Chapter 3: Carbon and Functional Groups/Biochemistry

What are organic compounds?

A compound containing carbon. Almost all organic compounds associated with life contain hydrogen atoms in addition to carbon atoms.

Define Polymer and monomer

A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bonds. Monomers are the repeating units that serve as the building blocks of a polymer.

What's the relationship between a polypeptide and a protein?

A protein is made up of polymers of amino acids called polypeptides. A protein is a biologically functional molecule that consists of one or more polypeptides folded and coiled into a specific three-dimensional structure.

Read and summarize the section on ATP

ATP consists of an organic molecule called adenine attached to a string of three phosphate groups. Where 3 phosphates are present, one phosphate may split off as a result of a reaction with water. Having lost a phosphate, ATP becomes adenine diphospahte, or ADP. ATP stores the potential to react with water, and this reaction releases energy that can be released by the cell.

Describe denaturation and explain how it happens

If the pH, salt concentration, temperature, or other aspects of its environment are altered, the weak chemical bonds and interactions within a protein may be destroyed, causing the protein to unravel and lose its native shape, a change called denaturation. The denatured shape is biologically inactive.

Describe the unifying characteristics of lipids: what makes a lipid a lipid?

Lipids are the one class of large biological molecules that does not include true polymers, and they are generally not big enough to be considered macromolecules. They are grouped together because they share on important trait: they mix poorly, if at all, with water. The hydrophobic behavior of lipids is based on their molecular structure.

Define macromolecule

Members of the carbohydrate, protein, or nucleic acid classes that are huge.

What are phospholipids? Why are they important in cells?

Phospholipids are essential for cells because they are major constituents of cell membranes. Cells could not exist without phospholipids. A phospholipid is similar to a fat molecule but has only two fatty acids attached to glycerol rather than three. The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell.

Using the text in the 1st paragraph of this section, and figure 3.17, list some of the functions of proteins.

Some proteins speed up chemical reactions, while others play a role in defense, storage, transport, cellular communication, movement, or structural support.

What are steroids? What is cholesterol, and what is good and bad about it?

Steroids are lipids characterized by a carbon skeleton consisting of four fused rings. Different steroids are distinguished by the particular chemical groups attached to this ensemble of rings. Cholesterol is a crucial steroid in animals and is a common component of animal cell membranes and is also the precursor from which other steroids are synthesized. A high level of cholesterol in the blood may contribute to atherosclerosis. Saturated fats exert their negative impact on health by affecting cholesterol level.s

What are the functions of fats in animals?

The major function of fats is energy storage. A gram of fat stores more than twice as much energy as a gram of a polysaccharide. Since animals must carry their energy stores with them, there is an advantage to having a more compact reservoir of fuel--fat.

In terms of properties and chemistry, compare and contrast saturated and unsaturated fatty acids.

The terms saturated fats and unsaturated fats refer to the structure of hydrocarbon chains of the fatty acids. If there are no double bonds between carbon atoms composing a chain, then as many hydrogen atoms as possible are bonded to the carbon skeleton, and such structure is said to be saturated with hydrogen, and the resulting fatty acid is called saturated fatty acid. An unsaturated fatty acid has one or more double bonds, with one fewer hydrogen atom on each double-bonded carbon. Saturated fats are usually solid at room temperature, while unsaturated fats are uusually liquid at room temperature.

Draw/Diagram alpha linkages AND beta linkages. Compare and contrast these diagrams.

When glucose forms a ring, the hydroxyl group attached to the number 1 carbon is positioned either below or above the plane of the ring. These two ring forms for glucose are called alpha and beta. In starch, all glucose monomers are in the alpha configuration, but in contrast the glucose monomers of cellulose are in the beta configuration, making every glucosse monomer "upside down'.

Describe the key traits (basic structure and function) of a. Monosaccharides (simple sugars) b. Disaccharides c. Polysaccharides

a. Monosaccharides generally have molecular formulas that are some multiple of the unit CH2O. Monosaccharides contain a carbonyl group (C=O) and multiple hydroxyl groups (-OH). The carbonyl group can be on the end of the linear sugar molecule or attached to interior carbon. Monosaccharides are major nutrients for cells. b. A disaccharide consists of two monosaccharides joined by a glycosidic linkage, a covalent bond formed between two monosaccharides by a dehydration reaction. c. Polysaccharides are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages. Some polysaccharides serve as storage material, hydrolyzed as needed to provide sugar for cells. Other polysaccharides serve as building materials for structures that protect the cell or the whole organism. The structure and function of a polysaccharide is determined by its sugar monomers and by the positions of its glycosidic linkages.

Describe the structure of a generalized amino acid, and explain how peptide bonds form (figure 5.17)

All amino acids share a common structure. An amino acid is an organic molecule with both an amino group and a carboxyl group. At the center of the amino acid is a carbon atom called the alpha carbon. Its four different partners are an amino group, a carboxyl group, a hydrogen atom, and a variable group symbolized by R. When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by dehydration reaction, with the removal of a water molecule. The resulting covalent bond is called a peptide bond.

What's a hydrogenated fat?

An unsaturated fat that was converted to a saturated fat by adding hydrogen.

There are only about 50 monomers that make up most of life's polymers. Yet polymers are astonishingly diverse. whats a good analogy for this? How does this analogy fall short? How is this related to the theme of unity and diversity?

Building a huge variety of polymers from such a limited number of monomers is analogous to creating hundreds of thousands of words from only 26 letters in the alphabet. This analogy falls short of describing the great diversity of macromolecules because most biological polymers have many more monomers than the number of letters in the longest word.

What are carbohydrates?

Carbohydrates include both sugars and polymers of sugars. The simplest of carbohydrates are the monosaccharides, or simple sugars, which are the monomers from which one or more complex carbohydrates are constructed.

Describe and draw examples showing how carbon atoms (and other atoms) can form chains, rings, and branched molecules.

Carbon chains form the skeletons of most organic molecules, and these skeletons vary in length and may be straight, branched, or arranged in closed rings.

Describe how the structure of carbon allows it to form such a wide variety of molecules

Carbon has 4 valence electrons in a shell that holds 8 electrons, so a carbon atom usually completes its valence shell by sharing its 4 electrons with other atoms so that 8 electrons are present. In organic molecules, carbon usually forms single or double covalent bonds. Each carbon atom acts as an intersection point from which a molecule can branch off in as many as four directions. This is a facet of carbon's versatility that makes large, complex molecules possible. A carbon atom can also use one or more valence electrons to form covalent bonds to other carbon atoms, linking the atoms into chains of seemingly infinite variety.

What are enzymes, and why are they important?

Enzymes are specialized macromolecules (usually proteins) that speed up chemical reactions. They are important because enzymatic proteins regulate metabolism by acting as catalysts, chemical agents that selectively speed up chemical reactions without being consumed by the reaction. Since an enzyme can perform its function over and over again, these molecules can be thought of as workhorses that keep cells running by carrying out the processes of life.

Describe the structure, properties, and biological importance of fats (AKA triglyceride or triacylglyceride)

Fats are large molecules assembled from smaller molecules by dehydration reactions. It is constructed from two kinds of smaller molecules: glycerol and fatty acids. The relatively nonpolar C-H bonds in the hydrocarbon chains of fatty acids are the reason fats are hydrophobic. Fats separate from water because the water molecules hydrogen-bond to one another and exclude the fats. In making a fat, three fatty acid molecules are each joined to glycerol by an ester linkage, a bond between a hydroxyl group and a carboxyl group. The resulting fat, also called triacylglycerol, thus consists of three fatty acids linked to one glycerol molecule.

For the following, be able to describe what type of carbohydrate and its overall function: glucose, fructose, sucrose, lactose, starch, glycogen, cellulose, chitin

Glucose is the most common monosaccharide. In the process known as cellular respiration, cells extract energy from glucose in a series of reactions that break down its molecules. Fructose is a monosaccharide. Sucrose is the most prevalent disaccharide. Plants generally transport carbohydrates from leaves to roots and other nonphotosynthetic organs in the form of sucrose. Lactose is a disaccharide. It is the sugar present in milk. Starch is a polysaccharide. It is a polymer of glucose monomers and it is stored by plants as granules within cells. Glycogen is a polysaccharide. It is a polymer of glucose that is like amylopectin but more extensively branched. Humans and other vertebrates store glycogen mainly in liver and muscle cells. Cellulose is a polysaccharide. It is a major component of the tough walls that enclose plant cells. Cellulose is a polymer of glucose with 1-4 glycosidic linkages. Chitin is a polysaccharide. It is the carbohydrate used by antropods to build their exoskeletons. It is also found in many fungi, which use this polysaccharid as the building material for theri cell walls.

What are hydrocarbons? Why are they important, both biologically and economically?

Hydrocarbons are organic molecules consisting of only carbon and hydrogen. Hydrocarbons are important because they are the major components of petroleum, which is called a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago. Although hydrocarbons aren't prevalent in most living organisms, many of a cell's organic molecules have regions consisting of only carbon and hydrogen. Also, they can undergo reactions that release a relatively large amount of energy. For example, the hydrocarbon tails of fats serve as stored fuel for animals.

Explain how cells synthesize and break down macromolecules (condensation synthesis vs hydrolysis)

Monomers are connected by a reaction in which two molecules are covalently bonded to each other, with the loss of a water molecule, and this is called dehydration reaction. When a bond forms between two monomers, each monomer contributes part of the water molecule that is released druing the reaction: one monomer provides the hydroxyl group (-OH) while the other provides a hydrogen (-H). Polymers are disassembled into monomers by hydrolysis, which is a process that is essentially the reverse of the dehydration reaction. Hydrolysis means breakage using water. The bond between the monomers is broken by the addition of a water molecule, with a hydrogen from the water attaching to one monomer and the hydroxyl group attaching to the adjacent monomer.

Why can we use starch as an energy source, but not cellulose?

We can use starch as an energy because most animals, including humans, also have enzymes that can hydrolyze plant starch, making glucose available as a nutrient for cells. On the other hand, few organisms possess the enzymes that can digest cellulose. Animals, including humans, do not; the cellulose in our food passes through the digestive tract and is eliminated with the feces.