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The Molecules of Life: Physical and Chemical Properties

Cells are made of many complex molecules called macromolecules, such as proteins, nucleic acids RNA and DNA , carbohydrates, and lipids. The macromolecules are a subset of organic molecules any carbon-containing liquid, solid, or gas that are especially important for life. The fundamental component for all of these macromolecules is carbon. Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6 six electrons and six protons , the first two electrons fill the inner shell, leaving four in the second shell.

Therefore, carbon atoms can form up to four covalent bonds with other atoms to satisfy the octet rule. The methane molecule provides an example: it has the chemical formula CH 4.

Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell.

Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane CH 4 described above. We often use hydrocarbons in our daily lives as fuels—like the propane in a gas grill or the butane in a lighter. The many covalent bonds between the atoms in hydrocarbons store a great amount of energy, which is released when these molecules are burned oxidized.

The geometry of the methane molecule, where the atoms reside in three dimensions, is determined by the shape of its electron orbitals. The carbons and the four hydrogen atoms form a shape known as a tetrahedron, with four triangular faces; for this reason, methane is described as having tetrahedral geometry. As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both.

Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds, and each type of bond affects the geometry of the molecule in a specific way. This three-dimensional shape or conformation of the large molecules of life macromolecules is critical to how they function. Hydrocarbon chains are formed by successive bonds between carbon atoms and may be branched or unbranched.

The hydrocarbons ethane, ethene, and ethyne serve as examples of how different carbon-to-carbon bonds affect the geometry of the molecule. Thus, propane, propene, and propyne follow the same pattern with three carbon molecules, butane, butane, and butyne for four carbon molecules, and so on.

Double and triple bonds change the geometry of the molecule: single bonds allow rotation along the axis of the bond, whereas double bonds lead to a planar configuration and triple bonds to a linear one.

These geometries have a significant impact on the shape a particular molecule can assume. So far, the hydrocarbons we have discussed have been aliphatic hydrocarbons , which consist of linear chains of carbon atoms.

Another type of hydrocarbon, aromatic hydrocarbons , consists of closed rings of carbon atoms. Examples of biological molecules that incorporate the benzene ring include some amino acids and cholesterol and its derivatives, including the hormones estrogen and testosterone. The benzene ring is also found in the herbicide 2,4-D. Benzene is a natural component of crude oil and has been classified as a carcinogen.

Some hydrocarbons have both aliphatic and aromatic portions; beta-carotene is an example of such a hydrocarbon. Biochemistry is the discipline that studies the chemistry of life, and its objective is to explain form and function based on chemical principles. Organic chemistry is the discipline devoted to the study of carbon-based chemistry, which is the foundation for the study of biomolecules and the discipline of biochemistry.

The most abundant element in cells is hydrogen H , followed by carbon C , oxygen O , nitrogen N , phosphorous P , and sulfur S.

Some elements, such as sodium Na , potassium K , magnesium Mg , zinc Zn , iron Fe , calcium Ca , molybdenum Mo , copper Cu , cobalt Co , manganese Mn , or vanadium Va , are required by some cells in very small amounts and are called micronutrients or trace elements.

All of these elements are essential to the function of many biochemical reactions, and, therefore, are essential to life. Unlike carbon, nitrogen forms up to three bonds, oxygen forms up to two, and hydrogen forms one. These traits in combination permit the formation of a vast number of diverse molecular species necessary to form the structures and enable the functions of living organisms. Living organisms contain inorganic compounds mainly water and salts and organic molecules.

Organic molecules contain carbon; inorganic compounds do not. Carbon oxides and carbonates are exceptions; they contain carbon but are considered inorganic because they do not contain hydrogen. The atoms of an organic molecule are typically organized around chains of carbon atoms.

They are small, simple compounds that play important roles in the cell, although they do not form cell structures. Most of the carbon found in organic molecules originates from inorganic carbon sources such as carbon dioxide captured via carbon fixation by microorganisms.

Organic molecules in organisms are generally larger and more complex than inorganic molecules. Their carbon skeletons are held together by covalent bonds. They form the cells of an organism and perform the chemical reactions that facilitate life. All of these molecules, called biomolecules because they are part of living matter, contain carbon, which is the building block of life. Carbon is a very unique element in that it has four valence electrons in its outer orbitals and can form four single covalent bonds with up to four other atoms at the same time.

The carbon skeleton of organic molecules can be straight, branched, or ring shaped cyclic. Organic molecules are built on chains of carbon atoms of varying lengths; most are typically very long, which allows for a huge number and variety of compounds. No other element has the ability to form so many different molecules of so many different sizes and shapes.

Molecules with the same atomic makeup but different structural arrangement of atoms are called isomers. The concept of isomerism is very important in chemistry because the structure of a molecule is always directly related to its function. Slight changes in the structural arrangements of atoms in a molecule may lead to very different properties. Chemists represent molecules by their structural formula, which is a graphic representation of the molecular structure, showing how the atoms are arranged.

Compounds that have identical molecular formulas but differ in the bonding sequence of the atoms are called structural isomers. Isomers that differ in the spatial arrangements of atoms are called stereoisomers; one unique type is enantiomers. The properties of enantiomers were originally discovered by Louis Pasteur in while using a microscope to analyze crystallized fermentation products of wine.

Enantiomers are molecules that have the characteristic of chirality, in which their structures are nonsuperimposable mirror images of each other. Many organisms are only able to use one enantiomeric form of certain types of molecules as nutrients and as building blocks to make structures within a cell. Some enantiomeric forms of amino acids have distinctly different tastes and smells when consumed as food. For example, L-aspartame, commonly called aspartame, tastes sweet, whereas D-aspartame is tasteless.

Drug enantiomers can have very different pharmacologic affects. For example, the compound methorphan exists as two enantiomers, one of which acts as an antitussive dextro methorphan, a cough suppressant , whereas the other acts as an analgesic levo methorphan, a drug similar in effect to codeine.

Enantiomers are also called optical isomers because they can rotate the plane of polarized light. Some of the crystals Pasteur observed from wine fermentation rotated light clockwise whereas others rotated the light counterclockwise.

The d and l labels are derived from the Latin words dexter on the right and laevus on the left , respectively. These two different optical isomers often have very different biological properties and activities. Certain species of molds, yeast, and bacteria, such as Rhizopus , Yarrowia , and Lactobacillus spp. Another important reason to be aware of optical isomers is the therapeutic use of these types of chemicals for drug treatment, because some microorganisms can only be affected by one specific optical isomer.

Biological macromolecules are large molecules, necessary for life, that are built from smaller organic molecules. There are four major classes of biological macromolecules carbohydrates, lipids, proteins, and nucleic acids ; each is an important cell component and performs a wide array of functions.

Biological macromolecules are organic, meaning they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, and additional minor elements. They also share the use of functional groups and nearly identical building and deconstructing reactions. In addition to containing carbon atoms, biomolecules also contain functional groups—groups of atoms within molecules that are categorized by their specific chemical composition and the chemical reactions they perform, regardless of the molecule in which the group is found.

R might symbolize just a single hydrogen atom or it may represent a group of many atoms. Notice that some functional groups are relatively simple, consisting of just one or two atoms, while some comprise two of these simpler functional groups. It is present in several classes of organic compounds as part of larger functional groups such as ketones, aldehydes, carboxylic acids, and amides. In ketones, the carbonyl is present as an internal group, whereas in aldehydes it is a terminal group.

Hydrogen bonds between functional groups within the same molecule or between different molecules are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Most macromolecules are made from single subunits, or building blocks, called monomers. The monomers combine with each other using covalent bonds to form larger molecules known as polymers.

In doing so, monomers release water molecules as byproducts. At the same time, the monomers share electrons and form covalent bonds. As additional monomers join, this chain of repeating monomers forms a polymer. Different types of monomers can combine in many configurations, giving rise to a diverse group of macromolecules.

Even one kind of monomer can combine in a variety of ways to form several different polymers: for example, glucose monomers are the constituents of starch, glycogen, and cellulose.

These reactions are similar for most macromolecules, but each monomer and polymer reaction is specific for its class. For example, in our bodies, food is hydrolyzed, or broken down, into smaller molecules by catalytic enzymes in the digestive system.

This allows for easy absorption of nutrients by cells in the intestine. Each macromolecule is broken down by a specific enzyme. For instance, carbohydrates are broken down by amylase, sucrase, lactase, or maltase. Proteins are broken down by the enzymes pepsin and peptidase, and by hydrochloric acid. Lipids are broken down by lipases. Breakdown of these macromolecules provides energy for cellular activities. Visit this site to see visual representations of dehydration synthesis and hydrolysis.

Learning Objectives Explain why carbon is important for life Identify common elements and structures found in organic molecules Explain the concept of isomerism Understand the synthesis of macromolecules Explain the importance and use of functional groups Explain dehydration or condensation and hydrolysis reactions.

Hydrocarbons Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane CH 4 described above. Hydrocarbon Chains Hydrocarbon chains are formed by successive bonds between carbon atoms and may be branched or unbranched. When two carbon atoms form a double bond, the shape is planar, or flat.


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Garland Science: New York and London. ISBN: Paperback As we enter the age of molecular medicine, in which the time between identification of a molecular target and generation of a site-specific intervention is becoming increasingly small, a well-integrated understanding of the physical and chemical processes that govern molecular interactions is becoming exceedingly important. The Molecules of Life: Physical and Chemical Properties seeks to approach our current understanding of life by uniting fundamental concepts in thermodynamics and kinetics commonly taught in introductory physical chemistry courses with biological processes functioning at the level of molecular structure frequently taught in undergraduate biochemistry courses. Unlike other biochemistry textbooks, this text aims to present the concepts of thermodynamics through applied analysis of biological systems. The authors have taught a course at the University of California at Berkeley for the last few years using this approach that integrates thermodynamics and molecular systems and have found this strategy widely appealing to students from biology, chemistry, and biomedical engineering.


Biochemistry or biological chemistry , is the study of chemical processes within and relating to living organisms. Over the last decades of the 20th century, biochemistry has become successful at explaining living processes through these three disciplines. Almost all areas of the life sciences are being uncovered and developed through biochemical methodology and research.

The Molecules of Life: Physical and Chemical Properties

2.3: Carbon and Organic Molecules

When two atoms approach each other closely, the 8. The central dogma of molecular biology states that energy goes up because the nuclei of the atoms RNA is translated from proteins. Which of these types of molecules serve as a 2. Ionic interactions are stronger in water than in template for messenger RNA?

This crucial dependence on water broadly governs all life forms. Clearly water is vital for survival, but what makes it so necessary? Water is a simple molecule composed of two small, positively charged hydrogen atoms and one large negatively charged oxygen atom.

The field of biochemistry is entering an exciting era in which genomic information is being integrated into molecular-level descriptions of the physical processes that make life possible. The Molecules of Life is a new textbook that provides an integrated physical and biochemical foundation for undergraduate students majoring in biology or health sciences. This new generation of molecular biologists and biochemists will harness the tools and insights of physics and chemistry to exploit the emergence of genomics and systems-level information in biology, and will shape the future of medicine. The book integrates fundamental concepts in thermodynamics and kinetics with an introduction to biological mechanism at the level of molecular structure. The central theme is that the ways in which proteins, DNA, and RNA work together in a cell are connected intimately to the structures of these biological macromolecules. The structures, in turn, depend on interactions between the atoms in these molecules, and on the interplay between energy and entropy, which results in the remarkable ability of biological systems to self-assemble and control their own replication. The Molecules of Life deepens our understanding of how life functions by illuminating the physical principles underpinning many complex biological phenomena, including how nerves transmit signals, the actions of chaperones in protein folding, and how polymerases and ribosomes achieve high fidelity.

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Contact info. Fundamentally, chemistry is the study of matter and change. The way that chemists study matter and change and the types of systems that are studied varies dramatically. Over the last several years, additional concentrations have begun to emerge, including Nuclear chemistry, Polymer chemistry, Biophysical chemistry, Bioinorganic chemistry, Environmental chemistry, etceteras. The following descriptions of the five major subdisciplines were written by several of our faculty members in their field of expertise. It is mainly concerned with looking at the structure and behavior of these molecules, which are composed of only a few different types of atoms: carbon, hydrogen, oxygen, nitrogen, and a few miscellaneous others.

Water , a substance composed of the chemical elements hydrogen and oxygen and existing in gaseous, liquid, and solid states. It is one of the most plentiful and essential of compounds. A tasteless and odourless liquid at room temperature, it has the important ability to dissolve many other substances. Indeed, the versatility of water as a solvent is essential to living organisms. Water also exists on other planets and moons both within and beyond the solar system.

Not a MyNAP member yet? Register for a free account to start saving and receiving special member only perks. Similarly, understanding a process at any scale requires awareness of the interactions occurring—in terms of the forces between objects, the related energy transfers, and their consequences. In this way, the physical sciences—physics and chemistry—underlie all natural and humancreated phenomena, although other kinds of information transfers, such as those facilitated by the genetic code or communicated between organisms, may also be critical to understanding their behavior. An overarching goal for learning in the physical sciences, therefore, is to help students see that there are mechanisms of cause and effect in all systems and processes that can be understood through a common set of physical and chemical principles. The committee developed four core ideas in the physical sciences—three of which parallel those identified in previous documents, including the National Science Education Standards and Benchmarks for Science Literacy [ 1 , 2 ].


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Jcharland 06.06.2021 at 01:52

The molecules of life: physical and chemical principles, by John Kuriyan, Boyana Konforti and David Wemmer, New York and London, Garland Science (Taylor.

JehovГЎ A. 07.06.2021 at 13:00

Cells are made of many complex molecules called macromolecules, such as proteins, nucleic acids RNA and DNA , carbohydrates, and lipids.