The Cell

Genetics: Reproducing Life and Producing Variation

Questions addressed in this chapter:
What is the genetic code?
What does the genetic code (DNA) do?
How does understanding genes help us understand variation?

The last chapter ended with a brief introduction to DNA. But, what is DNA? What is it made of? And how can a small molecule like DNA ‘code’ for all of the traits in a living organism? We will address these and other questions in this chapter. Ultimately, what we are doing in this chapter is understanding how the genetic code (DNA) results in variation, because it is this variation that natural selection can act upon and lead to evolutionary changes. We will start by looking at the fundamental unit of all life on Earth: the cell. Inside each cell, the DNA code is structured into packages known as chromosomes. We will see how the DNA molecule can copy itself so that each cell in an organism’s body contains the same DNA information. We will then look at how DNA codes for proteins, which all living organisms are made of. Finally, we will look at a concrete example of how DNA impacts our lives by examining human blood types. Though we have to dive into the microscopic world, do not lose sight of the big picture: DNA is a code for making proteins, and we are made of proteins. If the DNA slightly changes (through mutation, which we met in the last chapter), the protein changes, and thus the organism can change.

The Cell: Prokaryotes

Prokaryotes
3.5 billion years old
Single-celled bacteria
No nucleus or organelles

All living organisms are made of cells; they are the basic units of life. There are many, many organisms that are made of just one cell, and many (including you) that are made of trillions of cells. All of life can be divided into two big categories, depending on the kind of cell they have. The first kind are organisms called prokaryotes. Prokaryotes are single-celled bacteria without nuclei or any special structures called organelles. They often have structures shown here in this image, like a cell wall, an outer membrane, a cytoplasm within which the DNA resides, and they often have locomotor structures like a flagellum. On this slide is a microscopic image of a prokaryotic cell that we have all heard of: Escherichia coli (E. coli), which lives in the guts of many mammals, including humans. Though prokaryotic cells live within us, and have been instrumental factors in driving human evolution, we will turn now to the cells we are made of: eukaryotic cells.

The Cell: Eukaryotes

Eukaryotes
1.2 billion years ago.
Some single-celled; all multicellular organisms (including humans)
DNA contained in a nucleus
Organelles

All animals, plants, fungi, and many single-celled organisms called protists are made of eukaryotic cells. These cells have a nucleus that contains DNA, and often have membrane-bound parts of the cell called organelles. These include chloroplasts (found in plants) and mitochondria, which help produce the molecular energy that powers cellular processes. Notice in this image that the eukaryotic cell is a bit more complicated than a prokaryotic cell. The microscopic image here is of kidney cells, which clearly have a nucleus, a membrane keeping the components of the cell contained, and a fluid within the cell called a cytoplasm.

The Cell: Somatic Cells and Gametes

Somatic cells
Body cells
Full DNA (humans: 46 chromosomes)
Mitosis
Gametes
Eggs (ova) and sperm
Half DNA (humans; 23 chromosomes)
Meiosis

There are two types of eukaryotic cells in all animals and plants: somatic cells and gametes. Somatic cells, also called body cells, are found all over the body. Shown in the above image are the somatic cells found in the (clockwise from top left) brain, blood, bone, and skin. Somatic cells all contain a complete copy of the organism’s DNA. For example, in humans, somatic cells have all of the DNA packed in 46 chromosomes. Somatic cells also replicate through a process called mitosis, which we will learn about in just a moment. At the bottom right is an image of the other kind of eukaryotic cells: gametes. The large round cell is called an egg, or an ova. The small wiggly structures surrounding the egg are sperm. These are gametes. They contain only half of the organism’s DNA (23 chromosomes in humans) and replicate through a process known as meiosis.

Chromosomes

DNA packaged in chromosomes
Chromosome number varies by species
Number of chromosomes does not correlate with complexity

Since we just mentioned chromosomes, it is worth examining chromosome number in a bit more detail. Humans have 46 chromosomes in our somatic cells. 23 of these came from our mother, and 23 from our father, for a grand total of 46. But, this number, 46, is not special at all. Other apes, like chimpanzees, have 48 chromosomes. Some primates have fewer chromosomes, like the colobus monkey which has 44. Some organisms we would consider to be less complex than us have fewer chromosomes, like the house fly with 12 or the salamander with 24. But, plenty of organisms have more than we have, like the potato with 48, the camel with 70, or algae, which has 148 chromosomes. Classifying organisms by the number of chromosomes they have would be like organizing books in a library based on the number of pages they have, or by the color of its jacket cover. It wouldn’t make sense. What matters are not the number of chromosomes an organism has, but the similarity in DNA that is packaged in the chromosomes. For instance, humans and chimpanzees share about 98% of their DNA. This is remarkable, and, in some ways, indicates how important 2% of a difference can be.

DNA: The Blueprint of Life

• DNA

Genes

Chromosomes

Genome

• Nuclear DNA:

homoplasmic

• Mitochondrial DNA:

heteroplasmic

Most likely, you have all heard of DNA, and have probably heard that it is the “blueprint,” or “recipe,” or “code” for life? But, how does this work? It helps first to understand the structure of DNA, and to understand how it is packaged in your cells. It is estimated that there is six feet worth of DNA in every cell in your body. Six feet!? If cells are microscopic, how can this be? As shown in this image, the DNA molecule is wound up into compact structures that we have already encountered: chromosomes. Sections of that DNA specifically code for a specific protein in the body: These are called genes. The genome is all of the genes put together in all of the chromosomes. The DNA that is in the nucleus of our cells is called homoplasmic, meaning it is more or less the exact same in every cell in our body. But, the nucleus is not the only place in a cell that contains DNA. An organelle called the mitochondria also contains DNA. Mitochondrial DNA (mtDNA) is much, much smaller; it only contains 37 genes. And these genes are only inherited from your mother, meaning they can be used to trace one’s maternal lineage (called a matriline). Unlike nuclear DNA, mitochondrial DNA can differ from cell to cell, making it heteroplasmic.

DNA: The Blueprint of Life

DNA structure
Sugar
Phosphate
Nucleotide base
Adenine (A)
Thymine (T)
Guanine (G)
Cytosine (C)
A with T
C with G
CAAAT
GTTTA

We are finally ready to discuss what DNA actually is. It is a molecule; in fact, a very simple one. DNA is made of three things: a type of sugar, a phosphate group, and a nucleotide base pair. The sugar and phosphate form the backbone of the long DNA molecule and these do not vary along the chain. What varies along the chain are the nucleotide base pairs. These bases can be one of four types: adenine (A), thymine (T), guanine (G) and cytosine (C). You can think of DNA as a ladder with the sugar and phosphates forming the uprights, and the bases forming the rungs. The rungs are made of two base pairs that cling together using hydrogen bonds. Critical to understanding DNA is the fact that the base pairs do not randomly cling to each other. Instead, A only clings to T, and C only clings to G. These are called complementary bases. What this means is, if you know one side of the DNA chain, you know the other. If a DNA sequence is CAAAT, the other side MUST be GTTTA. Though any two humans may have over 99% of their DNA base pair order identical, there are, of course, differences. Differences in these single nucleotide regions are called SNPs (pronounced “snips” and short for single nucleotide polymorphisms). These are some of the areas of the genome that can be used to solve crimes using DNA evidence since they can vary from one individual to another.

The DNA Molecule: Replicating the Code

The very structure of DNA explains how it is so easily, and so accurately, replicated. When a cell is going to divide, it copies its entire genome. Remember those nucleotide base pairs? Well, there are 3 billion of them to copy each time a cell divides. And cells divide all the time. It happened when you went from a single fertilized zygote to two cells, to four, eight, sixteen and onwards until you were several trillion cells worth of newborn baby. It continues to happen as old cells divide to form replacement cells. Each time, the DNA faithfully replicates. DNA replicates so easily and accurately because of those As, Gs, Cs, and Ts we discussed a moment ago. A double stranded DNA molecule is unwound by enzymes, and the hydrogen bonds connecting the complementary base pairs are broken. What results are two template strands that have so-called sticky ends. Free floating nucleotide base pairs in the nucleus of the cell (which are acquired through the foods we eat- which have their own DNA), bind to the template strands following the rule of base pairs: A goes with T and C goes with G. In this case CTAT is separated from GATA. These sticky ends become templates to form two new strands that are identical to one another. Again, it is the very structure of DNA that explains how copies of it can be made. We often say that the replication process produces identical copies of DNA, but that is not entirely true. Copying mistakes can occasionally occur- yet another source for genetic variation.

Chromosome Types

Homologous pairs
Autosomes (22 pairs)
Sex chromosomes (1 pair)
X and Y
Male determines sex
Karyotype

Before we get into the nuts and bolts of mitosis, let’s consider those chromosomes one last time. In order to make sure that each copy of the full sequence of DNA gets into each cell, the chromosomes must pair up and replicate. 23 of these chromosomes were inherited from the mother, and 23 from the father and each chromosome number (1 to 23) are different in their length and the genes they contain. These chromosomes pair up into matching, or homologous pairings, in the somatic cells. Though these chromosome pairs (shown in the top image) may look identical, they may very well contain different versions of a gene (known as alleles), since one chromosome was inherited from the mother and the other from the father. 22 of the 23 homologous pairs of chromosomes are what are referred to as autosomes. The other pair determines the sex of the individual and are appropriately named the sex chromosomes X and Y. Females have two X chromosomes, one inherited from their mother and one from their father. Males have an X and a Y—the X from their mother and the Y from their father. Because females have two X chromosomes, they can only contribute an X in the egg cell they produce. Because the male has both an X and a Y, there is a 50-50 chance that a sperm will contain an X or a Y. It is therefore true that the male “determines” the sex of a child by either contributing an X (and therefore producing a female) or a Y (and therefore producing a male), though of course this is not a conscious decision the sperm cells make. One way to visualize the homologous chromosomes is to produce what is called a karyotype—this is shown in the bottom right of the slide. Notice the 22 homologous pairs of autosomes numbered according to their size, and last the sex chromosomes. Based on what you see here, is this karyotype from a female or a male?

LET THE STUDENTS THINK ABOUT THIS AND THEN DISCUSS (THIS IS A FEMALE KARYOTYPE SINCE THERE ARE TWO X CHROMOSOMES)

Mitosis

You started as a single fertilized egg, called a zygote. It had 46 chromosomes. Cells with this full set of chromosomes (46) are called diploid. As we’ll soon see, cells with half the number of chromosomes (23) are called haploid. These are the egg and sperm cells, and there is a very obvious reason that they have half the number of chromosomes, which we’ll encounter in just a moment. But, back to that zygote. During embryological development, this little zygote divided to form 2, 4, 8, 16, 32, 64, and eventually trillions of cells. These cells soon form tissues and organs in a process known as embryological development. If the DNA divided as the cells do, your chromosomes would go from 46 to 23 to 11.5 to 5.75. Of course, this did not happen. Instead, every cell contains 46 chromosomes. This occurs because, as we already discussed, DNA can replicate itself and does so before each cell division so that the cell goes from 46 chromosome to 92 before dividing into two cells, each with 46 chromosomes. The process by which this occurs is called mitosis.

Mitosis

As shown in this figure, mitosis starts with a single diploid cell that has 23 pairs or homologous chromosomes (or 46 chromosomes). These chromosomes duplicate by unwinding their DNA and attaching free nucleotide bases to the template strands in the manner already discussed. After chromosome duplication, the cells technically have 92 chromosomes, which all line up in the middle of the cells so that one full set is on one side and another full set is on the other side of the cell midline. The cell pulls apart into two daughter cells, each with identical DNA. The microscopic image is of skin cells dividing into two daughter cells. Each of these cells has 23 pairs of homologous chromosomes (or 46 total).

Meiosis

Haploid—23 chromosomes (no pairs)
Recombination via crossing-over
Haplotypes

Translocations and nondisjunctions

If an egg cell had 46 chromosomes and a sperm had 46 chromosomes, the resulting zygote would have 92 chromosomes. This simply would not work. So, gametes have to divide up the DNA a bit differently than somatic cells do. Instead of having a full copy of the organism’s DNA, gametes are haploid, meaning they only contain one chromosome from each pair of chromosomes. This one can be inherited from the mother or the one inherited from the father. With 23 chromosomes, the number of different combinations is exceptionally high, meaning that each egg and each sperm cell contains a unique combination of genes from the organisms’ mother and father. The process by which this occurs is called meiosis. Meiosis starts the same way as mitosis. The DNA replicates and the homologous chromosomes pair up. The cells then divide into two identical daughter cells, just as happens in mitosis. However, unlike mitosis, the cells then divide again, resulting in four daughter cells each with 23 chromosomes, but no pairs. Right before that final cell division, the homologous chromosomes can recombine their chromosomes in a process called crossing-over. A chunk of chromosome 2 from the mother’s line can switch with a chunk of chromosome 2 from the father’s line. So, not only are the 23 chromosomes in the gametes a random assortment of chromosomes from the mother and from the father, but within each chromosome there will be a combination of genes from the individual’s mother and father. Genes that are close together on a chromosome therefore tend to move together and cluster together. These clusters of genes are called haplotypes, which can be used to assess the history of genetic lineages. If chunks of DNA are exchanged on non-homologous chromosomes (called translocations) diseases such as leukemia can result. If the chromosomes fail to divide, the resulting gametes can have too few or too many chromosomes. Too few can result in a monosomy, and too many, a trisomy. Down syndrome is an example of a trisomy, in which there are three rather than two copies of chromosome 21.

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