Introduction

“Consider just three of Earth’s inhabitants: a bright yellow daffodil that greets the spring, the single-celled creature called Thermococcus that lives in boiling hot springs, and you. Even a science-fiction writer inventing a story set on a distant planet could hardly imagine three more different forms of life.

Yet you, Thermococcus, and the daffodil are related! Indeed, all of the Earth’s billions of living things are kin to each other!”

Underlying this cellular diversity is biochemical unity. All cells are made up of molecules that encode information and can be copied—the nucleic acids  DNA and its simpler relative, RNA. They contain proteins—workhorse molecules that perform important tasks. And encapsulating them all, there’s a membrane made from fatty acids. Further, the machinery used to generate energy, and carry out fundamental processes is the same in all cells.

Below are some overarching questions we will address this semester.

1. What shapes the characteristics of all living things? (Shared Biochemistry!)
2. How is the information in DNA expressed?
3. How do the differences in DNA lead to differences in characteristics? (Mutation, Heredity, Natural Selection)
4. In multicellular organisms (like us) how do our various cells perform specialized functions, even though all cells have the same genome? (Gene Regulation)

Make sure you watch the video below before you continue!

During this course we expand on many themes you may have encountered in earlier introductory classes. Below is a refresher of a few key concepts you should know well before we dive in

Domains of Life

All of life is either a single cell or made up of cells. We believe with good reason that all life on Earth evolved from a common ancestral cell that existed soon after the origins of life on our planet. At one time, all life was divided into two groups: the true bacteria and everything else! Now we group life into one of three domains:

• Prokaryotes are among the first descendants of that common ancestral cell. They lack nuclei (pro meaning before and karyon meaning kernel, or nucleus). They include bacteria and cyanobacteria (blue-green algae).
• Eukaryotes include all higher life forms, characterized by cells with true nuclei (Eu, true; karyon, nucleus).
• Archaea Originally classified as ancient prokaryotes, Archaebacteria were shown by 1990 to be separate from prokaryotes and eukaryotes, in fact, a third domain of life.

Chemical Components of Cells

Not only is all life cellular, all life is made up of the same stuff.  If you were to take any cell and vaporize it you will find that they are made up of relatively few types of atoms! These include carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. These atoms combine to form the building blocks of four major biological macromolecules: nucleic acids, proteins, carbohydrates, and lipids that are the fundamental components of a cell and therefore all of life.

All biological macromolecules are carbon containing. In addition to containing carbon, the small organic molecules contain special combinations of atoms called Functional Groups. Functional groups confer specific chemical properties to those molecules, influencing their behavior.

Knowing these groups and their properties is important. The video below briefly describes them.

Monomers to Polymers and Back: Dehydration Synthesis and Hydrolysis

Most macromolecules are made from single subunits, or building blocks, called monomers. The monomers combine using covalent bonds to form larger molecules known as polymers. In doing so, monomers release water molecules as byproducts. This type of reaction is dehydration synthesis, which means “to put together while losing water.”

Polymers break down into monomers during hydrolysis. A chemical reaction occurs when inserting a water molecule across the bond. Breaking a covalent bond with this water molecule in the compound achieves this. During these reactions, the polymer breaks into two components: one part gains a hydrogen atom (H+), and the other gains a hydroxyl molecule (OH–) from a split water molecule.

What is a Gene?

One of the features of life is the ability to pass on traits from one generation to another, and from one cell to another. We refer to observable traits as phenotypes. You may recall that it was Mendel’s early experiments with observable characteristics of pea plants (like seed color, seed coat, etc) followed by several others that established that ‘genes’ are the basic physical unit of inheritance. Genes are arranged, one after another, on structures called chromosomes.

A chromosome contains a single, long DNA molecule- only a portion of which corresponds to a single gene- as well as the structural proteins (called histones) that the DNA molecule wraps around. Humans have approximately 20,000 genes arranged on their chromosomes.

Watch the following brief video for an animated view of the relationship between chromosomes and genes.

The presence of genes alone does not result in traits.  Genes contain information needed to specify traits! It is the action of proteins inside the cell is responsible for the traits seen. Thus proteins are the link between genotype (the genes within a cell) and phenotype.

Basic Principles of Gene Expression

Gene expression is the mechanism for how the information coded in DNA is ‘brought to life’ or ‘expressed’ into proteins. It involves 2 processes: Transcription and Translation.

Because proteins are coded by genes, the term “gene expression” refers to protein synthesis (i.e., making proteins), including the regulation of that synthesis.

The first step in gene expression, transcription results in the production of  RNA. Note that DNA never “becomes” RNA; rather, the DNA is “read” to make an RNA copy.

For genes that code for proteins, this type of RNA is called messenger RNA or mRNA. It is important to note many genes code for RNA products like rRNA, tRNA, and microRNA, which are involved in protein synthesis and its regulation but do not carry code for proteins. In other words, they function as the RNA inside the cell.

Here it may help to pause and review the similarities and differences between DNA and RNA. The similarities between these two nucleic acids is what enable RNA to serve as a ‘messenger’ or copy.

DNA and RNA are comprised of monomers called nucleotides. The nucleotides combine to form a polynucleotide, DNA, or RNA.

Three components comprise each nucleotide: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group. Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.

Therefore, although the terms “base” and “nucleotide” are sometimes used interchangeably, a nucleotide contains a base as well as part of the sugar-phosphate backbone.

Comparison of RNA (left molecule) and DNA (right molecule). The color of the bases in RNA and DNA aligns with the colored boxes next to each base molecule

In eukaryotic cells, the mRNA leaves the nucleus, and then, through the process of translation,  is read to create an amino acid sequence that folds into a protein.

Consider what the terms “transcribe” and “translate” mean about language. To “transcribe” something means to rewrite text again in the same language while to “translate” something means to rewrite the text in a different language.

Similar to these meanings, in biology, DNA is transcribed into RNA: both DNA and RNA are made of nucleic acid (i.e., the same “language”). With the assistance of proteins, DNA is “read” and transcribed into an mRNA sequence.

To read RNA and create protein, though, we refer to it as being translated: RNA is made of nucleic acid, and protein is made of amino acids (i.e., different “languages”). Therefore, DNA is transcribed to create an mRNA sequence, and then the mRNA sequence is translated to make a protein.

Protein Synthesis Overview

Transcription and translation occur in all domains of life however,  since most studies have involved bacteria and eukaryotic cells, we will focus on those two in this course. Additionally, the basic mechanism of transcription and translation is universal regardless of the organism type. The few differences that arise are due to the organization of the cell. For example, in prokaryotes, both processes occur in the cytosol since these cells do not contain organelles.

In eukaryotic cells, transcription occurs in the nucleus (where the DNA is) and translation in the cytoplasm (where the protein synthesizing machinery is)! Hence the mRNA has to be exported out of the nucleus. This provides the eukaryotic cell with additional means to regulate gene expression.

Transcription

A gene is complex: it contains not only the code for the resulting protein but also several regulatory factors that determine if and when the region that codes for a protein is read to create protein.

What follows is a diagram of the components of a gene that are used in transcription.

Translation

Translation involves different types of RNA, and we will explain them in more detail in later chapters: rRNA, tRNA, mRNA, and microRNA.

After an mRNA is created, it leaves the nucleus and is attracted to or attracts a ribosome, which is a molecule made of rRNA and polypeptides. Then, in the ribosome, and with the assistance of tRNAs, the mRNA is read and an amino acid sequence is created.

DNA and mRNA create sequences with just four types of bases; yet, these bases code for 20 unique amino acids (the makeup of protein). How is this possible? Watch the following video to find out!

For closed captioning or to view the full transcript see the video on YouTube. Or click on the “YouTube” link in the video.

The mRNA is read in sets of three bases known as codons. Each codon codes for a single amino acid. In this way, the mRNA is read and the protein product is made. The following are two representations of the codon chart; move to the next slide for the second representation. These representations are commonly used in biology textbooks.

Regulation of Gene Expression

As we shall see throughout the semester, our cells resort to several ways and resources in controlling gene expression in space and time- what genes are expressed, when they are expressed and how robust is the expression. Regulation may occur at any point in the expression of a gene, from the start of the transcription phase of protein synthesis to the processing of a protein after synthesis occurs.

This tightly controlled regulation is key to the development as well as the smooth functioning of an already developed organism.

Watch this video that illustrates the concept of gene regulation.

(For closed captioning or to view the full transcript click on the document syllabus)

Attributions

This chapter is a modified derivative of the following:

Chapter 17. Gene Expression Overview from An Interactive Introduction to Organismal and Molecular Biology, 2nd ed. by Andrea Bierema is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

Modifications include additions of

“Domains of Life”  and “Monomers to Polymers and Back: Dehydration Synthesis and Hydrolysis” sections from Bergstrom, G. (2022) Cell and Molecular Biology: What We Know & How We Found Out  CC BY 4.0 Download the original at (CMB5e; digital versions, available at https://dc.uwm.edu/biosci_facbooks_bergtrom/

Genetic Science Learning Center. (2017, August 1) Shared Functions, Shared Genes. Retrieved December 16, 2021, from https://learn.genetics.utah.edu/content/evolution/sharedfunctions