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4.22: Introduction to Atomic Bonds - Biology

4.22: Introduction to Atomic Bonds - Biology


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Classify different types of atomic bonds

When atoms bond together, they create elements. Understanding the types of bonds that create things can help us understand those things themselves.

What You’ll Learn to Do

  • Describe the characteristics of ionic bonds and identify common ions
  • Describe the characteristics of covalent bonds and differentiate between polar and non-polar bonds
  • Model a Hydrogen bond and identify its unique qualities

Learning Activities

The learning activities for this section include the following:

  • Ionic Bonds
  • Covalent Bonds
  • Hydrogen Bonds
  • Self Check: Atomic Bonds

Chapter 4. Carbohydrates

Image 4.1 Foods such as grains, vegetables, fruits, beans, and sugary sweets are all rich in carbohydrates. (Credit: “gigantfotos”/Unsplash.)
  • Monosaccharides
  • Disaccharides
  • Polysaccharides
  • The Functions and Benefits of Carbohydrates

Most people are familiar with carbohydrates, one type of macromolecule, especially when it comes to what we eat. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have enough energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. Carbohydrates also have other important functions in humans, animals, and plants.

Carbohydrates can be represented by the chemical formula (CH2O)n, where n is the number of carbons in the molecule. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This formula also explains the origin of the term “carbohydrate”: the components are carbon (“carbo”) and the components of water (hence, “hydrate”). Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.


Introduction to PDB Data

The PDB archive is a repository of atomic coordinates and other information describing proteins and other important biological macromolecules. Structural biologists use methods such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy to determine the location of each atom relative to each other in the molecule. They then deposit this information, which is then annotated and publicly released into the archive by the wwPDB.

The constantly-growing PDB is a reflection of the research that is happening in laboratories across the world. This can make it both exciting and challenging to use the database in research and education. Structures are available for many of the proteins and nucleic acids involved in the central processes of life, so you can go to the PDB archive to find structures for ribosomes, oncogenes, drug targets, and even whole viruses. However, it can be a challenge to find the information that you need, since the PDB archives so many different structures. You will often find multiple structures for a given molecule, or partial structures, or structures that have been modified or inactivated from their native form.

Guide to Understanding PDB Data is designed to help you get started with charting a path through this material, and help you avoid a few common pitfalls. These chapters are intertwined with one another. To begin, select a topic from the right menu, or select a topic from below:

The primary information stored in the PDB archive consists of coordinate files for biological molecules. These files list the atoms in each protein, and their 3D location in space. These files are available in several formats (PDB, mmCIF, XML). A typical PDB formatted file includes a large "header" section of text that summarizes the protein, citation information, and the details of the structure solution, followed by the sequence and a long list of the atoms and their coordinates. The archive also contains the experimental observations that are used to determine these atomic coordinates.

While you can view PDB files directly using a text editor, it is often most useful to use a browsing or visualization program to look at them. Online tools, such as the ones on the RCSB PDB website, allow you to search and explore the information under the PDB header, including information on experimental methods and the chemistry and biology of the protein. Once you have found the PDB entries that you are interested in, you may use visualization programs to allow you to read in the PDB file, display the protein structure on your computer, and create custom pictures of it. These programs also often include analysis tools that allow you to measure distances and bond angles, and identify interesting structural features.

When you start exploring the structures in the PDB archive, you will need to know a few things about the coordinate files. In a typical entry, you will find a diverse mixture of biological molecules, small molecules, ions, and water. Often, you can use the names and chain IDs to help sort these out. In structures determined from crystallography, atoms are annotated with temperature factors that describe their vibration and occupancies that show if they are seen in several conformations. NMR structures often include several different models of the molecule.

You may run into several challenges as you explore the PDB archive. For example, many structures, particular those determined by crystallography, only include information about part of the functional biological assembly. Fortunately the PDB can help with this. Also, many PDB entries are missing portions of the molecule that were not observed in the experiment. These include structures that include only alpha carbon positions, structures with missing loops, structures of individual domains, or subunits from a larger molecule. In addition, most of the crystallographic structure entries do not have information on hydrogen atoms.

About PDB-101

PDB-101 helps teachers, students, and the general public explore the 3D world of proteins and nucleic acids. Learning about their diverse shapes and functions helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy.

Why PDB-101? Researchers around the globe make these 3D structures freely available at the Protein Data Bank (PDB) archive. PDB-101 builds introductory materials to help beginners get started in the subject ("101", as in an entry level course) as well as resources for extended learning.


Plastics and Covalent Chemical Bonds

In this lesson, we discuss the distribution of electrons in a carbon atom, introduce the students to examples of plastic materials made from organic compounds, explore environmentally safe materials that can mimic the same properties of plastic and explore the effects of bacteria and fungi on plastic materials. It is important that students are familiar with the periodic table of elements. The video is 25 minutes long with approximately 20 minutes of activities. Students should be prepared with pen and paper as they will be asked to draw electron distribution and ethane/propane.


Hair Biology & Bonds

Your hair is composed of keratin, a strong fibrous protein, and is built from cells similar to those of your skin. The average number of hairs on the human scalp is 120,000, although blondes tend to have more and redheads less. Hair is a remarkable fibre.

A healthy hair can stretch up to 30% of its length, can absorb its weight in water and swell up to 20% of its diameter. A single scalp hair can hold a weight of 100g and an average head of hair twisted together can support 23 tons. However, this is only if your hair is in good condition!

Disulphide and Hydrogen Bonds

‘Disulphide bonds are one of the strongest naturally-occurring bonds in nature.’ The protein structures of the hair shaft are held together by chemical bonds called disulphide and hydrogen bonds.

While the curliness (or straightness) of your hair depends on the shape of the follicle, it’s the disulphide bonds that keep the hair in the shape it was formed, and they can only be altered by perming or relaxing.

Disulphide bonds also give your hair its elasticity and strength. Hydrogen bonds, on the other hand, are easily broken by the application of water and can be temporarily reset with heat until they become wet again (either from washing or humidity).


Perceiving Depth

Depth perception is the ability to perceive three-dimensional space and to accurately judge distance. Without depth perception, we would be unable to drive a car, thread a needle, or simply navigate our way around the supermarket (Howard & Rogers, 2001). Research has found that depth perception is in part based on innate capacities and in part learned through experience (Witherington, 2005).

Psychologists Eleanor Gibson and Richard Walk (1960) tested the ability to perceive depth in 6- to 14-month-old infants by placing them on a visual cliff , a mechanism that gives the perception of a dangerous drop-off, in which infants can be safely tested for their perception of depth (Figure 4.22 “Visual Cliff”). The infants were placed on one side of the “cliff,” while their mothers called to them from the other side. Gibson and Walk found that most infants either crawled away from the cliff or remained on the board and cried because they wanted to go to their mothers, but the infants perceived a chasm that they instinctively could not cross. Further research has found that even very young children who cannot yet crawl are fearful of heights (Campos, Langer, & Krowitz, 1970). On the other hand, studies have also found that infants improve their hand-eye coordination as they learn to better grasp objects and as they gain more experience in crawling, indicating that depth perception is also learned (Adolph, 2000).

Depth perception is the result of our use of depth cues , messages from our bodies and the external environment that supply us with information about space and distance. Binocular depth cues are depth cues that are created by retinal image disparity—that is, the space between our eyes, and thus which require the coordination of both eyes. One outcome of retinal disparity is that the images projected on each eye are slightly different from each other. The visual cortex automatically merges the two images into one, enabling us to perceive depth. Three-dimensional movies make use of retinal disparity by using 3-D glasses that the viewer wears to create a different image on each eye. The perceptual system quickly, easily, and unconsciously turns the disparity into 3-D.

An important binocular depth cue is convergence , the inward turning of our eyes that is required to focus on objects that are less than about 50 feet away from us. The visual cortex uses the size of the convergence angle between the eyes to judge the object’s distance. You will be able to feel your eyes converging if you slowly bring a finger closer to your nose while continuing to focus on it. When you close one eye, you no longer feel the tension—convergence is a binocular depth cue that requires both eyes to work.

The visual system also uses accommodation to help determine depth. As the lens changes its curvature to focus on distant or close objects, information relayed from the muscles attached to the lens helps us determine an object’s distance. Accommodation is only effective at short viewing distances, however, so while it comes in handy when threading a needle or tying shoelaces, it is far less effective when driving or playing sports.

Although the best cues to depth occur when both eyes work together, we are able to see depth even with one eye closed. Monocular depth cues are depth cues that help us perceive depth using only one eye (Sekuler & Blake, 2006). Some of the most important are summarized in Table 4.2 “Monocular Depth Cues That Help Us Judge Depth at a Distance”.

Table 4.2 Monocular Depth Cues That Help Us Judge Depth at a Distance


Common Elements


Let's work with the alphabet idea again. If you read a book, you will find words on each page. Letters make up those words. In English, we only have twenty-six letters, but we can make thousands of words. In chemistry, you are working with almost 120 elements. When you combine them, you can make millions of different molecules.

Molecules are groups of atoms in the same way that words are groups of letters. An "A" will always be an "A" no matter what word it is in. A sodium (Na) atom will always be a sodium atom no matter what molecule it is in. While atoms from different elements have different masses and structures, they are all built with the same parts. Electrons, protons, and neutrons are the basic subunits for all atoms across the Universe.


4.22: Introduction to Atomic Bonds - Biology


This lesson will introduce you the student to basic chemistry principles. An understanding of this basic information will allow you to learn the more advanced topics in your course lectures.

This lesson focuses on a number of areas related to basic Chemistry. You should review each page in order as they build upon one another. Many of these topics will be review. Others may be new to you. Either way you will learn the fundamentals of chemistry needed in this course.

Atoms are the basic unit of chemistry. They consist of 3 smaller things:

  • Protons - these are positively charged (+)
  • Electrons - these are negatively charged (-)
  • Neutrons - these have no charge

These 3 smaller particles are arranged in a particular way. In the center is the Nucleus where you find the positive Protons and neutral Neutrons.

In orbit around the nucleus are the Electrons. These are found in a series of orbits (depending on the atom) with differing numbers of electrons as seen below.

Interaction of Atoms

It's the electrons in orbit around the nucleus that allow one atom to interact with other atoms so they can be linked together.

For example, H2O consists of an Oxygen atom linked to 2 Hydrogen atoms. The linkage or interaction between the electrons of the Hydrogen and Oxygen atoms is called a Chemical Bond. More on these later.

Atoms in the Human Body

The human body is made up of a couple dollars worth of chemicals.

The 12 most useful atoms for you to know about are listed below:

Sometimes atoms gain or lose electrons. The atom then loses or gains a "negative" charge. These atoms are then called ions.

  • Positive Ion - Occurs when an atom loses an electron (negative charge) it has more protons than electrons.
  • Negative Ion - Occurs when an atom gains an electron (negative charge) it will have more electrons than protons.

The following image shows Na losing an electron and Cl gaining an electron


4.22: Introduction to Atomic Bonds - Biology

Chemistry Based Animations

These animations support the teaching of concepts in chemistry in freshman through graduate level courses. Some of the QuickTime movie are without audio, and some of the audio--from a few of the sound augmented QuickTime movie--has been stripped and made available in Real Audio's streaming audio format. The chemistry courses that profit from these sorts of multimedia content include instrumental analysis, environmental chemistry, atmospheric chemistry and air quality. The gold foil experiment movie augments a completely on-line freshman chemistry course.

Animations By Thomas G. Chasteen, Analytical Environmental Chemistry, Sam Houston State University

Delights of Chemistry

Animations (Department of Chemistry, University of Leeds)

Chemical Reaction Animations

Animations (University of Texas, Austin)

Chemistry Quicktime Multimedia

Animated Catalytic reactions, Interesting Molecules, Explosive Chemistry, Multimedia Chemistry.

Animations (Department of Chemistry, University of Oxford)

Chemistry Video Collection

Chemistry comes alive! Bring chemistry to life - spark an interest.

Videos (Journal of Chemical Education)

Educational Materials in Organic Chemistry

Quicktime Animations organized by Lecture Topic

Acids, Alkalis and Neutralization

Aqueous Equilibrium Animations

Atom Builder

Build a carbon atom out of quarks and electrons, but watch out for radioactive decay.

Chemical Bonds

Because of the tendency of atoms to complete their outer energy shells with the stable number of electrons for each shell, atoms with incomplete shells have a tendency to gain electrons, lose electrons or share electrons. Atoms that have gained or lost electrons become ions. Oppositely charged ions form ionic bonds. Atoms that share electrons form covalent bonds. A much weaker, but very important bond in biological systems is the hydrogen bond.

Northland Community and Technical College

Essential Chemistry

Rutherford's Experiment, Limiting Reagent, Molecular View, Properties of Gases, Line Spectra, Atomic Radii, Hybridization, Vapor Pressure, Sphere Packing - Simple Cubic Packing, Sphere Packing - Body Centered Cubic Packing, Sphere Packing - Cubic Close Packing, Activation Energy, Orientation of Collision, Le Chatelier's Principle, Acid Ionization, Buffers, Galvanic Cell, Radioactive Decay.

Chirality - Chemistry 2001

The Nobel Prize in Chemistry 2001 concerns work with chiral molecules. These chiral molecules can be used to control or speed up different chemical reactions. In this game you can learn the basic principles of chirality.

Creative Chemistry

Whether you are a teacher, doing chemistry at school, or are simply just interested in chemistry, Creative Chemistry has lots for you.


Dissolving, Dissociating, and Diffusing

Ionic and covalent compounds also differ in what happens when they are placed in water, a common solvent. For example, when a crystal of sodium chloride is put into water, it may seem as though the crystal simply disappears. Three things are actually happening.

  1. A large crystal (Fig. 2.33 A) will dissolve, or break down into smaller and smaller pieces, until the pieces are too small to see (Fig. 2.33 B).
  2. At the same time, the ionic solid dissociates, or separates into its charged ions (Fig 2.33 C).
  3. Finally, the dissociated ions diffuse, or mix, throughout the water (Fig 2.34).

Ionic compounds like sodium chloride dissolve, dissociate, and diffuse. Covalent compounds, like sugar and food coloring, can dissolve and diffuse, but they do not dissociate. Fig. 2.34, is a time series of drops of food coloring diffusing in water. Without stirring, the food coloring will mix into the water through only the movement of the water and food coloring molecules.

Dissociated sodium (Na + ) and chloride (Cl - ) ions in salt solutions can form new salt crystals (NaCl) as they become more concentrated in the solution. As water evaporates, the salt solution becomes more and more concentrated. Eventually, there is not enough water left to keep the sodium and chloride ions from interacting and joining together, so salt crystals form. This occurs naturally in places like salt evaporation ponds (Fig. 2.35 A), in coastal tidepools, or in hot landlocked areas (Fig. 2.35 B). Salt crystals can also be formed by evaporating seawater in a shallow dish, as in the Recovering Salts from Seawater Activity.


Watch the video: Introduction to Covalent Bonds (May 2022).