3+Biochemistry

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**//Ch. 2//**
atom- the smallest unit of matter that still retains the properties of an element element- a substance that cannot be broken down by ordinary chemical means molecule- two or more atoms held together by a covalent bond compound- a substance containing two or more elements in a fixed ratio ion- an element having a charge as a result of reactions with other elements (gain or loss of one or more electrons) isotope- types of an element with the same number of protons and electrons but with a different number of neutrons Top four- C,H,O,N (96%) Most of the remaining- Ca,P,K,S,Na (also some other "trace elements"- essential elements that are present in minute quantities)
 * 1. Differentiate between the following terms: atom, element, molecule, compound, ion, isotope.**
 * 2. What are the most common elements in living organisms?**
 * 3. Be able to use a periodic table to determine the number of protons, neutrons and electrons in an element.

4. Differentiate between atomic mass and atomic weight as used in class.** atomic mass- number of protons + number of neutrons; whole number atomic weight- weighted average of all atomic masses (can change because of isotopes); decimal number They are used in research in medicine; however, they can be damaging to organs and molecules (especially DNA) Ionic- two ions of opposite charges attract eachother, holding them together; strong attraction; ex. NaCl - transfer of e- (jb) Covalent- two atoms share one or more pairs of outer shell electrons; strong attraction; ex. CH4 Hydrogen- the positively charged region (H+) is attracted to the negatively charged region (OH-) of polar water molecules; weak attraction Electronegativity is defined as an atoms attraction for its electrons, its own, transferred and shared. In covalent bonds, the electronegativity defines whether a bond is polar or non-polar. If the difference between the two electronegativities is very small, the bond is balanced and therefore non-polar (H2). If the electronegativity difference is slightly large that will cause a polar covalent bond (H2O). Finally, if the difference is greater than 2.0 the electron transfers and creates an ionic bond (NaCl). -expands when frozen=less dense=on surface -capillary action=climbing up thin tubes (adhesion-stick to SOMETHING, cohesion-stick to ITSELF) -high heat vaporization/high specific heat=lots of energy to change temp. -surface tension=measure of the difficulty in breaking the surface of a liquid, important for insects that walk on H2O concentration of hydrogen ions-used to describe how acidic or basic a solution is; (potential hydrogen scale) b/c the number of hydrogen ions changes by a TEN-FOLD each pH unit change...pH3 has 10x less H+ than pH2 and 100x less than pH1 (the lower the pH the higher the concentration of H+ ions)
 * 5. How are radioactive isotopes used in studying Biology?**
 * 6. Distinguish between the three types of bonds we have studied (ionic, covalent and hydrogen) with regard to how the participating atoms are bonded, and the strength of the bond. Be able to give examples.**
 * 7. How does electronegativity influence the bonding characteristics of elements? Distinguish between polar and non-polar covalent bonds. Be able to give examples.**
 * 8. Describe the special properties of water we discussed in class. Be able to give examples of their importance to living systems.**
 * 9. Define pH. Be able to work simple problems to determine either pH, [H+], or [OH-].**
 * 10. What does it mean that pH is a log scale? Be able to work simple problems regarding this concept.**

**//Ch. 3//**

 * 1. Be able to answer all of the questions on the Biochemistry Practice Worksheet.**


 * 2. Be able to circle and label all the functional groups we studied in class (hydroxyl, carbonyl, carboxyl, amino, phosphate, and sulfhydral).**

Dehydration synthesis is when cells link monomers together to form polymers and a water molecule is removed in the process. The primary product is the new polymer formed and the by product is water. Energy is stored; therefore, it is required for the reaction. The name is appropriate because when the two chains are linked together one loses a hydrogen and the other loses a hydroxide. The two bond together forming H2O and are lost from the chain. Hydrolysis is when a polymer separates into two pieces, breaking the bond by adding a split water molecule. Energy is released. The name is appropriate because hydro- refers to water, while -lysis refers to split, and water is literally split in the reaction.
 * 3. What is a condensation (aka dehydration synthesis) reaction? What is produced as the primary product and what is produced as the by product? Is energy released or required? Why is the name appropriate?**
 * 4. What is a hydrolysis reaction? What is produced as the primary product and what is required? Is energy released or required? Why is the name appropriate?**
 * 5. Be able to illustrate the concept of dehydration synthesis or hydrolysis. (ex. Text p.49 #16)**

Carbohydrates- monosaccharides; CHO; covalent (glycosidic linkage); quick-intermediate energy; ex. structural- cellulose (p) (alpha/ruffage-can't be broken down), chitin (a) (beta-can digest) Lipids- Fat (glycerol+3 fatty acids) and Phospholipids (glycerol+2 fatty acids+phosphate group); CHO; Polymers are fats, phospholipids, steroids, wax; covalent (ester); long term energy and builds cell membrane Proteins- amino acids; CHON; Polymers are proteins (polypeptide); covalent (peptide); service varies Nucleic Acids-monomers are nucleotides; CHONP; covalent (phosphodiester); genetics (mer-unit) monomer-one unit polymer-multiple units Carbohydrates- -momosaccharide=monomer-monosaccharide (CHO, gluclose, fructose, galactose) -disaccharride=monomer-monosaccharides (CHO, sucrose, maltose, lactose) -polysaccharide=monomer-monosaccharide (CHO, glycogen, starch, chitin, cellulose) Lipid -fat=monomer- 3 fatty acids + 1 glycerol (CHO, triglyceride) -phospholipid=monomer- 2 fatty acids + 1 glycerol +1 phosphate group (CHOP, phospholipid) -steriod=monomer-4 fused rings (CHO, cholesterol) Nucleic Acid -monomer=phosphate, sugar, nitrogenous base (CHONP, DNA and RNA) Protein -monomer=amino acids (CHON, leucine, etc)
 * 6. Know the characteristics of the 4 classes of macromolecules we talked about in class (ie. The Notes)**
 * 7. Be able to differentiate between a monomer and a polymer, know the monomers and examples of the polymers of the 4 classes of macromolecules.**
 * 8. Carbohydrates**

(CH2O)n 2:1 C, H, O Monosaccharides are single sugars: glucose, fructose, galactose Disaccharides have 2 sugars: maltose (glucose+glucose), sucrose (glucose+fructose), lactose (glucose+galactose) Polysaccharides have many sugars (thousands):: two types= storage (starch-p / glycogen-a) and structural (cellulose-p / chitin-a) Storage: starch=plants (not digestible), glycogen=animals Structural: cellulose= plants (not digestible), chitin=animals...the difference is based on which one is an alpha and which is beta alpha-the OH is pointing DOWN and beta-the OH is pointing UP Polar
 * a. What is the general formula? What is special about the H:O ratio?**
 * b. What elements are involved?**
 * c. Differentiate between mono-, di-, and polysaccharides and be able to give examples of each. Differentiate between pentose and hexose sugars and be able to identify diagrams of each.**
 * d. Differentiate between starch, glycogen and cellulose. What do each do, what kind of organisms have them, how are they structurally similar and how are they structurally different?**
 * e. How do alpha and beta glucose differ from each other?**
 * f. Are carbohydrates polar or non-polar?**

fat- CHO phospholipid- CHOP not 2:1 fat-3 fatty acids + 1 glycerol phos- 2 fatty acids + 1 glycerol + phosphate group fat- triglyceride phos- phospholipid saturated- no double bonds between carbons, straight chain, mostly animal fats, usually solid at room temp. unsaturated- at least 1 double bond in the carbon chain, hydrocarbon is bent, usually liquid at room temp, mostly plant fats, better for you H- has been added to unsaturated fats to make them more solid at room temp. ex. margarine
 * 9. Lipids**
 * a. What elements are involved in a fat and in a phospholipid? What is special about the H:O ratio?**
 * b. What monomers make up a fat? What monomers make up a phospholipid?**
 * c. Give examples of fats and phospholipids?**
 * d. Differentiate between saturated and unsaturated fats? Be able to recognize structures of each? What properties does this give?**
 * e. What is partially hydrogenated vegetable oil?**

a. What elements are involved in proteins?** C, H, O, N Amino acids; 20; H H O (all single bonds except O to C has a double bond) H-N-C-C-OH R
 * 10. Proteins
 * b. What are the monomers of proteins called? How many common versions of these are there? Some are essential; what does this mean?**
 * c. What is the basic structure of an amino acid? What is an R group? Be able to tell if an R group would be expected to be polar, non-polar, or charged? How does this affect the overall protein?**
 * d. Why is the name amino acid appropriate?

e. Be able to draw how you would join amino acids to form a polypeptide (ex. Study Guide Ch.3 #7 p.26) f. Why is there so much diversity among proteins?** Because just like with 26 letters in the alphabet endless words are made, with 20 R groups, tons of combinations are possible for protein structure Primary- sequence of amino acids Secondary- folding amino acid chain into alpha helix and beta pleated sheets; stabilized by hydrogen bonds Tertiary- 3-d; interactins of R groubs Quaternary- interactions of seperate protein subunits to form a functional protein
 * g. Be able to describe primary, secondary, tertiary, and quaternary levels of protein structure. What holds them together? (ex. Study Guide Ch.3 #8 p.27)**

a. What do DNA and RNA stand for?** deoxyribonucleic acid and ribonucleic acid C, H, O, N, P nucleotides; they consist of a five carbon sugar, a phosphate group, and a nitrogenious base double helix //Don't forget that there are some very good practice problems at the end of the chapter in the text and study guide.//**
 * 11. Nucleic Acids
 * b. What elements are involved?**
 * c. What is the monomer of DNA? The monomer consists of three parts; what are they?**
 * d. What is the basic shape of DNA?**