7.01SC | Fall 2011 | Undergraduate

Fundamentals of Biology

Biochemistry

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an illustration of the biochemical structures and molecules in a T cell receptor
An illustration showing the biochemical structures present in a T Cell Receptor (image by Michelle Mischke).

This unit will introduce the course and cover the basics of biochemistry and cell composition. First, we will introduce the levels of organization of life, and the different types of organisms. We will then cover the structure of biological molecules and the molecular forces involved in the formation of these molecules. We will learn about the general structure and function of lipids, carbohydrates, and nucleic acids, as well as the composition, structure, and function of proteins. After learning about the major groups of macromolecules, we will explore their interactions within a cell, starting with metabolism, Gibbs free energy, biochemical reactions, enzymes and ATP as the energy currency. We will outline the cellular mechanisms for harvesting energy from glucose and related sugars, briefly outline glycolysis as a mechanism to generate ATP, and discuss the fate of the pyruvate produced in glycolysis under anaerobic and aerobic conditions. Finally, we will cover the general ideas of both cyclic and non-cyclic photophosphorylation and how these two processes are used by cells to generate the ATP and the NADPH needed for the Calvin Cycle in photosynthesis.

During this unit, you will describe both the chemical and molecular composition of a cell, and define the basic components of biological macromolecules. You will identify the forces that act in biological systems: covalent bonds, ionic bonds, hydrogen bonds, van der Waal’s forces, and hydrophobicity. You will draw a generic amino acid and categorize each of the 20 amino acids appropriately based upon the nature of the side chain. You will also apply the general laws of thermodynamics to biological reactions. In addition, you will define Gibbs free energy, determine the Gibbs free energy change associated with a biochemical reaction, and identify spontaneous and non-spontaneous reactions.

At the end of this unit, you will be familiar with the different levels of organization of life, and the differences between eukaryotic and prokaryotic cells. You will understand the structures and properties of the major groups of macromolecules, including lipids and phospholipids, carbohydrates nucleic acids, and proteins, as well as their functions in the cell. You will be familiar with primary, secondary, tertiary, and quaternary levels of protein structure and know what types of bonds and forces stabilize each level. In addition, you will understand the effect of an amino acid substitution on the general structure and function of a protein. You will know how ATP provides the energy to power cellular work.

Finally, you will have a greater understanding of the reactions in cellular respiration and photosynthesis, when they occur, and why they are important. You will understand the relationships between cellular respiration and photosynthesis.

Looking for something specific in this course? The Resource Index compiles links to most course resources in a single page.

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Session Overview

Biochem_sess5.jpg

This session will introduce basic ideas of metabolism, Gibbs free energy, biochemical reactions, enzymes and ATP as the energy currency.

Learning Objectives

  • To understand that organisms, through their biochemistry, transform matter and energy.
  • To apply the general laws of thermodynamics to biological reactions.
  • To define Gibbs free energy, determine the Gibbs free energy change associated with a biochemical reaction, and identify spontaneous and non-spontaneous reactions.
  • To understand the role that enzymes play in biochemical reactions.
  • To understand how ATP provides the energy to power cellular work.

Session Activities

Lecture Video

Watch the lecture video excerpt

Check Yourself

Question 1

If the ΔG of a reaction is negative, which of the following is a true statement?

Question 2

Choose an ending that makes the following statement true. “In an enzyme catalyzed reaction…”

Question 3

Which of the following statements is true with respect to ATP? ATP is commonly used in coupled reactions1. The hydrolysis of ATP is an endergonic reaction 2. The hydrolysis of ATP produces inorganic phosphate and ATP. 3. ATP is used as an energy source and a building block in RNA. 4. ATP can donate a phosphate group that becomes covalently linked to a protein.

Session Activities

Practice Problems

Further Study

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Session Overview

Biochem_sess2.jpg

This session will introduce the structure of biological molecules and the molecular forces involved in the formation of these molecules.

Learning Objectives

  • To be able to identify the forces that act in biological systems: covalent bonds, ionic bonds, hydrogen bonds, van der Waal’s forces, and hydrophobicity.
  • To understand the properties of covalent bonds as well as the concepts of biological catalysts and chirality.
  • To be able to distinguish between a polar and non-polar molecule and understand the concept of electronegativity.
  • To be able to explain how hydrogen bonds are formed and describe their importance in biological systems.

Session Activities

Lecture Video

Watch the lecture video excerpt

Check Yourself

Question 1

Which of the following type of bond or interaction joins monomers together to form biological polymers?

Question 2

Which of the following does not accurately describe a covalent bond?

Session Activities

Help Session Video

Watch the short video of Nicole DeNisco explaining covalent bonds, chirality, electronegativity, and hydrogen bonding, that refers to the practice problem below.

Practice Problems

Further Study

Suggested topics for further study in an introductory-level Biology textbook

  • Forces: covalent bonds, ionic bonds, hydrogen bonds, van der Waal’s forces, and hydrophobicity
  • Catalysts
  • Chirality
  • Polarity

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Session Overview

For this exam, you will need to know the properties of amino acids, nucleic acids, and phospholipids, as well as bonds, polarity, respiration, and photosynthesis.

Check Yourself

Exam and Solutions

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Session Overview

Biochem_sess6.jpg

This session will outline the cellular mechanisms for harvesting energy from glucose and related sugars. It will briefly outline glycolysis as a mechanism to generate ATP and discuss the fate of the pyruvate produced in glycolysis under anaerobic and aerobic conditions.

Learning Objectives

  • To understand how cells harvest chemical energy by oxidizing glucose to pyruvate.
  • To know the different ways that pyruvuate is catabolized based upon the presence and absence of oxygen.
  • To understand what fermentation is, when it occurs, and why it is important.
  • To understand what the Citric acid cycle is, when it occurs, and why it is important.
  • To understand what Oxidative Phosphorylation is, when it occurs, and why it is important.

Session Activities

Lecture Video

Watch the lecture video excerpt

Check Yourself

Question 1

In the process of glycolysis, one glucose molecule is oxidized to form 2 pyruvates and which of the following?

Question 2

In a yeast cell under anaerobic conditions, the NADH (from glycolysis) donates electrons to __________, which produces _________ additional ATP?

In a yeast cell under anaerobic conditions, NADH donates electrons to pyruvate. Although this reaction does not produce any additional ATP, it regenerates the NAD+ needed for subsequent rounds of glycolysis.

Question 3

In a yeast cell under aerobic conditions, pyruvate is oxidized to Acetyl CoA which enters the _________. NADH donates electrons to __________. The total ATP/glucose produced from these processes and glycolysis is __________.

Session Activities

Practice Problems

Further Study

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Session Overview

Biochem_sess3.jpg

This session will introduce the general structure and function of the biological macromolecules: lipids, carbohydrates, and nucleic acids.

Learning Objectives

  • To understand the general structure and properties of lipids and phospholipids and their function in the cell.
  • To understand the general structure and properties of carbohydrates and their function in the cell.
  • To understand the general structure and properties of nucleic acids and their function in the cell.

Session Activities

Lecture Video

Watch the lecture video excerpt

Check Yourself

Question 1

Which of the following statements is true for phospholipid molecules? 1. The polar end of phospholipids would contain carbon and phosphorous and oxygen. 2. The non-polar end of phospholipids would contain almost exclusively carbon and hydrogen. 3. The polar end of phospholipids would form hydrogen bonds with water. 4. The non-polar end of phospholipids associate with the cytoplasm of the cell.

Question 2

Which of the following statements is true for carbohydrate molecules? 1. The general structure can abbreviated as (CH2O)n. 2. A disaccharide can be formed by a condensation reaction between two glucose molecules. 3. Carbohydrates can be used as an energy source for cells. 4. Carbohydrates can be used as a structural molecule.

Session Activities

Lecture Video

Watch the lecture video excerpt

Check Yourself

Question 1

Nucleotides and nucleic acid polymers have a polarity with respect to their structure. Which of the following would be attached to the 5’ carbon of the ribose of the first nucleotide in a polymer?

Question 2

How do the monomers found in DNA differ from the monomers found in RNA? Choose all that apply. 1. DNA incorporates four different nitrogenous bases, RNA incorporates three different nitrogenous bases. 2. Thymidine is found in DNA but not RNA. 3. There is a 3’ hydroxyl on the RNA monomer, but not on the DNA monomer. 4. There is a 2’ hydroxyl on the RNA monomer, but not on the DNA monomer.

Session Activities

Help Session Video

Watch the short video of Nicole DeNisco explaining phospholipids, phosphate, and nucleic acids, that refers to Question 1 in the practice problems below.

Practice Problems

Further Study

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Session Overview

Biochem_sess7.jpg

This session will introduce the general ideas of both cyclic and non-cyclic photophosphorylation and how these two processes are used by cells to generate the ATP and the NADPH needed for the Calvin Cycle in photosynthesis.

Learning Objectives

  • To know that photosynthesis can convert light energy into chemical energy.
  • To understand how the light reactions convert solar energy into ATP and NADPH.
  • To understand that the Calvin cycle uses the chemical energy of ATP and NADPH produced in the light reactions to reduce CO2 to sugar.
  • To understand the relationships between cellular respiration and photosynthesis.

Session Activities

Lecture Video

Watch the lecture video excerpt

Check Yourself

Question 1

The light reactions of non-cyclic photophosphorylation supply the Calvin Cycle with…

Question 2

Which of the following does not occur in the Calvin Cycle?

Question 3

Which of the following is not true?

Session Activities

Practice Problems

Further Study

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Session Overview

Biochem_sess4.jpg

This session will introduce the general composition, structure, and function of proteins. The relationship between structure and function of a protein will be emphasized.

Learning Objectives

  • To understand the general composition of a protein.
  • To draw a generic amino acid and categorize each of the 20 amino acids appropriately based upon the nature of the side chain.
  • To understand primary, secondary, tertiary, and quaternary levels of protein structure and know what types of bonds and forces stabilize each level.
  • To understand the effect of an amino acid substitution on the general structure and function of a protein.

Session Activities

Lecture Video

Watch the lecture video excerpt

Check Yourself

Question 1

How many different functional groups are attached to the alpha carbon of an amino acid?

Question 2

A polypeptide chain is polymerized in which direction?

Question 3

Which of the following can be described as “a localized region of three dimensional structure that is stabilized by hydrogen bonds formed between the amine of one amino acid and the carboxyl of another amino acid”?

Session Activities

Lecture Video

Watch the lecture video excerpt

Check Yourself

Structures of the 20 amino acids (PDF)

Question 1

The amino acids leucine, valine, and phenylalanine would best be described as…

Question 2

The side chain of serine can form a hydrogen bond with the side chain of which of the following amino acids? Choose all that apply. 1. isoleucine 2. alanine 3. threonine 4. asparigine 5. proline

Session Activities

Practice Problems

Further Study

Study Guides

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Session Overview

Biochem_sess1.jpg

This session will introduce the course and cover the basics of cell composition. It will also introduce the different types of organisms and the basic differences between them.

Learning Objectives

  • To understand the differences between eukaryotic and prokaryotic cells.
  • To be familiar with the different levels of organization of life.
  • To be able to describe both the chemical and molecular composition of a cell.
  • To be able to define the basic components of biological macromolecules.

Session Activities

Lecture Video

Watch the lecture video excerpt

Check Yourself

Question 1

Which of the following organisms is a prokaryote?

Question 2

Which is the correct order, from highest to lowest, of the different levels of biological organization?

Session Activities

Lecture Video

Watch the lecture video excerpt

Check Yourself

Question 1

Which element is not a common component of biological macromolecules?

Session Activities

Practice Problems

Further Study

Suggested topics for further study in an introductory-level Biology textbook

  • Levels of organization of life
  • Biological macromolecules
  • Cell composition
  • Prokaryotic and eukaryotic cells

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