D.+Biochemistry+(4-5)

toc =Target III - Basic Organic Chemistry (Ch. 4)=

1. Define the term organic chemistry. 2. State at least 5 reasons why carbon is ‘special.’ 3. Identify the valences for the major elements of organic molecules: C, H, O, N, P, S 4. Distinguish between structural isomers, geometric isomers, and enantiomers (chiral compounds). 5. Identify the 7 functional groups when presented with a structural formula (drawing) of their structures. Link each functional group to the types of molecules they form. Describe their functions and polarity.
 * Chapter 4- Carbon and the Molecular Diversity of Life (p. 58-65)**

=Target IV - Macromolecule Compesition, Synthesis, and Breakdown (Ch. 5)= 1. Recognize how dehydration synthesis can be used to build polymers from monomers and the name of the bond between monomer units for carbohydrates, lipids, and proteins. 2. Recognize how hydrolysis can be used to break down polymers into monomers. 3. Identify the elemental composition, general formula, structural formula (drawing), types, and functions of Carbohydrates. 4. Identify the elemental composition, structural formulas (drawings), types, and functions of Lipids. 5. Identify the elemental composition, structural formulas (drawings), levels of structure, and functions of Proteins.
 * Chapter 5- The Structure and Function of Large Biomolecules (p. 68-89)**

= Overall Review = =LINKS!=

__**Vocab Quizlet (may also include 2-3):**__ [|Biochemistry Vocabulary]
 * __Enzyme Quizlet! [|enzyme vocab quizlet]__**
 * __Chapter 4 quick review of basic things! (Youtube video) [|AP BIO CH. 4]__**
 * __Lipids review Youtube video! [|Lipids]__**
 * __Enzyme (Youtube Video)! [|Enzyme]__**
 * __Functional group jeopardy! [|functional group jeopardy]__**
 * __Basic Biochemistry Basic Biochemistry quiz__**
 * __Another biochem quiz__**
 * __[|Macromolecules Quiz]__**
 * __[|Basic but pretty nice overview of carbohydrates, lipids, proteins]__**

=__Review questions__=
 * __Quick fill in the blanks!__**

4 Unique properties of water: 1. Water is p_ and can dissolve other p_ substances. 2. Water has c __and a___ properties. 3. Water has a h_ h __capacity.__ __4. Water has a high s___ t__.__

__Answers: polar, polar, cohesive, adhesive, high, heat, surface, tension__

__**Simple review questions!**__ __-Monosaccharides, the simplest sugars, serve as an energy source for cells. The two most common sugars are__ __and__ __.__ __-Glucose can come in two forms: α-glucose and β-glucose. They differ by a reversal of what two elements on the first carbon?__ __-Fructose is a common sugar in__. -How many carbon molecules should both ring form and the straight-chain form of glucose have? -The two molecules of monosaccharides are chemically linked and form a __.__ __-Maltose is formed by linking two glucose molecules, forming a__. -Plants "stockpile" α glucose in the form of a starch called __.__

__Answers: glucose, fructose; H and OH; fruits; 6 carbon molecules; disaccharide; glycosidic bond; plastids__

__**Bio chem overall review quiz!**__

__1. Which of the following organic molecules is a major storage carbohydrate used to store energy in plants?__ __A) Cellulose__ __B) Maltose__ __C) Fructose__ __D) Starch__ __E) Glycogen__

__2. All of the following organic compounds contain a hydroxyl functional group EXCEPT__ __A) Maltose__ __B) Glucose__ __C) Fructose__ __D) Glycerol__ __E) Triglyceride__

__3. The conversion of lactose to glucose and galactose involves the addition of which of the following molecules to the lactose molecule?__ __A) NADH__ __B) H2O__ __C) ATP__ __D) O2__ __E) H2__

__4. Weak bond formed between polar molecules are__.

5. What is the name of the process by which an organic compound is "split" into two or more compounds?

6. What is the general formula for monosaccharides?

7. A chain of more than 50 amino acids is referred to as a(n) A) Protein B) Hormone C) Enzyme D) Peptide

8. Bonds that are the key to the Secondary Structure of Proteins are called: A) Glycosidic Linkages B) Hydrophobic interactions C) Ionic Bonds D) Disulfide Bonds E) Hydrogen Bonds

9. Acids and Bases denature a Protein by disrupting which of the following bonds: A) Ionic bonds and hydrophobic interactions B) Hydrogen and peptide bonds C) Peptide and Ionic Bonds D) Ionic and Hydrogen Bonds E) Hydrophobic interactions and peptide bonds

10. The amino acids which cannot be naturally manufactured in the body and must be consumed in the diet are known as A) Perfect Amino Acids B) Polar Amino Acids C) Ionic Amino Acids D) Hydrophobic Amino Acids E) Essential Amino Acids

11. Which of the following chemical groups is not normally found as a component in ALL amino acids? A) Amino Group B) R-Group C) Methyl Group D) Carboxyl Group

12. Which of the following cannot be digested by humans? A) Amylose B) Cellulose C) Monosaccharides D) Fiber E) Fructose

Answers: 1. D 2. E 3. B 4. Hydrogen Bond 5. Hydrolysis 6. CH2O 7. A 8. E 9. D 10. E 11. C 12. B

1. The connecting CO-NH bond in an organic molecule is a peptide bond. 2. Properties of water contain cohesion, adhesion, polarity, and low heat capacity. 3. Glycine is a polymer. 4. Ester linkage connects the fatty acid to glycerol in a tricylglycerol. 5. Peptide Bond is a basic functional unit of organic molecule.
 * True or False__**

Answers: 1.T 2.F 3.T 4.T 5.F

=__**OTHERS!**__=

This isn't really specified for Biochem... but I thought it was a good review for the whole exam check it out :) [|overall final exam review]

Really nice site that has a bunch of sets of flashcards on many different topics [|AP Bio Exam Review]

Fantastic site that covers a bunch of stuff we learned this year. There's a pretty lengthy Biochemistry section [|Bio tutorials, animations, explanations]

=** TARGET BY TARGET REVIEW **= = = = Target 3 Basic Organic Chemistry (Ch 4) REVIEW! =

Powerpoint for Ch. 4!




 * 1. __Define the term organic chemistry__**: Compounds containing carbons are said to be organic, and the branch of chemistry that specializes in the study of carbon compounds is called **organic chemistry.**


 * -What are the major elements used in organic chemistry? List 6.**
 * -What are the difference between organic and inorganic compounds?**

Answers: -C,H,O,N,S,P (CHOP SON! I have no idea... I just kinda made that up... At least it's a bit easier to memorize?) C - Carbon H - Hydrogen O - Oxygen N - Nitrogen S - Sulfur P - Phosphorus

Diagram! Basic shapes of organic molecules 2. State at least 5 reasons carbon is special. media type="youtube" key="gP8H7xj97pA" height="315" width="560"

media type="youtube" key="XKh3mjBaimY" height="315" width="560"

Quiz: Why is carbon special?? [|carbon quiz.docx]

Why is carbon so special?


 * Just a couple:**
 * Carbons can form long chains
 * Carbons don't have to bind to each other in straight chains, they can "branch" or create rings
 * Carbons aren't limited to single bonds, there can be double and triple bonds by sharing multiple electrons
 * Carbons have isomers. Isomers are compounds that have the same atoms and same elements but different structures, which give the isomers different properties.
 * Carbons bond to each other, and any electrons that are not used to bond the carbons together are used to form bonds with atoms of different elements

3. Identify the valences for the major elements of organic molecules: C, H, O, N, P, S media type="youtube" key="ZZ6g70BXbW8" height="315" width="560"



In the periodic table, the number of the column is the number of valence electrons of the elements in that column. C - 4 valence electrons H - 1 valence electron O - 6 valence electrons N - 5 valence electrons P - 5 valence electrons S - 6 valence electrons

The number of valence electrons is important. It usually determines how the atoms will interact with other atoms. If a valence shell is nearly filled, then the atom will be less reactive and less likely to share or give electrons to other atoms.

4. Distinguish between structural isomers, geometric isomers, and enantiomers (chiral compounds).



-Biochemistry of vision involves a light-induced change of rhodospin, chemical compound in the eye, from the cis to trans isomer. -Enantiomers important in pharmaceutical industry
 * Isomers** are compounds that have the same numbers of atoms of the same elements but different structures and hence different properties.
 * Structural isomers** are isomers that have different covalent arrangement of their atoms.
 * Geometric isomers**: as you can see in Figure 4.7, double bonds are key in geometric isomers. Single bonds allow atoms to rotate freely around the atom they are attached to, while double bonds are relatively rigid and do not allow much movement.
 * **Cis isomer:** The arrangement with both Xs on the same side of the double bond
 * **Trans isomer:** The arrangement with the Xs on opposite sides
 * Enantiomers** are literally mirror images of each other.

[|Identifying Isomers] This may not be the best, but it's for identifying if the structures are isomers or not.

media type="youtube" key="yHiRYSfA1tk" height="315" width="560"

[|QUIZ!] [|QUIZ 2!]

5.Identify the 7 functional groups when presented with a structural formula (drawing) of their structures. Link each functional group to the types of molecules they form. Describe their functions and polarity.

Here's a very easy way to quiz yourself on the functional groups! [|Udraw Functional groups!] [|Online flashcards on functional groups]
 * __^^If you can't see clearly this refer to page 64-65 in the book!__**
 * __[|FUNctional group Jeopardy! :)]__** (It's also at the top of the wiki page)

=Target IV - Macromolecule Compesition, Synthesis, and Breakdown (Ch. 5) REVIEW!= Target IV-1

Dehydration Synthesis removes a water molecule and bonds two (or more) organic monomers together. media type="youtube" key="UyDnnD3fMaU" height="315" width="420"

Target IV-2

Hydrolysis adds a water molecule and splits an organic polymer into two (or more) smaller organic compounds.


 * Carbohydrates, Lipids, and Proteins, and How to Tell them Apart - Target IV-3, IV-4, and IV-5**


 * || Carbohydrates || Lipids || Proteins ||
 * Monomer Units || Monosaccharides || Fatty Acids (and glycerol) || Amino Acids ||
 * Functional Groups || Carbonyl, Hydroxyl || Methyl || Carboxyl, Amine ||
 * Linkage name || Glycosidic linkage || Ester bonds || Peptide bonds ||
 * Functions || Broken down so the body can use energy || Protection, long-term energy storage, or as componenets in a cell membrane. || Used for just about anything not covered by carbohydrates and/or lipids. ||
 * Structure || Long chains of repeating monossacharides (usually glucose) || One glycerol molecule and 3 fatty acids || Long chains of amino acids ||

Target IV-3

Carbohydrates are composed of long chains of monosaccharides, such as glucose. Monosaccharides have the general formula C_H2_O_; every monosaccharide, regardless of which monosaccharide it is, has 2 hydrogens and 1 oxygen for every carbon the monosaccharide contains. Glucose, shown below, has the formula C6H12O6.

Carbon, Hydrogen, and Oxygen are the only elements in a carbohydrate.

Polysaccharides, such as starch or cellulose, are long chains of monosaccharides joined together by glycosidic linkages. Shown below are amylose and amylopectin, two types of starches. Each hexagon reperesents a molecule of glucose used in the chain.

Carbohydrates are used as the primary food source for cellular respiration, used in all aerobic organisms. When food is not needed by the organism, the carbohydrates are stored as starch in plants and glycogen in animals. Cellulose, also a carbohydrate, is used in plants' cell walls to provide structure and protection for the cells.

Amylopectin is turned into blood-sugar extremely quickly when compared with amylose. Within humans, carbohydrates are most often stored within the body in glycogen, a branched polysaccharide. Most carbohydrates are broken down in the human body by the enzyme amylase (sometimes seen as salivary amylase and sometimes it is seen as pancreatic amylase).

media type="youtube" key="c1WEL2CQeDc" height="315" width="560" Target IV-4

Lipids consist of 3 fatty acids and one glycerol molecule - EXCEPT in one case: Phospholipids, used in the cell membrane, contain only two fatty acids.

Phospholipid:

The fatty acids are hydrocarbons that can be of three types: Saturated fats (containing no double bonds), Unsaturated fats (containing at least one double bond, where the hydrogens are on the same side of the carbon chain), and Trans fats (containing at least one double bond, where the hydrogens are on opposite sides of the carbon chain) (These units are part of a larger chain) Also note: the unsaturated fat molecule will be physically bent due to it being the cis isomer

Lipids are used in the cell membrane (phospholipids), in long-term energy storage, and in protection.

[|Some basics about lipids]

Target IV-5

Proteins are composed always of carbon, hydrogen, oxygen, and nitrogen. Structurally, all amino acids are identical except for one thing. The R-group at the side of the amino acid varies depending on what amino acids are used.

Amino acids, joined together by peptide bonds, form a polypeptide chain otherwise known as a "protein". The specific sequence of the amino acids is "primary structure". Hydrogen bonds between the R-groups, forming structures such as alpha-helices and beta-pleated-sheets, form the secondary structure. Van der Waals interactions and attractions and repulsions by the various amino acids cause the three-dimensional structure of the protein to form: the tertiary structure. Quaternary structure does not exist in all proteins, but some proteins are composed of two or more smaller proteins, which wrap together via interactions between the two proteins to form the quaternary structure.
 * Primary structure** of a protein is the sequence of amino acids. These chains of acids are very long, and the primary structure of a protein isn't random. Inherited genetic information determinds the shape.
 * Secondary structure** of a protein is a bunch of coils and folds. The coils and folds are due to hydrogen bonds. Although hydrogen bonds are weak, there are many of these bonds along the chain, so the bonds are able to support a particular shape or structure for the protein. The two types of secondary structures are a-helix and B-pleated sheets. In the a-helix, a coil is formed through hydrogen bonds, which occur every fourth amino acid. In the B-pleated sheets, two or more regions of the polypeptide chain are connected side by side through hydrogen bonds.
 * Tertiary structure** of a protein is the overall shape of polypeptides. The tertiary structure looks like a mass of coils and folds. Amino acids with hydrophobic side chains usually move towards the middle of the protein, because they're hydrophobic. Now that the nonpolar amino acids are close together in a clump, van der Waals interactions keeps the structure together. The structure is stabilized by hydrogen bonds between polar side chains and ionic bonds between positively charged side chains and negatively charged side chains.
 * Quaternary structure** is the overall protein structure that is the conglomeration of the previous structures.

A protein's function is determined by its structure. When a proteins is denatured; that is, loses its shape, the protein ceases to work properly. Proteins are denatured by heat.

Proteins are used in cells as enzymes, in cell signaling, in cellular active transport and facilitated diffusion, in macroscopic structure, and various other functions.

media type="youtube" key="Tj1IekkRe_c" height="315" width="420"
 * A cute video, don't know how much help it'll be but it's pretty amusing (:**

//**__Target 5 review quiz__**// //**[|Self quiz for polypeptides and proteins]**//