Figure 2.15
(D) DNA (nucleic acid).
The
Figure 2.16
A healthy diet includes protein, fat, and carbohydrate.
Enzyme Reactions
The oxidation reaction occurs readily, but not all reactions move so quickly. Others can take quite a while. Since many of the body’s necessary chemical reactions would take years to happen on their own, you need the help of enzymes. Enzymes speed up chemical reactions, often by bringing the reactants closer together so they can interact more easily (Figure below). Enzymes attach to, or bind, specifically to the reactants. Because enzymes are so specific, you have a different enzyme for every chemical reaction in your body. A single cell may contain hundreds or thousands of different enzymes.
When an enzymes attaches, or binds, to another molecule, that molecule is referred to as the substrate. The enzyme is usually much bigger than the substrate.
Figure 2.17
The enzyme (green) binds to the substrate (red) to speed up a chemical reaction.
How Enzymes Work
How do enzymes speed up biochemical reactions so dramatically? Like all catalysts, enzymes work by lowering the activation energy of chemical reactions. This is illustrated in Figure below. The biochemical reaction shown in the figure requires about three times as much energy without the enzyme as it does with the enzyme. An animation of this process can be viewed at http://www.stolaf.edu/people/giannini/flashanimat/enzymes/transition%20state.swf.
Figure 2.18
The reaction represented by this graph involves the reactants glucose (CHO) and oxygen (O). The products of the reaction are carbon dioxide (CO) and water (HO). Energy is also released during the reaction. The enzyme speeds up the reaction by lowering the activation energy needed for the reaction to start. Compare the activation energy with and without the enzyme.
As discussed above, enzymes lower activation energy by reducing the energy needed for reactants to come together and react. For example:
Enzymes bring reactants together so they don’t have to expend energy moving about until they collide at random. Enzymes bind both reactant molecules (called substrate), tightly and specifically, at a site on the enzyme molecule called the active site (Figure below).
By binding reactants at the active site, enzymes also position reactants correctly, so they do not have to overcome the forces that would otherwise push them apart. This allows the molecules to interact with less energy.
Figure 2.19
This enzyme molecule binds reactant moleculescalled substrateat its active site, forming an enzyme-substrate complex. This brings the reactants together and positions them correctly so the reaction can occur. After the reaction, the products are released from the enzymes active site. This frees up the enzyme so it can catalyze additional reactions.
The activities of enzymes also depend on the temperature, ionic conditions, and the pH of the surroundings.
Some enzymes work best at acidic pHs, while others work best in neutral environments.
Digestive enzymes secreted in the acidic environment (low pH) of the stomach help break down proteins into smaller molecules. The main digestive enzyme in the stomach is pepsin, which works best at a pH of about 1.5 (see the Digestive and Excretory Systems chapter). These enzymes would not work optimally at other pHs. Trypsin is another enzyme in the digestive system which break protein chains in the food into smaller parts. Trypsin works in the small intestine, which is not an acidic environment. Trypsin's optimum pH is about 8.
Biochemical reactions are optimal at physiological temperatures. For example, most biochemical reactions work best at the normal body temperature of 98.6˚F. Many enzymes lose function at lower and higher temperatures. At higher temperatures, an enzyme’s shape deteriorates and only when the temperature comes back to normal does the enzyme regain its shape and normal activity.
Lesson Summary
Elements are substances that cannot be broken down into simpler substances with different properties.
Elements have been organized by their properties to form the periodic table.
Two or more atoms can combine to form a molecule.
Molecules consisting of more than one element are called compounds.
Reactants can combine through chemical reactions to form products.
Enzymes can speed up a chemical reaction.
Living things are made of just four classes of macromolecules: proteins, carbohydrates, lipids, and nucleic acids.
Review Questions
What is density?
What are the 4 main classes of organic compounds?
Would water, with the symbol H2O, be considered an element or a compound?
How many types of atoms make up gold?
Why do you need fats in your diet?
Sugar is what kind of organic compound?
What is an atom?
What monomers make up proteins?
Name a few examples of proteins.
Name a few examples of lipids in organisms.
What are two nucleic acids?
Further Reading / Supplemental Links
http://ghr.nlm.nih.gov/handbook/howgeneswork/protein
http://ghr.nlm.nih.gov/handbook/basics/dna
http://publications.nigms.nih.gov/thenewgenetics/chapter1.html
Vocabulary
amino acids
Monomers that combine to make protein chains.
atom
The simplest and smallest particle of matter that still retains the physical and chemical properties of the element; the building block of all matter.
ATP
Adenosine triphosphate, the energy "currency" of the cell.
carbohydrates
Class of organic compound that includes sugar, starch, cellulose and chitin.
electron
A negatively charged particle in the atom, found outside of the nucleus.
element
A substance that cannot break down into a simpler substance with different properties.
enzyme
Protein that speeds up a chemical reaction by binding to the reactants (substrates).
functional groups
Groups of atoms that give a compound its unique chemical properties.
lipids
Class of organic compound that includes fats, oils, waxes and phospholipids.
matter
Anything that takes up space and has mass.
neutrons
The non-charged particle of the atom; located in nucleus of the atom.
nucleic acid
Class of organic compound that includes DNA and RNA.
organic compounds
Compounds made up of a carbon backbone and associated with living things.
phospholipids
Lipid molecule that makes up cell membranes.
product
The end result formed from a chemical reaction.
protein
Class of organic compound consisting of a chain of amino acids; includes enzymes and antibodies.
Proton
The positively charged particle of the atom; located in nucleus of the atom.
Reactants
The raw ingredients in a chemical reaction.
Waxes
A water-proof lipid.
Points to Consider
Do you expect the genetic information in the DNA of a cow to be the same or different from that in a crow?
If we are all composed of the same chemicals, how do all organisms look so different?
What characteristics would you use to distinguish and classify living things?
Lesson 2.3: Classification of Living Things
Lesson Objectives
Explain what makes up a scientific name.
Explain what defines a species.
List the information scientists use to classify organisms.
List the three domains of life and the chief characteristics of each.
Check Your Understanding
What are the basic characteristics of life?
What are the four main classes of organic molecules that are building blocks of life?
Introduction
When you see an organism that you’ve never seen before, you probably automatically classify it into a specific group. If it’s green and leafy, you would probably call it a plant. If it’s long and slithers, you would probably classify it as a snake. How do you make such assignments? You look at the physical features of the organism and think about what it has in common with other organisms. Scientists do the same thing when they classify living things. But scientists classify organisms not only by their physical features, but also by their evolutionary history and relatedness. Lions and tigers look like each other more than they look like bears. But it's not just appearance. The two cats are actually more closely related to each other than to bears. How related organisms are is an important basis for classifying them.
Classifying Organisms
People have been concerned with classifying organisms back to the time of the Greeks and Romans. The Greek philosopher Aristotle developed a classification system that divided living things into several groups that we still use today, including mammals, insects, and reptiles. Carl Linnaeus (1707-1778) (Figure below) built on Aristotle’s work to produce his own extensive classification system and invented the way we name organisms by their genus and species. For example, a coyote's species name is Canis latrans. "Latrans" is the species and "canis" is the genus, a larger group that includes dogs, wolves, and other dog-like animals. Linnaeus is considered the inventor of modern taxonomy, the science of naming and grouping organisms. He was especially interested in plants, and he used differences in flowers to classify each plant into groups. Modern taxonomists have reordered many groups of organisms since Linnaeus. The main categories biologists use are listed here from the most specific to the broadest category (Figure below). In other words, there are many species in each genus, many genera (plural for "genus") in each family, and so on. The broadest and most inclusive category is the domain. It is currently believed that there are three domains and six kingdoms. We will discuss these groups more later.
Figure 2.20
In the 18th century, Carl Linnaeus invented the two-name system of naming organisms (genus and species) and introduced the most complete classification system then known.
Figure 2.21
This diagram illustrates the classification categories for organisms, with the broadest category (Life) at the bottom, and the most specific category (Species) at the top.
But how do taxonomists decide what domain or family an organism belongs to? Like Linnaeus, they still look at the physical features of the organisms and group organisms that look similar together (Figure below). But taxonomists also try to piece together evolutionary relationships when assigning organisms to a specific group. By looking at fossils, ancient remains of living things, they can tell if organisms share a recent common ancestor--sort of like a "grandparent" species. A common ancestor is an ancestor shared by two groups of organisms. For example lions and tigers share a common ancestor; both species are descended from an ancient cat. If two species share a recent common ancestor, it means they are closely related and they will be placed in the same group.
Another way to determine evolutionary relationships is by looking for similarities or differences in organisms’ DNA. The number of differences in two organisms’ DNA can show how closely related the two organisms are. You might expect, for example, that human DNA is more similar to chimpanzee DNA than to bacterial DNA. (And it is.) How biologists determine evolutionary history will be discussed in more detail in the Evolution chapter.
Figure 2.22
Darwin suggested that these Galapagos Island finches share a common ancestor and evolved different beaks because they were eating different foods. Modern research confirms this hypothesis.
Naming Organisms
Carl Linnaeus recognized a need for a system of names for each species. If we just used common names, we would have many different names in many different languages for the same species. To solve this problem, Linnaeus developed binomial nomenclature, a way to give a scientific name to every organism. Each species receives a two-part name in which the first word is the genus (a group of species) and the second word refers to one species in that genus. For example, the red maple, Acer rubra, and the sugar maple, Acer saccharum, are both in the same genus (Figures below, below and below). Notice that the genus is capitalized and the species is not, and that the whole scientific name is in italics. The names are nearly always in Latin, the universal language of scholars throughout European history. Sometimes, biologists use Greek or other words. For example, Microtus pennsylvanicus is a species of mouse in Pennsylvania and nearby states.
Figure 2.23
Figure 2.24
Figure 2.25
These leaves in the top and middle photographs are from two different species trees in the Acer, or maple, genus. One of the characteristics of the maple genus is winged seeds (bottom).
Even though naming species is straightforward, deciding if two organisms are the same species can sometimes be difficult. Linnaeus defined each species by the distinctive physical characteristics shared by these organisms. But two members of the same species may look quite different. For example, people from different parts of the world sometimes look very different, but we are all the same species (Figure below ).
So how is a species defined? A species is group of individuals that can interbreed with one another and produce fertile offspring; a species does not interbreed with other groups. By this definition, two species of animals or plants that do not interbreed are not the same species. For example, tigers and lions can mate in zoos and produce kittens that are half tiger and half lion. But we still consider tigers and lions separate species. The two cats look and behave differently and are not known to interbreed in the wild, even though they can. Groups of lions and tigers do not interbreed.
Figure 2.26
These children are all members of the same species, .
Domains of Life
All life can be divided into 3 domains: Bacteria, Archaea, and Eukarya (Figures below, below and below). This is the largest and least specific classification, so the organisms might not look much alike, but they do have some very important traits in common. For example, you might be surprised that mushrooms, plants, and people are all in the same domain. But when you look at the cells of mushrooms, plants, and people, you will see that they do have some similar features. They are all eukaryotic organisms, or in the domain Eukarya. The other two domains are composed of prokaryotic organisms. Prokaryotic and eukaryotic cells will be discussed in the chapter titled Cells and Their Functions.
Figure 2.27
The "Group D" Streptococcus organism is in the domain , one of the three domains of life.
Figure 2.28
The Halobacterium is in the domain , one of the three domains of life.
Figure 2.29
The Western Gray Squirrel is in the domain , one of the three domains of life.
All the cells in the domain Eukarya keep their DNA inside a membrane, a structure called the nucleus. The cells of other domains have DNA, but it is not inside a nucleus. The domain Eukarya is made up of four diverse kingdoms: plants, fungi, animals, and protists.
Plants, such as trees and grasses, survive by capturing energy from the sun, a process called photosynthesis. Animals survive by eating other organisms or the remains of other organisms. Animals range from tiny worms to insects, dogs, and the largest dinosaurs and whales. Fungi, such as mushrooms and molds, also survive by eating other organisms or the remains of other organisms. The last group listed here are the protists. Protists are not all descended from a single common ancestor in the way that plants, animals, and fungi are. Protists are a sort of miscellaneous group; they are all the organisms that are not something else. Protists are a diverse group of organisms that include many kinds of microscopic o
ne-celled organisms, such as algae and plankton, but also giant seaweeds that can grow to be 200 feet long (an alga protist is shown in Figure below). Plants, animals, fungi, and protists might seem very different, but remember that if you look through a microscope, you would find cells with a membrane-bound nucleus in all them.
Figure 2.30
This microscopic alga is a protist in the domain Eukarya.
The cells of the two other domains - the Archaea and the Bacteria - do not have a nucleus. All the cells in both domains are tiny, microscopic one-celled organisms that can reproduce without sex by dividing in two. The difference between the archaea and the bacteria is in their cell walls. Also, archaea often live in extreme environments like hot springs, geysers, and salt flats, while bacteria are abundant and live almost everywhere. A teaspoon of soil can contain 100 million to a billion individual bacteria. Bacteria obtain energy in lots of different ways. Some infect plants and animals and cause disease. Others break down dead organisms. The cyanobacteria photosynthesize, like plants. In fact, the ancestors of today's cyanobacteria invented photosynthesis more than two billion years ago.
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