Unit: Biochemistry & Metabolism (Intro to Energy & Enzymes)

(reorganized from the College Board AP Biology Curriculum Framework 2012 by David Knuffke)

Jump to Origin of Life; Lesson 1: Intro to Biochem & Water; Lesson 2: Macromolecules; Lesson 3: Energetics; Lesson 4: Enzymes; Not on the National Exam


Origin of Life

Enduring understanding 1.D: The origin of living systems is explained by natural processes.

Essential knowledge 1.D.1: There are several hypotheses about the natural origin of life on Earth, each with supporting scientific evidence.

a. Scientific evidence supports the various models.

Evidence of student learning is a demonstrated understanding of each of the following:

1. Primitive Earth provided inorganic precursors from which organic molecules could have been synthesized due to the presence of available free energy and the absence of a significant quantity of oxygen.

2. In turn, these molecules served as monomers or building blocks for the formation of more complex molecules, including amino acids and nucleotides. [See also 4.A.1]

3. The joining of these monomers produced polymers with the ability to replicate, store and transfer information.

4. These complex reaction sets could have occurred in solution (organic soup model) or as reactions on solid reactive surfaces. [See also 2.B.1]

5. The RNA World hypothesis proposes that RNA could have been the earliest genetic material.


Learning Objectives:

LO 1.27 The student is able to describe a scientific hypothesis about the origin of life on Earth. [See SP 1.2]

LO 1.28 The student is able to evaluate scientific questions based on hypotheses about the origin of life on Earth. [See SP 3.3]

LO 1.29 The student is able to describe the reasons for revisions of scientific hypotheses of the origin of life on Earth. [See SP 6.3]

LO 1.30 The student is able to evaluate scientific hypotheses about the origin of life on Earth. [See SP 6.5]

LO 1.31 The student is able to evaluate the accuracy and legitimacy of data to answer scientific questions about the origin of life on Earth. [See SP 4.4]

Essential knowledge 1.D.2: Scientific evidence from many different disciplines supports models of the origin of life.

a. Geological evidence provides support for models of the origin of life on Earth.

Evidence of student learning is a demonstrated understanding of each of the following:

1. The Earth formed approximately 4.6 billion years ago (bya), and the environment was too hostile for life until 3.9 bya, while the earliest fossil evidence for life dates to 3.5 bya. Taken together, this evidence provides a plausible range of dates when the origin of life could have occurred.

2. Chemical experiments have shown that it is possible to form complex organic molecules from inorganic molecules in the absence of life.

b. Molecular and genetic evidence from extant and extinct organisms indicates that all organisms on Earth share a common ancestral origin of life.

Evidence of student learning is a demonstrated understanding of each of the following:


Learning Objective:

LO 1.32 The student is able to justify the selection of geological, physical, and chemical data that reveal early Earth conditions. [See SP 4.1]


Lesson 1: Introduction to Biochemistry, Properties of Water

Enduring understanding 2.A: Growth, reproduction and maintenance of the organization of living systems require free energy and matter.


Essential knowledge 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization.

a. Molecules and atoms from the environment are necessary to build new molecules.

Evidence of student learning is a demonstrated understanding of each of the following:

1. Carbon moves from the environment to organisms where it is used to build

carbohydrates, proteins, lipids or nucleic acids. Carbon is used in storage

compounds and cell formation in all organisms.

2. Nitrogen moves from the environment to organisms where it is used in building proteins and nucleic acids. Phosphorus moves from the environment to organisms where it is used in nucleic acids and certain lipids.

3. Living systems depend on properties of water that result from its polarity and hydrogen bonding.

To foster student understanding of this concept, instructors can choose an

illustrative example such as:

b. Surface area-to-volume ratios affect a biological system’s ability to obtain necessary resources or eliminate waste products.

Evidence of student learning is a demonstrated understanding of each of the following:

1. As cells increase in volume, the relative surface area decreases and demand for material resources increases; more cellular structures are necessary to adequately exchange materials and energy with the environment. These limitations restrict cell size.

To foster student understanding of this concept, instructors can choose an

illustrative example such as:

2. The surface area of the plasma membrane must be large enough to adequately exchange materials; smaller cells have a more favorable surface area-to-volume ratio for exchange of materials with the environment.


Learning Objectives:

LO 2.6 The student is able to use calculated surface area-to-volume ratios to predict which cell(s) might eliminate wastes or procure nutrients faster by diffusion. [See SP 2.2]

LO 2.7 Students will be able to explain how cell size and shape affect the overall

rate of nutrient intake and the rate of waste elimination. [See SP 6.2]

LO 2.8 The student is able to justify the selection of data regarding the types of

molecules that an animal, plant or bacterium will take up as necessary building

blocks and excrete as waste products. [See SP 4.1]

LO 2.9 The student is able to represent graphically or model quantitatively

the exchange of molecules between an organism and its environment, and the

subsequent use of these molecules to build new molecules that facilitate dynamic

homeostasis, growth and reproduction. [See SP 1.1, 1.4]



Lesson 2: Macromolecules

Enduring understanding 4.A: Interactions within biological systems lead to complex properties.

Essential knowledge 4.A.1: The subcomponents of biological molecules and their sequence determine the properties of that molecule.

a. Structure and function of polymers are derived from the way their monomers are assembled.

Evidence of student learning is a demonstrated understanding of each of the following:

4. Carbohydrates are composed of sugar monomers whose structures and bonding with each other by dehydration synthesis determine the properties and functions of the molecules. Illustrative examples include: cellulose versus starch.

b. Directionality influences structure and function of the polymer.

Evidence of student learning is a demonstrated understanding of each of the following:

3. The nature of the bonding between carbohydrate subunits determines their relative orientation in the carbohydrate, which then determines the secondary structure of the carbohydrate.

a. Structure and function of polymers are derived from the way their monomers are assembled.

Evidence of student learning is a demonstrated understanding of each of the following:

3. In general, lipids are nonpolar; however, phospholipids exhibit structural properties, with polar regions that interact with other polar molecules such as water, and with nonpolar regions where differences in saturation determine the structure and function of lipids. [See also 1.D.1, 2.A.3, 2. B.1]

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a. Structure and function of polymers are derived from the way their monomers are assembled.

Evidence of student learning is a demonstrated understanding of each of the following:

1. In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate and a nitrogen base (adenine, thymine, guanine, cytosine or uracil). DNA and RNA differ in function and differ slightly in structure, and these structural differences account for the differing functions. [See also 1.D.1, 2.A.3, 3.A.1]

b. Directionality influences structure and function of the polymer.

Evidence of student learning is a demonstrated understanding of each of the following:

1. Nucleic acids have ends, defined by the 3' and 5' carbons of the sugar in the nucleotide, that determine the direction in which complementary nucleotides are added during DNA synthesis and the direction in which transcription occurs (from 5' to 3'). [See also 3.A.1]

a. Structure and function of polymers are derived from the way their monomers are assembled.

Evidence of student learning is a demonstrated understanding of each of the following:

2. In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall shape of the protein, which also involves secondary tertiary and quaternary structure and, thus, its function. The R group of an amino acid can be categorized by chemical properties (hydrophobic, hydrophilic and ionic), and the interactions of these R groups determine structure and function of that region of the protein. [See also 1.D.1, 2.A.3, 2.B.1]

b. Directionality influences structure and function of the polymer.

Evidence of student learning is a demonstrated understanding of each of the following:

2. Proteins have an amino (NH2) end and a carboxyl (COOH) end, and consist of a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the amino and carboxyl groups of adjacent monomers.


Learning Objectives:

LO 4.1 The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. [See SP 7.1]

LO 4.2 The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. [See SP 1.3]

LO 4.3 The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecule. [See SP 6.1, 6.4]


Unit: Metabolism (Energy, Enzymes)


Lesson 3: Energetics of Life Introduction


Enduring understanding 2.A: Growth, reproduction and maintenance of the organization of living systems require free energy and matter.

Day 1: “Theory”

Essential knowledge 2.A.1: All living systems require constant input of free energy.

a. Life requires a highly ordered system.

Evidence of student learning is a demonstrated understanding of each of the following:

1. Order is maintained by constant free energy input into the system.

2. Loss of order or free energy flow results in death.

3. Increased disorder and entropy are offset by biological processes that maintain or increase order.

b. Living systems do not violate the second law of thermodynamics, which states that entropy increases over time.

Evidence of student learning is a demonstrated understanding of each of the following:

1. Order is maintained by coupling cellular processes that increase entropy (and so have negative changes in free energy) with those that decrease entropy (and so have positive changes in free energy).

2. Energy input must exceed free energy lost to entropy to maintain order and power cellular processes.

3. Energetically favorable exergonic reactions, such as ATP→ADP, that have a negative change in free energy can be used to maintain or increase order in a system by being coupled with reactions that have a positive free energy change.

c. Energy-related pathways in biological systems are sequential and may be entered at multiple points in the pathway. [See also 2.A.2]

To foster student understanding of this concept, instructors can choose an illustrative example such as:

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Practice”

d. Organisms use free energy to maintain organization, grow and reproduce.

Evidence of student learning is a demonstrated understanding of each of the following:

1. Organisms use various strategies to regulate body temperature and metabolism.

To foster student understanding of this concept, instructors can choose an illustrative example such as:

2. Reproduction and rearing of offspring require free energy beyond that used for maintenance and growth. Different organisms use various reproductive strategies in response to energy availability.

To foster student understanding of this concept, instructors can choose an illustrative example such as:

3. There is a relationship between metabolic rate per unit body mass and the size of multicellular organisms — generally, the smaller the organism, the higher the metabolic rate.

4. Excess acquired free energy versus required free energy expenditure results in energy storage or growth.

5. Insufficient acquired free energy versus required free energy expenditure results in loss of mass and, ultimately, the death of an organism.

e. Changes in free energy availability can result in changes in population size.

f. Changes in free energy availability can result in disruptions to an ecosystem.

To foster student understanding of this concept, instructors can choose an illustrative example such as:


Learning Objectives:

LO 2.1 The student is able to explain how biological systems use free energy based on empirical data that all organisms require constant energy input to maintain organization, to grow and to reproduce. [See SP 6.2]

LO 2.2 The student is able to justify a scientific claim that free energy is required for living systems to maintain organization, to grow or to reproduce, but that multiple strategies exist in different living systems. [See SP 6.1]

LO 2.3 The student is able to predict how changes in free energy availability affect organisms, populations and ecosystems. [See SP 6.4]


Lesson 4: Enzyme Structure and Function

Enduring understanding 4.B: Competition and cooperation are important aspects of biological systems.


Essential knowledge 4.B.1: Interactions between molecules affect their structure and function.

a. Change in the structure of a molecular system may result in a change of the function of the system. [See also 3.D.3]

b. The shape of enzymes, active sites and interaction with specific molecules are essential for basic functioning of the enzyme.

Evidence of student learning is a demonstrated understanding of each of the

following:

1. For an enzyme-mediated chemical reaction to occur, the substrate must be complementary to the surface properties (shape and charge) of the active site. In other words, the substrate must fit into the enzyme’s active site.

2. Cofactors and coenzymes affect enzyme function; this interaction relates to a structural change that alters the activity rate of the enzyme. The enzyme may only become active when all the appropriate cofactors or coenzymes are present and bind to the appropriate sites on the enzyme.

c. Other molecules and the environment in which the enzyme acts can enhance or inhibit enzyme activity. Molecules can bind reversibly or irreversibly to the active or allosteric sites, changing the activity of the enzyme.

d. The change in function of an enzyme can be interpreted from data regarding the concentrations of product or substrate as a function of time. These representations demonstrate the relationship between an enzyme’s activity, the disappearance of substrate, and/or presence of a competitive inhibitor.


Learning Objective:

LO 4.17 The student is able to analyze data to identify how molecular interactions affect structure and function. [See SP 5.1]


Untested on the National College Board AP Biology Exam:

The molecular structure of specific nucleotides is beyond the scope of the course and the AP Exam.

The molecular structure of specific amino acids is beyond the scope of the course and the AP Exam.

The molecular structure of specific lipids is beyond the scope of the course and the AP Exam.

The molecular structure of specific carbohydrate polymers is beyond the scope of the course and the AP Exam.

No specific cofactors or coenzymes are within the scope of the course and the AP Exam.

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