New+Chapter+Three

NAME: Note: The graphics didn't come across from this chapter. Please just try and find the blank you are filling in and go for it! Thanks!@ Definition Quiz Chapter 3: Place the number of the below term with its definition.

1. Organic Compound: Compounds that do contain carbon with hydrogen (for example, carbohydrates, lipids, proteins, nucleic acids) 2. Inorganic Compound:Compounds that do not contain carbon with hydrogen (for example, trace mineral complexes) 3. Molecular Formula:This is the representation of a molecule showing the type of element present and the amount. For example: C6H12O6, H2O, CO2, CH4. 4. Structural Formula: The picture below shows this type of representation of a molecule. 5. Isomer: Two molecules with the SAME molecular formula but DIFFERENT arrangements in space (structure) such as glucose and fructose 6. Functional Group: This is the name of particular atoms or groups of atoms covalently bonded to carbon (e.g. carboxyl, carbonyl, alcohol, amine) in an organic compound 7. Condensation (dehydration synthesis): chemical reaction covalent bond 8. Hydrolysis (cleavage) Reaction: //hydro// "water" + //lysis// "separation") is a chemical reaction in which molecules of water (H2O) are split into hydrogen cations (H+, identical to protons) and hydroxide anions (OH−) in the process of a chemical mechanism 9. Monomer: Large molecules that consist of many subunits 10. Polymer: This is when a large organic molecule is broken apart (like with a sharp kitchen knife) into smaller subunits. Energy is released. 11. Monosaccharide: the monomer of a carbohydrate 12. Polysaccharide: Polymers of simple sugars. This group includes starch, glycogen, cellulose and chitin 13. Lipids: Nonpolar organic compounds which include waxes, fats, and sterols. Many are long chains of hydrocarbons with groups attached to one end (triglyceride, for example). 14. Saturated Fatty Acid: This is the description given to a fatty acid in which there are no double bonds in the chain at all. This type should be avoided overall, because it is harder for our body to break these down. 15. Unsaturated Fatty Acid:This is the description given to a fatty acid in which there are one or more double bonds in the chain. These are easier for our body to break down. 16. Protein: are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. 17. Amino Acid: This is the monomer of proteins. They contain an amine group and a carboxylic acid group, with a central Carbon to which is attached a functional group. 18. Denaturation: (any disruption of Hydrogen) of proteins involves the disruption and possible destruction of both the secondary and tertiary structures. 19. Enzyme: are biological molecules that catalyze (i.e., increase the rates of) chemical reactions.In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. 20. Hormone: blood borne chemical messengers. 21. Nucleic Acid:is made of alternating **sugar** and **phosphate** molecules bonded together in a long chain, represented below 22. Purine: These are organic compounds with lots of Nitrogens. They are sometimes called nitrogenous bases and include Adenine and Guanine. They have a double ring structure, and are an important component of DNA and RNA. 23. Pyrimidine: These are organic compounds with lots of Nitrogens. They are sometimes called nitrogenous bases and include Thymine and Cytosine. They have a single ring structure.__They are also an important component of nucleic acids.__

Please put the number of the correct term next to the definition. A. This is the monomer of proteins. They contain an amine group and a carboxylic acid group, with a central Carbon to which is attached a functional group. **17** B. This is the name of particular atoms or groups of atoms covalently bonded to carbon (e.g. carboxyl, carbonyl, alcohol, amine) in an organic compound. **6** D. This is when a large organic molecule is broken apart (like with a sharp kitchen knife) into smaller subunits. Energy is released. **10** E. Polymers of simple sugars. This group includes starch, glycogen, cellulose and chitin.**12**

__F. Compounds that do not contain carbon with hydrogen (for example, trace mineral complexes)__ **2** __G. Compounds that do contain carbon with hydrogen (for example, carbohydrates, lipids, proteins, nucleic acids)__ **1** H. Large molecules that consist of many subunits. **9** __I. The picture below shows this type of representation of a molecule. **4**__ . J. Nonpolar organic compounds which include waxes, fats, and sterols. Many are long chains of hydrocarbons with groups attached to one end (triglyceride, for example). **13** K. Two molecules with the SAME molecular formula but DIFFERENT arrangements in space (structure) such as glucose and fructose. **5** L. This is when we put small molecules together to form larger molecules (like in forming polymers). We need to add energy to make this happen. **18** __M. DNA, RNA, ATP are all this type of molecule**.**__ **21** __N. These are organic compounds with lots of Nitrogens. They are sometimes called nitrogenous bases and include Adenine and Guanine. They have a double ring structure, and are an important component of DNA and RNA.__ **22** __O. These are organic compounds with lots of Nitrogens. They are sometimes called nitrogenous bases and include Thymine and Cytosine. They have a single ring structure.__ __They are also an important component of nucleic acids. **23**__ P. This is the term to describe a protein that has been heated too much, the pH in the environment has changed too much or you have added a detergent and caused this to happen to the protein. When this happens, the protein is often not able to function any longer.**16** __Q. This is a type of organic compound that contains **many amino acids**. This includes insulin and many other hormones, enzymes, hemoglobin, collagen, keratin, elastin, membrane channels, just to name a few!__ _**10** __R. This is the description given to a fatty acid in which there are no double bonds in the chain at all. This type should be avoided overall, because it is harder for our body to break these down.__ **14** __S. This is the description given to a fatty acid in which there are one or more double bonds in the chain. These are easier for our body to break down.__ **15** T. These are protein molecules that help reactions proceed more rapidly. Examples include lactase, maltase, carbonic anhydrase.**3** __U. Glucose and fructose are examples of this type of organic compound, in which there is one subunit, and the generalized formula follows Cn (H2O) n .__ **21** __V. This is the representation of a molecule showing the type of element present and the amount. For example: C6H12O6, H2O, CO2, CH4.__ **4** __W. This is the basic building block (individual subunits) from which any polymer is constructed.__. **19** X. Chemical messengers that send signals in our body to perform metabolic functions. Examples include testosterone, estrogen, insulin, aldosterone, and thyroxine. **20**
 * [[image:file:///C:/Users/family/AppData/Local/Temp/msohtmlclip1/01/clip_image002.jpg width="124" height="80" caption="See full size image" link="http://www.1-formula.com/upl/Image/800px-Acetone-structural.png"]] ||
 * See full size image ||

**CHAPTER 3** __** : Basic Introduction to Organic Chemistry **__
 * By Zaynah Somani**

__1. ORGANIC COMPOUNDS:__ __What is an organic compound?__
 * The carbon in living organisms is part of the molecules of life- complex carbohydrates lipids, proteins and nucleic acids. These molecules consist primarily of hydrogen and carbon atoms so they are organic**

__Living things are mainly made out of 3 elements:__
 * oxygen, hydrogen, and carbon**

__Take away the elements that make up water, what is left?__
 * carbon makes up more than half of what is left**

__What physical and chemical characteristics of carbon make it the leading molecule in living organisms?__ __a. how many covalent bonds can carbon form with other atoms?__
 * The carbon in living organisms is part of the molecules of life= complex carbohydrates, lipids, proteins and nucleic acids**
 * Each carbon atoms can form covalent bonds with one, two, three, or four organisms.**

__b. Can carbon form polar covalent bonds with other atoms?__
 * Yes, depending on the elements in the resulting molecules**

__c. Can carbon form nonpolar covalent bonds with other atoms?__ __d. What is a carbon backbone? Why is it important that carbon can form a ring, connecting a backbone into a circle?__
 * Yes, depending on the elements in the resulting molecules**
 * A chain of carbon atoms to which other atoms attach. The ends of a backbone may join so that the carbon chain forms one or more ring structures this means that carbon atoms can be assembled and remodeled into a variety of organic compounds**

__e. What is a hydrocarbon? Are they hydrophilic or hydrophobic?__ __f. Make sure__ __you study the different ways of representing carbon-based molecules:__
 * is an organic compound consisting entirely of hydrogen and carbon**
 * hydrophobic**
 * Kate talked about this in class, looking at the differences!!**
 * Type of model || Advantage || Limitation ||
 * Molecular model ||  ||   ||
 * Structural model ||  ||   ||
 * Ball-and-stick models ||  ||   ||
 * Space-filling models ||  ||   ||
 * Surface model ||  ||   ||
 * Ribbon model ||  ||   ||

__2. Functional Groups:__ __What is a functional group?__ __Why is it important to study the functional groups attached to a carbon backbone on an organic molecule?__
 * a cluster of atoms covalently bonded to a carobn atom of an organic molecule**
 * All biological systems are based on the same organic molecules**


 * Functional group || Character || Location || Water soluble?* || Structure ||
 * hydroxyl || **polar** || **amino acids** || **yes** || **(-OH)** ||
 * methyl || **non polar** || **fatty acids some amino acids** || **no** || (**CH3)** ||  ||
 * carbonyl || **polar, reactive** || **sugars, amino acids** || **yes** || **(CH 02)** ||  ||   ||
 * carboxyl || **acidic** || **amino acids, fatty acids, carbohydrates** || **yes** ||  ||
 * amine || **basic** || **amino acids, some nucleotide bases** || **yes** || -NH2 ||
 * phosphate || **higher energy, polar** || **nucleotides, many proteins, phospholipids** || **yes** ||  ||
 * sulfhydryl || **forms disulfide bridges** || **cysteine (an amino acid)** || **yes** || -SH ||

__As a general rule, polar or ionic substances dissolve in polar solvents; nonpolar substances dissolve in nonpolar solvents. As a result, hydrocarbons (being nonpolar) don't dissolve in water. They are often said to be **immiscible** (literally, "not mixable") in water.__

__3. Organic molecules can be described as having a simple structure or a complex structure. Those with a simple structure tend to be much smaller in size and serve as “building blocks” (subunits) for making the larger more complex molecules.__ __A. The smaller subunits are more commonly known as__ _**Monomers;** and the larger more complex molecules are known as **polymers** B. The main “building blocks” or subunits of the major biological molecules include the following. (you may need to look ahead in the chapter to find these) 1. SIMPLE **Sugars**___: join together to form complex carbohydrates__ __2. FATTY **ACIDS**_____: join together with other molecules to form lipids (except for cholesterol and other sterols)__ __3. **Amino**__ ACIDS: join together to form protein molecules 4**._DNA/RNA:** join together to form nucleic acids

4. Metabolism What is metabolism?
 * Refers to activities by which cells acquire and use energy as they construct, rearrange, and split organic compounds.**


 * Types of metabolic reactions || What happens? ||
 * Condensation || **two molecules convalently bond into a large one** ||
 * Cleavage (Hydrolysis is an example) || **a molecule splits into two smaller one, hydrolysis is an example** ||
 * Functional group transfer || **a functional group is transferred from one molecule to another** ||
 * Electron transfer || **electrons are transferred from one molecule to another** ||
 * Rearrangement || **juggling of covalent bonds, convert one organic compound into another** ||

D. **Hydrolysis** __occurs when two monomers combine to form a larger more complex molecule. This type of reaction generally occurs as one monomer loses a hydroxyl group (-OH) while another monomer loses a hydrogen__ __atom (H) and the two join together to form a molecule of__ **water**_. It is for this reason that this type of reaction is also commonly known as a DEHYDRATION SYNTHESIS reaction. The diagram below illustrates this type of reaction

E. **Clevage** occurs when a large complex molecule splits into smaller ones. A common form of this type of reaction is the reverse of a condensation (dehydration) reaction. In this reaction, a molecule of water is used to break a covalent bond. The water breaks apart, adding the Hydrogen atom to one of the monomers and the hydroxyl group to the other monomer. Because water is used to break the bond, this type of reaction is also commonly known as a  _**condensation** reaction. The diagram below illustrates this type of reaction.

5. CARBOHYDRATES:
 * 1) These are the most abundant of all the macromolecules found in the biosphere.


 * 1) Carbon + (2 Hydrogens + Oxygen)n



How do cells utilize carbohydrates?
 * Cells use different kinds of structural materials and as sources of instant energy**


 * 1) Complete the following table.


 * Carbohydrate type || How many sugar units? || examples || Picture ||
 * Monosaccharide || 1 || fructose || [[image:file:///C:/Users/family/AppData/Local/Temp/msohtmlclip1/01/clip_image009.gif width="67" height="120" caption="clip_image009.gif" link="http://en.wikipedia.org/wiki/File:D-glucose-chain-2D-Fischer.png"]] glucose ||
 * Disaccharide || **2** || **lactose in milk** || [[image:file:///C:/Users/family/AppData/Local/Temp/msohtmlclip1/01/clip_image011.jpg width="190" height="107" caption="clip_image011.jpg" link="http://images.google.com/imgres?imgurl=http://www.southernmatters.com/sugarcane/images/sucrose2.jpg&imgrefurl=http://www.southernmatters.com/sugarcane/essays-sugars.htm&usg=__Gef2rtbNza3Vd4jZq809Ye3Yq-g=&h=337&w=600&sz=39&hl=en&start=13&um=1&tbnid=NPwRhWN6ZrQhtM:&tbnh=76&tbnw=135&prev=/images%3Fq%3Dpicture%2Bof%2Bsimple%2Bsugars%26hl%3Den%26rls%3Dcom.microsoft:en-us%26rlz%3D1I7ADFA_en%26sa%3DX%26um%3D1"]] ||
 * Oligosaccharide || **2** |||| [[image:file:///C:/Users/family/AppData/Local/Temp/msohtmlclip1/01/clip_image013.gif width="247" height="232" caption="clip_image013.gif"]]**maltose sucrose lactose** ||
 * Polysaccharide || **hundreds to thousands** |||| cellulose [[image:file:///C:/Users/family/AppData/Local/Temp/msohtmlclip1/01/clip_image015.gif width="278" height="114" caption="clip_image015.gif" link="http://en.wikipedia.org/wiki/File:Cellulose-3D-balls.png"]] ||

a. **_**__material that is tough, insoluble in water and used in plant cells walls for structural strength. This compound is NOT a source of energy for humans because we lack the needed enzymes to break the bonds connecting the glucose molecules together; however it is needed by the body to keep the digestive system working properly. This compound is commonly called “dietary fiber.__
 * 1) What type of bond holds sugar subunits together?
 * Covalent bonds**
 * 1) Ahich type of sugar is part of DNA and RNA?
 * Sugar that are part of DNA and RNA are monosaccharides with carbon atoms**
 * 1) There is one simple sugar that the body uses as an energy source and also as a starter material for use in building bigger materials. What is this simple sugar?
 * glucose**
 * 1) Complex Carbohydrates:**Cellulose**: a structural

__b.__ branched coiled chain of glucose molecules or highly branched chains of glucose that are easily hydrolyzed into individual glucose molecules. This complex carbohydrate is used as a storage form of energy for **water** __. Due to a large number of hydroxyl groups (-OH) it is soluble in water, but due to its large size it is sometimes difficult to get it to dissolve.__ __Starch molecules can be used by humans as an energy source, and due to their size they can provide energy for a sustained period of time. This is why marathon runners often eat large amounts of pasta the night before the race. This practice is called “carbohydrate loading”.__ __c.__ **Glycogen**_: a highly branched chain of glucose molecules used as a storage form of energy by animals. It is found in highest concentrations in **muscle** and **liver** cells. When blood sugar levels drop, the liver cells break down glycogen into individual glucose molecules and release them into the blood.
 * Polysaccharides** an un


 * By: Zaynah Somani**

By: Hashimi E. Complete the following table by entering the name of the carbohydrate class, the specific carbohydrate, or the main function. Mono? || Sucrose || The most plentiful sugar in nature; also known as table sugar; formed by joining together glucose and fructose ||
 * //Carbohydrate Class// || //Specific Carbohydrate// || //Function// ||
 * Polysachharide
 * Monosaccharide || Glucose || The main energy source for most organisms; serves as building blocks (monomers) for larger carbohydrates ||
 * || Cellulose || Structural material of plant cell walls; formed from long straight chains of glucose; unable to be used by humans as a source of energy; also known as dietary fiber ||
 * Monosaccharide || Ribose || Five Carbon. Sugar found in RNA ||
 * Polysaccharide || Glycogen || The complex carbohydrate found in animals, stored especially in liver and muscle tissue; formed from many branched glucose chains ||
 * Disaccharide || Lactose ||  ||
 * || Starch || The storage form for sugars produced by plants using photosynthesis, able to be used by animals as a source of energy ||

6. LIPIDS: A. How do you describe lipids? Lipids are molecules that are oily and waxy to touch. Organic compounds that are Insoluble in water.

B. Are lipids soluble in water? Why or why not? Contain mostly of carbon, hydrogen. Less oxygen than carbohydrates. Not able to form hydrogen with water (hydrophobic)

C. What is a fatty acid? carboxylic acids with long hydrocarbon chains.

D. What is a triglyceride? glycerol and three fatty acids

E. These molecules make up about 12-25% of the total body weight. F. Oils, fats and waxes are all classified as lipids. Oils tend to be smaller in size and liquid at room temperature, fats are larger and are “soft” solids at room temperature, while waxes are much larger and are solids at room temperature. G. Lipids serve several functions in the body: 1. Reservoir for long-term storage of potential __ENERGY__ __2.__ INSULATE the body (think of whale blubber). 3. Act as a “shock absorber” (padding around sensitive organs like the kidneys) and as space fillers (especially around joints). 4. Are a major part of cell MEMBRANE 5. Some act as hormones (chemical messengers in the body) F. There are several classes of lipids: FATTY ACIDS (triglyceride) 1. : have a long hydrocarbon backbone of as many as 36 carbon atoms and a carboxyl group (acid group) attached to the end of the chain (tail). These molecules can be further divided into two main groups: a. __SATURATED: those that have all single bonds in the carbon chain, therefore containing the maximum number of hydrogen atoms possible. When something is full, it is saturated (filled to capacity).__ __ b. ____UNSATURATED: those that have at least one double bond in the carbon chain, therefore containing fewer hydrogen atoms. When something is not full, it is unsaturated (not filled to capacity).__ 

__** Saturated Unsaturated Polyunsaturated **__

BY: HASHIMI

 __2.__ FATS __(also known as glycerides): these molecules__ __have one, two or three fatty acid molecules attached to a__ __glycerol (3 carbon sugar) backbone by a condensation__ __(dehydration synthesis) reaction. The triglycerides are the__ __most plentiful lipid found in the body and are stored in__ ADIPOSE tissue. Gram for gram, they provide more than __TWICE the amount of energy when__ __compared to complex carbohydrates, which is why a high__ __fat diet tends to cause a person to gain weight. The body__ __doesn’t use all the energy available, so stores it for later use.__ __This type of lipid is also used by the body to act as a shock__ __absorber (padding) to protect organs, and provide thermal insulation. There are several types of fat:__ __a. SATURATED__ __b.__ UNSATURATED FATS: have at least one double bond in the carbon chain. The double bond causes the “tail” to bend or kink, keeping these molecules slightly separated from each other. These molecules tend to be easier for the body to digest and less likely to lead to heart or vascular conditions. They tend to be found in plants (olive oil, safflower oil, vegetable oil, etc.). c. __POLYUNSATURATED FATS: produced by a chemical process called “hydrogenation” where an unsaturated fat (vegetable oil) are forced to accept extra hydrogen atoms, breaking the double bonds to form straight chains. This process causes vegetable oils to pack tightly together, forming a solid at room temperature. They are unhealthy because the body treats them like animal fat.__ __3.__ PHOSPHOLIPIDS: are similar to triglycerides except that one of the fatty acid tails is replaced with a phosphate group and another very polar group. These groups cause the glycerol portion of the molecule to like water, so it is often referred to as the _ or polar head. These molecules are the main component of cell membranes that will be discussed in more detail in the next chapter.  4. STEROIDS (STEROLS): this class of lipid does NOT contain any fatty acid molecules, rather it has a rigid backbone of four fused-together carbon rings. CHOLESTEROL is the most common type found in the body and is modified into various hormones (estrogen and testosterone), bile salts, as well as the activated form of vitamin D. 5. WAXES: have very long fatty acid tails that are tightly packed together allowing them to be firm yet pliable. They repel water and therefore act as a good barrier against dehydration and when warmed, serve as a good lubricant. In the ear canal it serves as a sticky covering trapping dust and foreign objects before they reach the ear drum. 6. EICOSANOIDS: these are short chain fatty acid molecules that are released by damaged tissues and function to stimulate nerve endings producing the sensation of “pain”. They are also released by uterus to initiate labor contractions and the secretion of various other hormones.

G.
 * **Type of lipid** || **Description** ||
 * FATS || Lipids with one, two, or three fatty acids that dangle like tails from a small alcohol called glycerol ||
 * TRIGLY || Fats with three fatty acid tails linked to glycerol ||
 * TRIGLY || Concentrated in adipose tissue that insulates and cushions part of the body ||
 * SAT || Fatty acid tails of this type of fat has only single covalent bonds ||
 * UNSAT || Fatty acid tails of thes types of fats have one or more double covalent bond ||
 * UNSAT || Most vegetable oils ||
 * TRANS || Partially hydrogenated vegetable oils ||
 * PHOSPHO || A polar head and two nonpolar fatty acid tails ||
 * WAX || Complex, varying mixtures of lipids with long fatty acid tails bonded to long-chain alcohols or carbon rings ||
 * STEROIDS || Lipids with a rigid backbone of four carbon rings and no fatty acid tails ||
 * CHOLEST || This molecule is remodeled into many molecules such as bile salts and vitamin D. Steroid hormones are derived from this molecule. ||
 * MONO || Oleic acid ||
 * SAT || Stearic acid ||
 * TRANS || Elaidic acid ||
 * WAX || Lipid in the cuticle of plant tissue ||
 * WAX || Protect, lubricate and soften skin and hair ||
 * WAX || honeycomb ||
 * PHOSPHO || Lipid in cell membranes (bilayer) ||

BY: HASHIMI

7. PROTEINS: In what type of metabolic reaction are chains of amino acids put together to form polypeptides (proteins)? CONDENSATION What type of bond is a peptide bond? COVALENT BOND C. Proteins perform numerous functions in the body: 1. Structural support (especially at the cellular level): within most cells is a cytoskeleton made of protein fibers. (Collagen & Elastin) 2. Movement: muscle contraction is caused by protein fibers sliding against each other. (Actin & Myosin) 3. Transport: especially of substances that do not dissolve in water like fats and most of the oxygen is transported in the blood attached to a protein called hemoglobin. (High & Low Density Lipoproteins: HDL & LDL) 4. Enzymes: protein molecules that speed chemical reactions (metabolism) in the body. (Lipase & Protease) 5. Hormones (chemical messengers): released by cells and travel throughout the body signaling cells to modify their activities. (Insulin) 6. Antibodies: one mechanism used by the body for protection against foreign pathogens (disease causing substances or organisms). (Gammaglobulins) 7. Buffering the blood: proteins help to stabilize the pH of the blood.
 * 1) [[image:file:///C:/Users/family/AppData/Local/Temp/msohtmlclip1/01/clip_image023.jpg width="114" height="106" caption="clip_image023.jpg"]] These are the most diverse of all the macromolecules in the body. There are estimated to be more than 140,000 different protein molecules in the body, and they make up more than 50% of the total body weight.
 * 2) What is the monomer of protein? AMINO ACID

D. With this many and very different functions to perform, there must be more than one kind of amino acid and proteins must have a very complex structure. When a cell needs to make a protein, enzymes in the cell join together one amino acid after another forming a long chain of amino acids, also known as a __POLYPEPTIDEchain.__  __E. There are__20 different amino acids, however each one has an amino group (-NH2), a carboxyl or acid group (-COOH) and one or more atoms called its “R” group (for the “rest” of the molecule). All three “side groups” are covalently bonded to a central carbon atom. Each amino acid has only one R group, but it is the characteristic of the “R Group” that determines the overall characteristic of each amino acid molecule. The vast majority of amino acids are neutral, but some are acidic and some are basic, some are hydrophilic and some are hydrophobic.

BY: HASHIMI

F. For each of the following diagrams, circle the “R” group part of the amino acid. 

H. The structure of protein molecules is divided into four levels of complexity. Actin and myosin silk ||
 * **Structural Level** || **Shape(s)** || **Type of bond holding form together** || **Once taken apart, can it reassemble?** || **Examples** ||
 * Primary ||  || Peptide (covalent) || NO ||   ||
 * Secondary || Polypeptide chain twists, bends, loops and folds into a-helices or b-pleated sheets || Hydrogen bonds || //Yes// || Keratin
 * Tertiary || Domains, barrels, tunnels || Four factors are responsible for the tertiary structure of proteins: || 1. Disulfide linkages ||
 * 2. Hydrogen Bonding ||
 * 3. Electrostatic interactions ||
 * 4. Hydrophobic interactions ||

DNA polymerase; ion channels; microtubules; some enzymes ||
 * Membrane transport proteins ||
 * Quaternary || More than one polypeptide chain joined together, strands or sheets || result of interactions between hydrophobic substituents on these polymer chains; also hydrogen bonding or ionic interactions between amino-acid side chains on the surfaces of adjacent polymer chains || NO || Hemoglobin

[] Great link about protein structure with good pictures

The primary structure of a protein is nothing more than the sequence of amino acids, read off one at a time, as if printed on ticker-tape. Insulin obtained from cows, for example, consists of two chains (//A// and //B//). There is more to the structure of a protein, however, than the sequence of amino acids. The polypeptide chain folds back on itself to form a secondary structure. Interactions between amino acid side chains then produce a tertiary structure. For some proteins, such as hemoglobin, interactions between individual polypeptide chains give rise to a quaternary structure. Human hair is composed primarily of proteins known as the -keratins that are about 14% cysteine. Hair curls as it grows because of the disulfide (S-S) links between cysteine residues on adjacent protein molecules. The first step in changing the way hair curls involves shaping the hair to our satisfaction and then locking it into place with curlers. The hair is then treated with a mild reducing agent that reduces the S-S bonds to pairs of -SH groups. This relaxes the proteins in the hair, allowing them to pick up the structure dictated by the curlers. The -SH side chains on cysteine residues that are now adjacent to each other are then oxidized by the O2 in air. New S-S linkages form, locking the hair permanently in place; at least until new hair grows. The a -keratins are divided into two categories, "hard" and "soft," on the basis of the amount of cysteine they contain. The -keratins in skin are soft because they contain relatively small amounts of sulfur, and disulfide cross-links are uncommon. Although hair is classified as a hard keratin, horn and hoof, which contain even more sulfur, are much less pliable because of the extensive disulfide cross-links that form. []

H. is any process that disrupts or destroys the hydrogen bonds or the overall three-dimensional shape of a protein molecule, and thereby changes the overall function of the protein. In most cases the process is irreversible and the protein is destroyed. This process can be caused by changing the _ __or the__ _(acidity) of the cell, or exposing a protein to certain detergents.

I. Match the following descriptions with the most appropriate term related to proteins and protein structure. acids in a protein molecule ||
 * 1. _ __amino acid__ || A. || A coiled or pleated structure caused by regular intervals of hydrogen bonds ||
 * 2. _ denaturation || B. || Three or more amino acids joinded in a linear chain ||
 * 3. _ __dipeptide__ || C. || Proteins with oligosaccharides covalently bonded to them ||
 * 4. _ glycoproteins || D. || Folding of a protein molecule into domains, following interactions between the “R” groups of the amino acids in the protein chain ||
 * 5. _ __lipoproteins__ || E. || Proteins with cholesterol or phospholipids covalently bonded to them ||
 * 6. _ peptide bond || F. || Another name for a covalent bond between two amino acids ||
 * 7. _ __polypeptide chain__ || G. || The globular protein hemoglobin with four protein chains is an example of a protein with this level of organization ||
 * 8. _ primary structure || H. || Breaking of protein bonds thereby changing the shape and function of the protein ||
 * 9. _ __quaternary structure__ || I. || Formed by joining together two amino acids ||
 * 10. _ secondary structure || J. || The linear arrangement or sequence of amino
 * 11. _ __tertiary structure__ || K. || The monomer of all proteins, composed of an amino, phosphate and “R” group. ||

What causes sickle cell anemia? Explain what happens to produce faulty hemoglobin. What does this say about the importance of the primary structure of a polypeptide being assembled correctly? 8. NUCLEIC ACIDS: A. These macromolecules are made of “building blocks” (monomers) known as _ __that consist of three parts.__ __1. A five carbon__ _ __(ribose or deoxyribose)__ __2. One or more__ _ __groups (PO4)__ __3. A__ _ __base (a single or double ring structure that contains a few nitrogen atoms)__ __a. There are five different nitrogenous bases used to make nucleotides.__ __(See chapter 13, section 13.2 for details)__ __1. Two of these are called //Purines// and have a double ring structure:__ _ __(A) and__ _ __(G) found in DNA and RNA__ __2. Three of them are called //Pyrimidines// and have a single ring structure:__ (T) and _(C) found in DNA and (U) only found in RNA


 * Example of a Pyrimidine Example of a Purine **

B. Nucleic acids perform several functions in the body: 1. DNA (deoxyribonucleic acid): stores the genetic information needed for survival. 2. RNA (ribonucleic acid): carries the “working copy” of the genetic information and instructs the production of specific protein molecules. 3. __(adenosine triphosphate): the energy form used by cells to drive specific cellular reactions or activities.__ __4.__ _ __(nicotinamide adenine dinucleotide) and__ ___(flavin adenine dinucleotide): act as coenzymes in metabolic reactions.__ __5.__ _ (cyclic adenosine monophosphate): acts as a chemical messenger within the cell.

C. DNA and RNA structure: 1. These are very large molecules made of many nucleotides connected to each other by strong covalent bonds forming long strands. Since they contain many nucleotides, they are also called _. 2. The covalent bonds form between the sugar group of one nucleotide and the phosphate group of the next nucleotide, forming a “backbone” of the molecules with alternating sugar and phosphate groups. 3. RNA is a molecule that has a ___strand of nucleotides.__ __4. DNA is a molecule that has a__ __strand of nucleiotides.__ __a. The sugar-phosphate backbone forms the side chains (like the legs of a ladder)__ __b. The two “backbones” (legs of the ladder) are connected to each other by__ __forming__ _ __bonds between the nitrogenous bases (like the steps on a ladder). Remember that these bonds are **weak** bonds however when there are many of them working together they are quite strong.__

__D. Review the structure and function of nucleic acids by matching each of the phrases on the right with a word or phrase from the list on the left. Answers may be used more than once.__

_ __2. Describes the overall structure of DNA__ _ __3. Short for ribonucleic acid__ _ __4. Genetic material passed on from parent to offspring__ _ __5. Nitrogenous bases found in RNA__ _ __6. Sugar found in DNA__ _ __7. Nitrogenous bases found in DNA__ _ __8. Short for deoxyribonucleic acid__ _ __9. Some act as intermediates that contain protein- building instructions__ _ __10. Nucleotides contain a 5-carbon sugar, a phosphate group, and a__ _ _ 11. The sugar of one nucleotide bonds to the _ of the next nucleotide in the chain, forming the backbone of a nucleic acid. _ 12. Is a monomer (building block) of nucleic acids || A. Phosphate group B. Deoxyribose C. A, T, C, G D. DNA E. Nucleotide F. A, U, C, G G. Double helix H. Ribose I. Nitrogenous base J. RNA ||
 * _ __1. Sugar found in RNA__

9. As you have seen in this chapter, there are four main classes of macromolecules. Most are polymers, assembled from smaller monomers (building blocks) in a process called a //condensation// reaction or //dehydration synthesis//. Water is produced as a bi-product of these reactions. The process by which the large polymers are broken back down into monomers is called a //cleavage// reaction or //hydrolysis//. This process requires that water also be broken down and its parts (the H– and –OH) be used to satisfy the bonds that are broken in the polymer. State whether each of the following statements relates to dehydration synthesis reactions (D) or hydrolysis reactions (H). 1. Connects monomers to form a polymer 2. Produces water as a by-product 3. Breaks up polymers, forming monomers 4. Water is used to break bonds between monomers 5. Joins amino acids to form a protein 6. Glycerol and fatty acids combine this way to form a fat. 7. Occurs when polysaccharides are digested to form monosaccharides 8. ―H and ―OH groups are removed, forming a water molecule 9. Nucleic acid breaks up to form nucleotides. 10. Water breaks up, forming ―H and ―OH groups on separate monomers.

1. The four main categories of macromolecules in a cell are
 * //Sample Test Questions for Chapter 3 and Lab #7://**
 * 1) proteins, DNA, RNA and steroids
 * 2) RNA, DNA, proteins and carbohydrates
 * 3) monosaccharides, lipids, polysaccharides and proteins
 * 4) nucleic acids, carbohydrates, monosaccharides and proteins
 * 5) proteins, nucleic acids, carbohydrates and lipids

2. Of the following molecules, which are the only ones that contain phosphorous?
 * 1) fatty acids
 * 2) saccharides
 * 3) proteins
 * 4) DNA
 * 5) all of the above

3. Proteins are built from how many different kinds of amino acids? a. 4 b. 10 c. 20 d. 30

4. In a hydrolysis reaction, _, and in this process water _.
 * 1) a polymer breaks up to form monomers…………is consumed
 * 2) a polymer breaks up to form monomers……….. is produced
 * 3) a monomer breaks up to form polymers…………is produced
 * 4) monomers are assembled to produce a polymer…….is consumed
 * 5) monomers are assembled to produce a polymer……..is produced

5. Proteins are to amino acids as _ are to glucose.
 * 1) fatty acids
 * 2) lipids
 * 3) starches
 * 4) nucleic acids
 * 5) monosaccharides

6. When dehydration synthesis takes place what is happening? a. water has been added to break the polymer into monomers b. chemical takes up excess hydrogen ions c. water is removed to link monomers into polymers d. two amino acids are joining together e. more than one of the above

7. Lipids are: a. commonly known as fats b. hydrophobic c. molecules that mostly have carbon and hydrogen, very little oxygen d. include molecules known as triglycerides e. all of the above 8. TRUE or FALSE: A functional group is generally more reactive than the rest of the molecule.

9. What are the three parts that make up a nucleotide? a. five carbon sugar, phosphate group, and a double helix b. phosphate group, nitrogenous base, and a double helix c. five carbon sugar, nitrogenous base, and enzymes d. phosphate group, nitrogenous base, and five carbon sugar

10. Which of the following protein structures is (are) reversible? a. primary b. secondary c. tertiary d. quarternary e. more than one of the above

11. A molecule with a formula C18H38O is probably a a. monosaccharide b. polysaccharide c. protein d. fat e. nucleic acid

12. The type of lipid that composes the bilayer in a cell membrane is called a: a. steroid b. triglyceride c. phospholipid d. glycerol

13. Peptide bonds a. hold the polypeptide chains of complex proteins together b. form between fatty acids c. are formed by a hydrolysis reaction d. link amino acids together e. none of the above

14. What sugar is it that we humans cannot digest? a. glycogen b. starch c. cellulose d. glucose

15. Depakene 0.75 grams is prescribed by a physician. The bottle of Depakene syrup is labeled 250 mg per 5 ml. How many ml should be given the patient? a. 1 ml b. 2 ml c. 3 ml d. 5 ml e. 15 ml

Definition Worksheet #4: Chapter 4 Identify the major function of the following organelles and structures commonly found in cells. 1. Cell Membrane 2. Nucleus 3. Nucleolus 4. Ribosomes 5. Rough Endoplasmic Reticulum 6. Smooth Endoplasmic Reticulum 7. Golgi Body (Apparatus) 8. Vesicles 9. Lysosomes 10. Peroxisomes 11. Mitochondria 12. Centrioles 13. Cytoskeleton: Microtubules 14. Cytoskeleton: Intermediate filaments 15. Cytoskeleton: Microfilaments 16. Cilia 17. Flagella 18. Tight cell junctions 19. Adhering cell junctions 20. Gap (communicating) cell junctions