BIO - Biochemistry [OVERVIEW]

Biochemistry

Introduction

In this biochemistry module, you will learn about the chemistry, molecules, and chemical processes necessary for life to exist. You’ll also learn about substances like carbohydrates, fats, proteins, and the nucleic acids that make up the genetic code. All living things are composed of these same four biomolecules and they are combined together using the same chemical processes. You’ll understand the atoms that each is composed of, the major functions, and the building blocks that form each one by the end of the module. With proteins, you will dive deep into the relationship between structure and function, one of the core themes of biology. We’ll learn about how proteins fold into 3-dimensional space and also how enzymes, a subclass of proteins, work to speed up chemical reactions. The laboratory activity embedded in this module explores the relationship between environmental factors such as pH and temperature and enzyme activity.

List of Lessons

In this module, we will study the following topics:

1. 1. Review of Chemistry – this lesson will review the prerequisite, relevant chemistry knowledge acquired from your introductory chemistry class.
   2. Water – this lesson will explain the structure of water, intermolecular forces between molecules, and explanations of the unique properties of water that result.
   3. Introduction to Biomolecules – this lesson will describe the basics of biomolecules, the difference between a monomer and polymer, and both dehydration synthesis and hydrolysis reactions that join and break them.
   4. Carbohydrates and Lipids – this lesson will describe the structure and function of both carbohydrates and lipid biomolecules.
   5. Proteins – this lesson will describe the structure and function of protein biomolecules, including the four levels of protein structure and how proteins fold up into 3-dimensional space.
   6. Enzymes – this lesson will describe the function of enzyme proteins and explore the effects of temperature and pH on enzyme activity.
   7. Math – this lesson will review the Standard Error of the Mean statistical test.
   8. Nucleic Acids – this lesson will describe the structure and function of nucleic acid biomolecules.

Module Objectives

By the end of this module, students will be able to:

• • Explain how the properties of water that result from its polarity and hydrogen bonding affect its biological function.
  • Describe the composition of macromolecules required by living organisms.
  • Describe the properties of the monomers and the type of bonds that connect the monomers in biological macromolecules.
  • Explain how a change in the subunits of a polymer may lead to changes in the structure or function of the macromolecule.
  • Describe the structural similarities and differences between DNA and RNA.
  • Describe the properties of enzymes.
  • Explain how changes to the structure of an enzyme may affect its function.
  • Explain how the cellular environment affects enzyme activity.
  • MATH SKILL: Use confidence intervals and/or error bars (both determined using standard errors) to determine whether sample means are statistically different.

Key Terms

Monomer – one repeating unit (building block) of a polymer

Polymer – a chain of repeating monomers connected to each other

Dehydration Synthesis (Condensation) Reaction – a chemical reaction that combines two monomers into a chain and releases a water molecule in the process

Hydrolysis – a chemical reaction that splits a water molecule as well as a bond connecting two monomers in order to break down the polymer

Monosaccharide – one single-ringed sugar monomer such as glucose and fructose

Disaccharide – two monosaccharides put together such as lactose or sucrose

Polysaccharide – larger carbohydrate formed by chains or sheets of monosaccharides put together

Glycogen – long chains or branches of glucose connected together for temporary storage in animals and fungi

Starch - long chains or branches of glucose connected together for temporary storage in plants

Cellulose – long chains or branches of glucose connected together to provide support and structure to the cell wall in plants

Phospholipid – a major component of the cell membrane and formed from two hydrocarbon tails attach to a polar phosphate head

Polypeptide – name for an incomplete protein or one that has not folded up yet

Protein – long sequence of amino acids, folded up into a 3-dimensional shape

Amino acid – monomer of a protein and consists of an amino and carboxyl group plus a central carbon attached to an R group

Peptide bond – a bond between the amino group of one amino acid and the carboxyl group of the next one

Primary structure – linear sequence of amino acids lined up according to the DNA code

Secondary structure – α helices and β pleated sheets held in place by hydrogen bonding in the backbone of the protein

Tertiary structure – interactions between the R groups of the amino acids

Quaternary structure – when some proteins join together and function as subunits of a larger protein

Denaturation – when an enzyme protein unfolds and loses its shape upon exposure to extreme environments

Enzyme – a specific class of proteins that serve as biological catalysts and speed up chemical reactions

Catalyst – any factor that can speed up a chemical reaction

Substrate – molecule(s) that fits into the active site of an enzyme and become products after the chemical reaction occurs

Active site – binding site on an enzyme where the substrate fits and transforms into products

Allosteric site – a binding site where an activator or inhibitor molecule can bind to regulate enzyme activity

Competitive inhibitor – a molecule that fits into the active site and blocks the substrate from binding

Noncompetitive inhibitor – a molecule that binds to the allosteric site which changes the shape of the active site and prevents the substrate from binding

DNA – nucleic acid that contains the code for determining the order of amino acids in proteins

mRNA – takes the DNA code out of the nucleus after transcription

Deoxyribose – 5 carbon sugar in DNA

Ribose – 5 carbon sugar in RNA

Nucleotide – monomer for nucleic acid and composed of a 5 carbon sugar, a phosphate, and a nitrogen-base

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