foundational Concept 1, 55%

▪ Foundational Concept 2, 20%
▪ Foundational Concept 3, 25%

Scientific Inquiry and Reasoning Skill:

▪ Skill 1, 35%
▪ Skill 2, 45%
▪ Skill 3, 10%
▪ Skill 4, 10%

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 Biological and Biochemical Foundations of Living Systems Framework of Foundational
Concepts and Content Categories
Foundational Concept 1: Biomolecules have unique properties that determine how they contribute to
the structure and function of cells and how they participate in the processes necessary to maintain life.

The content categories for this foundational concept include:

1A. Structure and function of proteins and their constituent amino acids.

1B. Transmission of genetic information from the gene to the protein.

1C. Transmission of heritable information from generation to generation and the processes that
increase genetic diversity.

1D. Principles of bioenergetics and fuel molecule metabolism.

Foundational Concept 2: Highly organized assemblies of molecules, cells, and organs interact to carry
out the functions of living organisms.

The content categories for this foundational concept include:

2A. Assemblies of molecules, cells, and groups of cells within single cellular and multicellular organisms.

2B. The structure, growth, physiology, and genetics of prokaryotes and viruses.

2C. Processes of cell division, differentiation, and specialization.

Foundational Concept 3: Complex systems of tissues and organs sense the internal and external
environments of multicellular organisms, and through integrated functioning, maintain a stable internal
environment within an ever-changing external environment.

The content categories for this foundational concept include:

3A. Structure and functions of the nervous and endocrine systems and ways these systems coordinate
the organ systems.

3B. Structure and integrative functions of the main organ systems.

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 How Foundational Concepts and Content Categories Fit Together
The MCAT exam asks you to solve problems by combining your knowledge of concepts with your
scientific inquiry and reasoning skills. The figure below illustrates how foundational concepts, content
categories, and scientific inquiry and reasoning skills intersect when test questions are written.

Foundational Concept 1 Foundational Concept 2

Content Content Content Content Content Content

Category 1A Category 1B Category 1C Category 2A Category 2B Category 2C
Skill
Skill 1
▪ Each cell represents the point at which foundational
Skill 2 concepts, content categories, and scientific inquiry and
reasoning skills cross.
Skill 3 ▪ Test questions are written at the intersections of the
Skill 4 knowledge and skills.

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 Understanding the Foundational Concepts and Content Categories in the Biological and
Biochemical Foundations of Living Systems Section
The following are detailed explanations of each foundational concept and related content categories
tested in the Biological and Biochemical Foundations of Living Systems section. To help you prepare for
the MCAT exam, we provide content lists that describe specific topics and subtopics that define each
content category for this section. The same content lists are provided to the writers who develop the
content of the exam. Here is an excerpt from the content list.

EXCERPT FROM BIOLOGICAL AND BIOCHEMICAL FOUNDATONS OF LIVING SYSTEMS OUTLINE

Metabolism of Fatty Acids and Proteins (BIO, BC) Topic

▪ Description of fatty acids (BC) Subtopic

▪ Digestion, mobilization, and transport of fats
▪ Oxidation of fatty acids
o Saturated fats
o Unsaturated fats
▪ Ketone bodies (BC)
▪ Anabolism of fats (BIO)
▪ Nontemplate synthesis: biosynthesis of lipids and polysaccharides (BIO)
▪ Metabolism of proteins (BIO)

The abbreviations in parentheses indicate the courses in which undergraduate students at many
colleges and universities learn about the topics and associated subtopics. The course abbreviations are:

▪ BC: first-semester biochemistry

▪ BIO: two-semester sequence of introductory biology
▪ GC: two-semester sequence of general chemistry
▪ OC: two-semester sequence of organic chemistry

In preparing for the MCAT exam, you will be responsible for learning the topics and associated subtopics
at the levels taught at many colleges and universities in the courses listed in parentheses. A small
number of subtopics have course abbreviations indicated in parentheses. In those cases, you are
responsible only for learning the subtopics as they are taught in the course(s) indicated.

Using the excerpt above as an example:

▪ You are responsible for learning about the topic Metabolism of Fatty Acids and Proteins at the
level taught in a typical two-semester introductory biology sequence and in a typical first-
semester biochemistry course.

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 ▪ You are responsible for learning about the subtopics Anabolism of fats, Nontemplate synthesis:
biosynthesis of lipids and polysaccharides, and Metabolism of proteins only at the levels taught
in a typical two-semester sequence of introductory biology.
▪ You are responsible for learning about the subtopics Description of fatty acids and Ketone
bodies only at the levels taught in a typical first-semester biochemistry course.

Remember that course content at your school may differ from course content at other colleges and
universities. The topics and subtopics described in this and the next two chapters may be covered in
courses with titles that are different from those listed here. Your prehealth advisor and faculty are
important resources for your questions about course content.

Please Note
Topics that appear on multiple content lists will be treated differently. Questions will focus on the
topics as they are described in the narrative for the content category.

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 Biological and Biochemical Foundations of Living Systems

Foundational Concept 1

Biomolecules have unique properties that determine how they contribute to the structure and function of
cells and how they participate in the processes necessary to maintain life.

The unique chemical and structural properties of biomolecules determine the roles they play in cells. The
proper functioning of a living system depends on the many components acting harmoniously in response to a
constantly changing environment. Biomolecules are constantly formed or degraded in response to the
perceived needs of the organism.

Content Categories

▪ Category 1A focuses on the structural and functional complexity of proteins, which is derived from
their component amino acids, the sequence in which the amino acids are covalently bonded, and the
three-dimensional structures the proteins adopt in an aqueous environment.
▪ Category 1B focuses on the molecular mechanisms responsible for the transfer of sequence-specific
biological information between biopolymers that ultimately result in the synthesis of proteins.
▪ Category 1C focuses on the mechanisms that function to transmit the heritable information stored in
DNA from generation to generation.
▪ Category 1D focuses on the biomolecules and regulated pathways involved in harvesting chemical
energy stored in fuel molecules, which serves as the driving force for all the processes that take place
within a living system.

With these building blocks, medical students will be able to learn how the major biochemical, genetic, and
molecular functions of the cell support health and lead disease.

1A: Structure and function of proteins and their Amino Acids (BC, OC)
constituent amino acids
▪ Description
Macromolecules formed from amino acids adopt well- o Absolute configuration at the α position
defined, three-dimensional structures with chemical o Amino acids as dipolar ions
properties that are responsible for their participation in o Classifications
virtually every process occurring within and between ▪ Acidic or basic
cells. The three-dimensional structure of proteins is a ▪ Hydrophobic or hydrophilic
direct consequence of the nature of the covalently ▪ Reactions
bonded sequence of amino acids, their chemical and o Sulfur linkage for cysteine and cystine
physical properties, and the way the whole assembly o Peptide linkage: polypeptides and proteins
interacts with water. o Hydrolysis

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 Enzymes are proteins that interact in highly regio- and Protein Structure (BIO, BC, OC)
stereo-specific ways with dissolved solutes. They either
▪ Structure
facilitate the chemical transformation of these solutes
o 1° structure of proteins
or allow for their transport innocuously. Dissolved
o 2° structure of proteins
solutes compete for protein-binding sites, and protein
o 3° structure of proteins; role of proline, cystine,
conformational dynamics give rise to mechanisms
hydrophobic bonding
capable of controlling enzymatic activity.
o 4° structure of proteins (BIO, BC)
The infinite variability of potential amino acid ▪ Conformational stability
sequences allows for adaptable responses to o Denaturing and folding
pathogenic organisms and materials. The rigidity of o Hydrophobic interactions
some amino acid sequences makes them suitable for o Solvation layer (entropy) (BC)
structural roles in complex living systems. ▪ Separation techniques
o Isoelectric point
Content in this category covers a range of protein
o Electrophoresis
behaviors that originate from the unique chemistry of
amino acids themselves. Amino acid classifications and Nonenzymatic Protein Function (BIO, BC)
protein structural elements are covered. Special
▪ Binding (BC)
emphasis is placed on enzyme catalysis, including
▪ Immune system
mechanistic considerations, kinetics, models of
▪ Motors
enzyme-substrate interaction, and regulation.
Enzyme Structure and Function (BIO, BC)

▪ Function of enzymes in catalyzing biological

reactions
▪ Enzyme classification by reaction type
▪ Reduction of activation energy
▪ Substrates and enzyme specificity
▪ Active Site Model
▪ Induced-Fit Model
▪ Mechanism of catalysis
o Cofactors
o Coenzymes
o Water-soluble vitamins
▪ Effects of local conditions on enzyme activity

Control of Enzyme Activity (BIO, BC)

▪ Kinetics
o General (catalysis)
o Michaelis-Menten
o Cooperativity

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 ▪ Feedback regulation
▪ Inhibition ― types
o Competitive
o Noncompetitive
o Mixed (BC)
o Uncompetitive (BC)
▪ Regulatory enzymes
o Allosteric enzymes
o Covalently modified enzymes
o Zymogen

1B: Transmission of genetic information from the gene Nucleic Acid Structure and Function (BIO, BC)
to the protein
▪ Description
Biomolecules and biomolecular assemblies interact in ▪ Nucleotides and nucleosides
specific, highly regulated ways to transfer sequence o Sugar phosphate backbone
information between biopolymers in living organisms. o Pyrimidine, purine residues
By storing and transferring biological information, DNA ▪ Deoxyribonucleic acid (DNA): double helix,
and RNA enable living organisms to reproduce their Watson-Crick model of DNA structure
complex components from one generation to the next. ▪ Base pairing specificity: A with T, G with C
The nucleotide monomers of these biopolymers, being ▪ Function in transmission of genetic information
joined by phosphodiester linkages, form a (BIO)
polynucleotide molecule with a “backbone” composed ▪ DNA denaturation, reannealing, hybridization
of repeating sugar-phosphate units and “appendages”
DNA Replication (BIO)
of nitrogenous bases. The unique sequence of bases in
each gene provides specific information to the cell. ▪ Mechanism of replication: separation of strands,
specific coupling of free nucleic acids
DNA molecules are composed of two polynucleotides
▪ Semiconservative nature of replication
that spiral around an imaginary axis, forming a double
▪ Specific enzymes involved in replication
helix. The two polynucleotides are held together by
▪ Origins of replication, multiple origins in
hydrogen bonds between the paired bases and van der
eukaryotes
Waals interactions between the stacked bases. The
▪ Replicating the ends of DNA molecules
pairing between the bases of two polynucleotides is
very specific, and its complementarity allows for a Repair of DNA (BIO)
precise replication of the DNA molecule.
▪ Repair during replication
The DNA inherited by an organism leads to specific ▪ Repair of mutations
traits by dictating the synthesis of the biomolecules
(RNA molecules and proteins) involved in protein Genetic Code (BIO)
synthesis. While every cell in a multicellular organism ▪ Central Dogma: DNA → RNA → protein
inherits the same DNA, its expression is precisely ▪ The triplet code

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 regulated such that different genes are expressed by ▪ Codon-anticodon relationship
cells at different stages of development, by cells in ▪ Degenerate code, wobble pairing
different tissues, and by cells exposed to different ▪ Missense, nonsense codons
stimuli. ▪ Initiation, termination codons
▪ Messenger RNA (mRNA)
The topics included in this category concern not only
the molecular mechanisms of the transmission of Transcription (BIO)
genetic information from the gene to the protein
▪ Transfer RNA (tRNA); ribosomal RNA (rRNA)
(transcription and translation), but also the
▪ Mechanism of transcription
biosynthesis of the important molecules and molecular
▪ mRNA processing in eukaryotes, introns, exons
assemblies involved in these mechanisms. The control
▪ Ribozymes, spliceosomes, small nuclear
of gene expression in prokaryotes and eukaryotes is
ribonucleoproteins (snRNPs), small nuclear RNAs
also included.
(snRNAs)
Broadly speaking, the field of biotechnology uses ▪ Functional and evolutionary importance of
biological systems, living organisms, or derivatives introns
thereof to make or modify products or processes for
Translation (BIO)
specific use. The biotechnological techniques
emphasized in this category, however, are those that ▪ Roles of mRNA, tRNA, rRNA
take advantage of the complementary structure of ▪ Role and structure of ribosomes
double-stranded DNA molecules to synthesize, ▪ Initiation, termination co-factors
sequence, and amplify them and to analyze and ▪ Post-translational modification of proteins
identify unknown polynucleotide sequences. Included
within this treatment of biotechnology are those Eukaryotic Chromosome Organization (BIO)
practical applications that directly impact humans, such ▪ Chromosomal proteins
as medical applications, human gene therapy, and ▪ Single copy vs. repetitive DNA
pharmaceuticals. ▪ Supercoiling
Content in this category covers the biopolymers, ▪ Heterochromatin vs. euchromatin
including ribonucleic acid (RNA), deoxyribonucleic acid ▪ Telomeres, centromeres
(DNA), proteins, and the biochemical processes Control of Gene Expression in Prokaryotes (BIO)
involved in carrying out the transfer of biological
information from DNA. ▪ Operon Concept, Jacob-Monod Model
▪ Gene repression in bacteria
▪ Positive control in bacteria

Control of Gene Expression in Eukaryotes (BIO)

▪ Transcriptional regulation
▪ DNA binding proteins, transcription factors
▪ Gene amplification and duplication
▪ Post-transcriptional control, basic concept of
splicing (introns, exons)

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 ▪ Cancer as a failure of normal cellular controls,
oncogenes, tumor suppressor genes
▪ Regulation of chromatin structure
▪ DNA methylation
▪ Role of noncoding RNAs

Recombinant DNA and Biotechnology (BIO)

▪ Gene cloning
▪ Restriction enzymes
▪ DNA libraries
▪ Generation of cDNA
▪ Hybridization
▪ Expressing cloned genes
▪ Polymerase chain reaction
▪ Gel electrophoresis and Southern blotting
▪ DNA sequencing
▪ Analyzing gene expression
▪ Determining gene function
▪ Stem cells
▪ Practical applications of DNA technology: medical
applications, human gene therapy,
pharmaceuticals, forensic evidence,
environmental cleanup, agriculture
▪ Safety and ethics of DNA technology

1C: Transmission of heritable information from Evidence That DNA Is Genetic Material (BIO)
generation to generation and the processes that
Mendelian Concepts (BIO)
increase genetic diversity
▪ Phenotype and genotype
The information necessary to direct life functions is
▪ Gene
contained within discrete nucleotide sequences
▪ Locus
transmitted from generation to generation by
▪ Allele: single and multiple
mechanisms that, by nature of their various processes,
▪ Homozygosity and heterozygosity
provide the raw materials for evolution by increasing
▪ Wild-type
genetic diversity. Specific sequences of
▪ Recessiveness
deoxyribonucleic acids store and transfer the heritable
▪ Complete dominance
information necessary for the continuation of life from
▪ Co-dominance
one generation to the next. These sequences, called
▪ Incomplete dominance, leakage, penetrance,
genes ― being part of longer DNA molecules ― are
expressivity
▪ Hybridization: viability

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 organized, along with various proteins, into ▪ Gene pool
biomolecular assemblies called chromosomes.
Meiosis and Other Factors Affecting Genetic
Chromosomes pass from parents to offspring in Variability (BIO)
sexually reproducing organisms. The processes of
▪ Significance of meiosis
meiosis and fertilization maintain a species’
▪ Important differences between meiosis and
chromosome count during the sexual life cycle.
mitosis
Because parents pass on discrete heritable units that
▪ Segregation of genes
retain their separate identities in offspring, the laws of
o Independent assortment
probability can be used to predict the outcome of
o Linkage
some, but not all, genetic crosses.
o Recombination
The behavior of chromosomes during meiosis and ▪ Single crossovers
fertilization is responsible for most of the genetic ▪ Double crossovers
variation that arises each generation. Mechanisms that ▪ Synaptonemal complex
contribute to this genetic variation include ▪ Tetrad
independent assortment of chromosomes, crossing o Sex-linked characteristics
over, and random fertilization. Other mechanisms, such o Very few genes on Y chromosome
as mutation, random genetic drift, bottlenecks, and o Sex determination
immigration, exist with the potential to affect the o Cytoplasmic/extranuclear inheritance
genetic diversity of individuals and populations. ▪ Mutation
Collectively, the genetic diversity that results from o General concept of mutation — error in DNA
these processes provides the raw material for evolution sequence
by natural selection. o Types of mutations: random, translation error,
transcription error, base substitution, inversion,
The content in this category covers the mechanisms by
addition, deletion, translocation, mispairing
which heritable information is transmitted from
o Advantageous vs. deleterious mutation
generation to generation and the evolutionary
o Inborn errors of metabolism
processes that generate and act on genetic variation.
o Relationship of mutagens to carcinogens
▪ Genetic drift
▪ Synapsis or crossing-over mechanism for
increasing genetic diversity

Analytic Methods (BIO)

▪ Hardy-Weinberg Principle
▪ Testcross (Backcross; concepts of parental, F1,
and F2 generations)
▪ Gene mapping: crossover frequencies
▪ Biometry: statistical methods

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 Evolution (BIO)

▪ Natural selection
o Fitness concept
o Selection by differential reproduction
o Concepts of natural and group selection
o Evolutionary success as increase in percentage
representation in the gene pool of the next
generation
▪ Speciation
o Polymorphism
o Adaptation and specialization
o Inbreeding
o Outbreeding
o Bottlenecks
▪ Evolutionary time as measured by gradual
random changes in genome

1D: Principles of bioenergetics and fuel molecule Principles of Bioenergetics (BC, GC)
metabolism
▪ Bioenergetics/thermodynamics
Living things harness energy from fuel molecules in a ▪ Free energy/Keq
controlled manner that sustains all the processes o Equilibrium constant
responsible for maintaining life. Cell maintenance and o Relationship of the equilibrium constant and
growth is energetically costly. Cells harness the energy ΔG°
stored in fuel molecules, such as carbohydrates and ▪ Concentration
fatty acids, and convert it into smaller units of chemical o Le Châtelier’s Principle
potential known as adenosine triphosphate (ATP). ▪ Endothermic and exothermic reactions
▪ Free energy: G
The hydrolysis of ATP provides a ready source of energy
▪ Spontaneous reactions and ΔG°
for cells that can be coupled to other chemical
▪ Phosphoryl group transfers and ATP
processes that make them thermodynamically
o ATP hydrolysis ΔG << 0
favorable. Fuel molecule mobilization, transport, and
o ATP group transfers
storage are regulated according to the needs of the
▪ Biological oxidation-reduction
organism.
o Half-reactions
The content in this category covers the principles of o Soluble electron carriers
bioenergetics and fuel molecule catabolism. Details of o Flavoproteins
oxidative phosphorylation including the role of
chemiosmotic coupling and biological electron transfer
reactions are covered, as are the general features of
fatty acid and glucose metabolism. Additionally,

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 regulation of these metabolic pathways, fuel molecule Carbohydrates (BC, OC)
mobilization, transport, and storage are covered.
▪ Description
o Nomenclature and classification, common
names
o Absolute configuration
o Cyclic structure and conformations of hexoses
o Epimers and anomers
▪ Hydrolysis of the glycoside linkage
▪ Monosaccharides
▪ Disaccharides
▪ Polysaccharides

Glycolysis, Gluconeogenesis, and the Pentose

Phosphate Pathway (BIO, BC)

▪ Glycolysis (aerobic), substrates and products

o Feeder pathways: glycogen, starch metabolism
▪ Fermentation (anaerobic glycolysis)
▪ Gluconeogenesis (BC)
▪ Pentose phosphate pathway (BC)
▪ Net molecular and energetic results of respiration
processes

Principles of Metabolic Regulation (BC)

▪ Regulation of metabolic pathways (BIO, BC)

o Maintenance of a dynamic steady state
▪ Regulation of glycolysis and gluconeogenesis
▪ Metabolism of glycogen
▪ Regulation of glycogen synthesis and breakdown
o Allosteric and hormonal control
▪ Analysis of metabolic control

Citric Acid Cycle (BIO, BC)

▪ Acetyl-CoA production (BC)

▪ Reactions of the cycle, substrates and products
▪ Regulation of the cycle
▪ Net molecular and energetic results of respiration
processes

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 Metabolism of Fatty Acids and Proteins (BIO, BC)

▪ Description of fatty acids (BC)

▪ Digestion, mobilization, and transport of fats
▪ Oxidation of fatty acids
o Saturated fats
o Unsaturated fats
▪ Ketone bodies (BC)
▪ Anabolism of fats (BIO)
▪ Nontemplate synthesis: biosynthesis of lipids and
polysaccharides (BIO)
▪ Metabolism of proteins (BIO)

Oxidative Phosphorylation (BIO, BC)

▪ Electron transport chain and oxidative

phosphorylation, substrates and products,
general features of the pathway
▪ Electron transfer in mitochondria
o NADH, NADPH
o Flavoproteins
o Cytochromes
▪ ATP synthase, chemiosmotic coupling
o Proton motive force
▪ Net molecular and energetic results of respiration
processes
▪ Regulation of oxidative phosphorylation
▪ Mitochondria, apoptosis, oxidative stress (BC)

Hormonal Regulation and Integration of

Metabolism (BC)

▪ Higher-level integration of hormone structure

and function
▪ Tissue-specific metabolism
▪ Hormonal regulation of fuel metabolism
▪ Obesity and regulation of body mass

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 Biological and Biochemical Foundations of Living Systems

Foundational Concept 2

Highly organized assemblies of molecules, cells, and organs interact to carry out the functions of living
organisms.

Cells are the basic unit of structure in all living things. Mechanisms of cell division provide not only for the
growth and maintenance of organisms, but also for the continuation of the species through asexual and
sexual reproduction. The unique microenvironment to which a cell is exposed during development and
division determines the fate of the cell by impacting gene expression and ultimately the cell’s collection and
distribution of macromolecules and its arrangement of subcellular organelles.

In multicellular organisms, the processes necessary to maintain life are executed by groups of cells organized
into specialized structures with specialized functions ― both of which result from the unique properties of
the cells’ component molecules.

Content Categories

▪ Category 2A focuses on the assemblies of molecules, cells, and groups of cells within single cellular
and multicellular organisms that function to execute the processes necessary to maintain life.
▪ Category 2B focuses on the structure, growth, physiology, and genetics of prokaryotes and the
structure and life cycles of viruses.
▪ Category 2C focuses on the processes of cell and nuclear division and the mechanisms governing cell
differentiation and specialization.

With these building blocks, medical students will be able to learn how cells grow and integrate to form tissues
and organs that carry out essential biochemical and physiological functions.

2A: Assemblies of molecules, cells, and groups of cells Plasma Membrane (BIO, BC)
within single cellular and multicellular organisms
▪ General function in cell containment
The processes necessary to maintain life are executed ▪ Composition of membranes
by assemblies of molecules, cells, and groups of cells, o Lipid components (BIO, BC, OC)
all of which are organized into highly specific ▪ Phospholipids (and phosphatids)
structures as determined by the unique properties of ▪ Steroids
their component molecules. The processes necessary ▪ Waxes
to maintain life require that cells create and maintain o Protein components
internal environments within the cytoplasm and o Fluid mosaic model
▪ Membrane dynamics

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 within certain organelles that are different from their ▪ Solute transport across membranes
external environments. o Thermodynamic considerations
o Osmosis
Cell membranes separate the internal environment of
▪ Colligative properties; osmotic pressure (GC)
the cell from the external environment. The
o Passive transport
specialized structure of the membrane, as described in
o Active transport
the fluid mosaic model, allows the cell to be
▪ Sodium/potassium pump
selectively permeable and dynamic, with homeostasis
▪ Membrane channels
maintained by the constant movement of molecules
▪ Membrane potential
across the membranes through a combination of
▪ Membrane receptors
active and passive processes driven by several forces,
▪ Exocytosis and endocytosis
including electrochemical gradients.
▪ Intercellular junctions (BIO)
Eukaryotic cells also maintain internal membranes o Gap junctions
that partition the cell into specialized regions. These o Tight junctions
internal membranes facilitate cellular processes by o Desmosomes
minimizing conflicting interactions and increasing
Membrane-Bound Organelles and Defining
surface area where chemical reactions can occur.
Characteristics of Eukaryotic Cells (BIO)
Membrane-bound organelles localize different
processes or enzymatic reactions in time and space. ▪ Defining characteristics of eukaryotic cells:
membrane-bound nucleus, presence of organelles,
Through interactions between proteins bound to the
mitotic division
membranes of adjacent cells or between membrane-
▪ Nucleus
bound proteins and elements of the extracellular
o Compartmentalization, storage of genetic
matrix, cells of multicellular organisms organize into
information
tissues, organs, and organ systems. Certain
o Nucleolus: location and function
membrane-associated proteins also play key roles in
o Nuclear envelope, nuclear pores
identifying tissues or recent events in the cell’s history
▪ Mitochondria
for purposes of recognition of “self” versus foreign
o Site of ATP production
molecules.
o Inner- and outer-membrane structure (BIO, BC)
The content in this category covers the composition, o Self-replication
structure, and function of cell membranes; the ▪ Lysosomes: membrane-bound vesicles containing
structure and function of the membrane-bound hydrolytic enzymes
organelles of eukaryotic cells; and the structure and ▪ Endoplasmic reticulum
function of the major cytoskeletal elements. It covers o Rough and smooth components
the energetics of and mechanisms by which o Rough endoplasmic reticulum site of ribosomes
molecules, or groups of molecules, move across cell o Double-membrane structure
membranes. It also covers how cell-cell junctions and o Role in membrane biosynthesis
the extracellular matrix interact to form tissues with o Role in biosynthesis of secreted proteins
▪ Golgi apparatus: general structure and role in
packaging and secretion

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 specialized functions. Epithelial tissue and connective ▪ Peroxisomes: organelles that collect peroxides
tissue are covered in this category.
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

Tissues Formed From Eukaryotic Cells (BIO)

▪ Epithelial cells
▪ Connective tissue cells

2B: The structure, growth, physiology, and genetics Cell Theory (BIO)
of prokaryotes and viruses
▪ History and development
The highly organized assembly of molecules that is the ▪ Impact on biology
cell represents the fundamental unit of structure,
Classification and Structure of Prokaryotic Cells
function, and organization in all living organisms. In
(BIO)
the hierarchy of biological organization, the cell is the
simplest collection of matter capable of carrying out ▪ Prokaryotic domains
the processes that distinguish living organisms. As o Archaea
such, cells have the ability to undergo metabolism; o Bacteria
maintain homeostasis, including ionic gradients; grow; ▪ Major classifications of bacteria by shape
move in response to their local environments; o Bacilli (rod-shaped)
respond to stimuli; reproduce; and adapt to their o Spirilli (spiral-shaped)
environment in successive generations. o Cocci (spherical)
▪ Lack of nuclear membrane and mitotic apparatus
Life at cellular levels arises from structural order and
▪ Lack of typical eukaryotic organelles
its dynamic modulation. This happens in response to
▪ Presence of cell wall in bacteria
signals, thereby reflecting properties that result from
▪ Flagellar propulsion, mechanism
individual and interactive features of molecular
assemblies, their compartmentalization, and their
Growth and Physiology of Prokaryotic Cells (BIO)
interaction with environmental signals at many spatial
and temporal scales. ▪ Reproduction by fission
▪ High degree of genetic adaptability, acquisition of
The content in this category covers the classification,
antibiotic resistance
structure, growth, physiology, and genetics of

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 prokaryotes and the characteristics that distinguish ▪ Exponential growth
them from eukaryotes. Viruses are also covered here. ▪ Existence of anaerobic and aerobic variants
▪ Parasitic and symbiotic
▪ Chemotaxis

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)

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

Viral Life Cycle (BIO)

▪ Self-replicating biological units that must

reproduce within specific host cell
▪ Generalized phage and animal virus life cycles
o Attachment to host, penetration of cell
membrane or cell wall, and entry of viral genetic
material
o Use of host synthetic mechanism to replicate
viral components
o 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

2C: Processes of cell division, differentiation, and Mitosis (BIO)

specialization
▪ Mitotic process: prophase, metaphase, anaphase,
telophase, interphase

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 The ability of organisms to reproduce their own kind is
the characteristic that best distinguishes living things. ▪ Mitotic structures
In sexually reproducing organisms, the continuity of o Centrioles, asters, spindles
life is based on the processes of cell division and o Chromatids, centromeres, kinetochores
meiosis. o Nuclear membrane breakdown and
reorganization
The process of cell division is an integral part of the
o Mechanisms of chromosome movement
cell cycle. The progress of eukaryotic cells through the
▪ Phases of cell cycle: G0, G1, S, G2, M
cell cycle is regulated by a complex molecular control
▪ Growth arrest
system. Malfunctions in this system can result in
▪ Control of cell cycle
unabated cellular division and, ultimately, the
▪ Loss of cell cycle controls in cancer cells
development of cancer.
Biosignaling (BC)
In the embryonic development of multicellular
organisms, a fertilized egg gives rise to cells that ▪ Oncogenes, apoptosis
differentiate into many different types of cells, each
Reproductive System (BIO)
with a different structure, corresponding function, and
location within the organism. During development, ▪ Gametogenesis by meiosis
spatial-temporal gradients in the interactions between ▪ Ovum and sperm
gene expression and various stimuli result in the o Differences in formation
structural and functional divergence of cells into o Differences in morphology
specialized structures, organs, and tissues. The o Relative contribution to next generation
interaction of stimuli and genes is also explained by ▪ Reproductive sequence: fertilization, implantation,
the progression of stem cells to terminal cells. development, birth
The content in this category covers the cell cycle; the Embryogenesis (BIO)
causes, genetics, and basic properties of cancer; the
processes of meiosis and gametogenesis; and the ▪ Stages of early development (order and general
mechanisms governing cell specialization and features of each)
differentiation. o Fertilization
o Cleavage
o Blastula formation
o 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

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 Mechanisms of Development (BIO)

▪ Cell specialization
o Determination
o Differentiation
o 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

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 Biological and Biochemical Foundations of Living Systems

Foundational Concept 3

Complex systems of tissues and organs sense the internal and external environments of multicellular
organisms and, through integrated functioning, maintain a stable internal environment.

As a result of the integration of a number of highly specialized organ systems, complex living things are able to
maintain homeostasis while adapting to a constantly changing environment and participating in growth and
reproduction. The interactions of these organ systems involve complex regulatory mechanisms that help
maintain a dynamic and healthy equilibrium, regardless of the organ systems’ current state and environment.

Content Categories

▪ Category 3A focuses on the structure and functions of the nervous and endocrine systems and the
ways the systems work together to coordinate the responses of other body systems to both external
and internal stimuli.
▪ Category 3B focuses on the structure and functions of the organ systems ― circulatory, respiratory,
digestive, immune, lymphatic, muscular, skeletal, and reproductive ― and the ways these systems
interact to fulfill their concerted roles in the maintenance and continuance of the living organism.

With these building blocks, medical students will be able to learn how the body responds to internal and
external stimuli to support homeostasis and the ability to reproduce.

3A: Structure and functions of the nervous and Nervous System: Structure and Function (BIO)
endocrine systems and ways these systems coordinate
▪ Major functions
the organ systems
o High-level control and integration of body
The nervous and endocrine systems work together to systems
detect external and internal signals, transmit and o Adaptive capability to external influences
integrate information, and maintain homeostasis. They ▪ Organization of vertebrate nervous system
do all this by producing appropriate responses to ▪ Sensor and effector neurons
internal and external cues and stressors. The ▪ Sympathetic and parasympathetic nervous
integration of these systems both with one another systems: antagonistic control
and with the other organ systems ultimately results in ▪ Reflexes
the successful and adaptive behaviors that allow for o Feedback loop, reflex arc
the propagation of the species. o Role of spinal cord and supraspinal circuits
▪ Integration with endocrine system: feedback
Animals have evolved a nervous system that senses
control
and processes internal and external information used
to facilitate and enhance survival, growth, and
reproduction. The nervous system interfaces with

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 sensory and internal body systems to coordinate Nerve Cell (BIO)
physiological and behavioral responses ranging from
▪ Cell body: site of nucleus, organelles
simple movements and small metabolic changes to
▪ Dendrites: branched extensions of cell body
long-distance migrations and social interactions. The
▪ Axon: structure and function
physiological processes for nerve signal generation and
▪ Myelin sheath, Schwann cells, insulation of axon
propagation involve specialized membranes with
▪ Nodes of Ranvier: propagation of nerve impulse
associated proteins that respond to ligands and/or
along axon
electrical field changes, signaling molecules, and, by
▪ Synapse: site of impulse propagation between
extension, the establishment and replenishment of
cells
ionic electrochemical gradients requiring ATP.
▪ Synaptic activity: transmitter molecules
The endocrine system of animals has changed over ▪ Resting potential: electrochemical gradient
time to produce chemical signals that function ▪ Action potential
internally to regulate stress responses, reproduction, o Threshold, all-or-none
development, energy metabolism, growth, and various o Sodium-potassium pump
individual and interactive behaviors. The integrated ▪ Excitatory and inhibitory nerve fibers: summation,
contributions of the nervous and endocrine systems to frequency of firing
bodily functions are exemplified by the process ▪ Glial cells, neuroglia
whereby the signaling of neurons regulates hormone
Electrochemistry (GC)
release and by the targeting of membrane or nuclear
receptors on neurons by circulating hormones. ▪ Concentration cell: direction of electron flow,
Nernst equation
The content in this category covers the structure,
function, and basic aspects of nervous and endocrine Biosignaling (BC)
systems and their integration. The structure and
function of nerve cells is also included in this category. ▪ Gated ion channels
o Voltage gated
o Ligand gated
▪ Receptor enzymes
▪ G protein-coupled receptors

Lipids (BC, OC)

▪ Description; structure
o Steroids
o Terpenes and terpenoids
Endocrine System: Hormones and Their Sources
(BIO)

▪ Function of endocrine system: specific chemical

control at cell, tissue, and organ level
▪ Definitions of endocrine gland, hormone

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 ▪ Major endocrine glands: names, locations,
products
▪ Major types of hormones
▪ Neuroendocrinology ― relation between neurons
and hormonal systems

Endocrine System: Mechanisms of Hormone Action

(BIO)

▪ Cellular mechanisms of hormone action

▪ Transport of hormones: blood supply
▪ Specificity of hormones: target tissue
▪ Integration with nervous system: feedback control
▪ Regulation by second messengers

3B: Structure and integrative functions of the main Respiratory System (BIO)
organ systems
▪ General function
Animals use a number of highly organized and o Gas exchange, thermoregulation
integrated organ systems to carry out the necessary o Protection against disease: particulate matter
functions associated with maintaining life processes. ▪ Structure of lungs and alveoli
Within the body, no organ system is an island. ▪ Breathing mechanisms
Interactions and coordination between organ systems o Diaphragm, rib cage, differential pressure
allow organisms to engage in the processes necessary o Resiliency and surface tension effects
to sustain life. For example, the organs and structures ▪ Thermoregulation: nasal and tracheal capillary
of the circulatory system carry out a number of beds; evaporation, panting
functions, such as transporting: ▪ Particulate filtration: nasal hairs, mucus-cilia
system in lungs
▪ Nutrients absorbed in the digestive system.
▪ Alveolar gas exchange
▪ Gases absorbed from the respiratory system and
o Diffusion, differential partial pressure
muscle tissue.
o Henry’s Law (GC)
▪ Hormones secreted from the endocrine system.
▪ pH control
▪ Blood cells, produced in bone marrow, to and from
▪ Regulation by nervous control
cells in the body to help fight disease.
o CO2 sensitivity
The content in this category covers the structure and
Circulatory System (BIO)
function of the major organ systems of the body,
including the respiratory, circulatory, lymphatic, ▪ Functions: circulation of oxygen, nutrients,
immune, digestive, excretory, reproductive, muscle, hormones, ions and fluids, removal of metabolic
skeletal, and skin systems. Also covered in this category waste
is the integration of these systems and their control ▪ Role in thermoregulation
▪ Four-chambered heart: structure and function

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 and coordination by the endocrine and nervous ▪ Endothelial cells
systems. ▪ Systolic and diastolic pressure
▪ Pulmonary and systemic circulation
▪ Arterial and venous systems (arteries, arterioles,
venules, veins)
o Structural and functional differences
o Pressure and flow characteristics
▪ Capillary beds
o Mechanisms of gas and solute exchange
o Mechanism of heat exchange
o Source of peripheral resistance
▪ Composition of blood
o Plasma, chemicals, blood cells
o Erythrocyte production and destruction; spleen,
bone marrow
o Regulation of plasma volume
▪ Coagulation, clotting mechanisms
▪ Oxygen transport by blood
o Hemoglobin, hematocrit
o Oxygen content
o Oxygen affinity
▪ Carbon dioxide transport and level in blood
▪ Nervous and endocrine control

Lymphatic System (BIO)

▪ Structure of lymphatic system

▪ Major functions
o Equalization of fluid distribution
o Transport of proteins and large glycerides
o Production of lymphocytes involved in immune
reactions
o Return of materials to the blood
Immune System (BIO)

▪ Innate (nonspecific) vs. adaptive (specific)

immunity
▪ Adaptive immune system cells
o T-lymphocytes
o B-lymphocytes

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 ▪ Innate immune system cells
o Macrophages
o Phagocytes
▪ Tissues
o Bone marrow
o Spleen
o Thymus
o Lymph nodes
▪ Concept of antigen and antibody
▪ Antigen presentation
▪ Clonal selection
▪ Antigen-antibody recognition
▪ Structure of antibody molecule
▪ Recognition of self vs. nonself, autoimmune
diseases
▪ Major histocompatibility complex

Digestive System (BIO)

▪ Ingestion
o Saliva as lubrication and source of enzymes
o Ingestion; esophagus, transport function
▪ Stomach
o Storage and churning of food
o Low pH, gastric juice, mucal protection against
self-destruction
o Production of digestive enzymes, site of
digestion
o Structure (gross)
▪ Liver
o Structural relationship of liver within
gastrointestinal system
o Production of bile
o Role in blood glucose regulation, detoxification
▪ Bile
o Storage in gall bladder
o Function
▪ Pancreas
o Production of enzymes
o Transport of enzymes to small intestine

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 ▪ Small intestine
o Absorption of food molecules and water
o Function and structure of villi
o Production of enzymes, site of digestion
o Neutralization of stomach acid
o Structure (anatomic subdivisions)
▪ Large intestine
o Absorption of water
o Bacterial flora
o Structure (gross)
▪ Rectum: storage and elimination of waste, feces
▪ Muscular control
o Peristalsis
▪ Endocrine control
o Hormones
o Target tissues
▪ Nervous control: the enteric nervous system

Excretory System (BIO)

▪ Roles in homeostasis
o Blood pressure
o Osmoregulation
o Acid-base balance
o Removal of soluble nitrogenous waste
▪ Kidney structure
o Cortex
o Medulla
▪ Nephron structure
o Glomerulus
o Bowman’s capsule
o Proximal tubule
o Loop of Henle
o Distal tubule
o Collecting duct
▪ Formation of urine
o Glomerular filtration
o Secretion and reabsorption of solutes
o Concentration of urine
o Counter-current multiplier mechanism
▪ Storage and elimination: ureter, bladder, urethra

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 ▪ Osmoregulation: capillary reabsorption of H2O,
amino acids, glucose, ions
▪ Muscular control: sphincter muscle

Reproductive System (BIO)

▪ Male and female reproductive structures and their

functions
o Gonads
o Genitalia
o Differences between male and female structures
▪ Hormonal control of reproduction
o Male and female sexual development
o Female reproductive cycle
o Pregnancy, parturition, lactation
o Integration with nervous control
Muscle System (BIO)

▪ Important functions
o Support: mobility
o Peripheral circulatory assistance
o Thermoregulation (shivering reflex)
▪ Structure of three basic muscle types: striated,
smooth, cardiac
▪ Muscle structure and control of contraction
o T-tubule system
o Contractile apparatus
o Sarcoplasmic reticulum
o Fiber type
o Contractile velocity of different muscle types
▪ Regulation of cardiac muscle contraction
▪ Oxygen debt: fatigue
▪ Nervous control
o Motor neurons
o Neuromuscular junction, motor end plates
o Sympathetic and parasympathetic innervation
o Voluntary and involuntary muscles

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 Specialized Cell ― Muscle Cell (BIO)

▪ Structural characteristics of striated, smooth, and

cardiac muscle
▪ Abundant mitochondria in red muscle cells: ATP
source
▪ Organization of contractile elements: actin and
myosin filaments, crossbridges, sliding filament
model
▪ Sarcomeres: “I” and “A” bands, “M” and “Z” lines,
“H” zone
▪ Presence of troponin and tropomyosin
▪ Calcium regulation of contraction

Skeletal System (BIO)

▪ Functions
o Structural rigidity and support
o Calcium storage
o Physical protection
▪ Skeletal structure
o Specialization of bone types, structures
o Joint structures
o Endoskeleton vs. exoskeleton
▪ Bone structure
o Calcium-protein matrix
o Cellular composition of bone
▪ Cartilage: structure and function
▪ Ligaments, tendons
▪ Endocrine control

Skin System (BIO)

▪ Structure
o Layer differentiation, cell types
o Relative impermeability to water
▪ Functions in homeostasis and osmoregulation
▪ Functions in thermoregulation
o Hair, erectile musculature
o Fat layer for insulation
o Sweat glands, location in dermis

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 o Vasoconstriction and vasodilation in surface
capillaries
▪ Physical protection
o Nails, calluses, hair
o Protection against abrasion, disease organisms
▪ Hormonal control: sweating, vasodilation, and
vasoconstriction

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