Chemistry you need to know Chapter 2

P 26: Know symbols for elements in table 2.1, oxygen to iron; know charge on ions: calcium, potassium, sodium, chlorine ^K^y-^.-^K

P 29 isotope radioisotopes p 29-30 - ' ^ ^ t r

P 30-31 mixtures, solutions, concentration in percent and molarity (in most medical applications, concentration is in percent)

P 33-36 types of bonds, difference between ionic and covalent; polar and nonpolar; hydrogen bond

P 38 oxidation-reduction or redox reactions - • Basis of all reactions in which food is catabolized (broken down)

; Reactant losing electron = electron donor is oxidized ' Reactant gaining electron = electron acceptor is reduced ^ Occur when ionic cmpds formed; NaCI;

sodium loses electron = ~ - * chlorine gains electron = * ^ ^ ' - '

also occur when substances change patterns of sharing electrons substance oxidized by losing H or combining with O

oxygen is very electronegative and so electrons spend more time around it Cellular respiration: glucose oxidized and oxygen reduced

P 39 Chemical equilibrium; represented in a reaction by double arrow Once equilibrium is reached..no net change Many biological reactions are irreversible for all practical purposes = Cellular respiration; ATP is used immediately and carbon dioxide is removed

P 39 Collision Theory and factors influencing rates of reactions

P 40-41 Biochemistry: difference between organic and inorganic Water: why is it so important?

2. 3. 4. -5. - ^^

Salt: Disassociate: Electrolyte: ' . 'r Common in body are: " '-' ' ' Proper ionic balance is job of

P 41-42 Acids and bases: electrolytes; disassociate in water Acids: release ions; proton donors; biological acids include: hydrochloric, acetic,

carbonic

Bases: release OH' ions called hydroxyl ions; protons acceptors; biological bases include bicarbonate and ammonia

P 42-43: pH Acid-Base concentration pH is a measure of hydrogen Ions in solution in moles per liter or molarity pH goes from 0-14 and is logarithmic or based on exponents . -pH negative log of hydrogen ion concentration in moles per liter or -log[H ] pH of 0-6 is acidic with 0,1,2 being strong 5,6 weak pH of 7 is neutral pH 8-14 is basic or alkaline with 8,9 weak bases, 12,13,14 strong bases neutralization: acids and bases combined in proper proportions yield water and a salt

p 43 Buffers Living cells are very sensitive to slight changes in pH; strong acids and bases are very

damaging to tissues; acid-base balance is regulated by kidneys, lungs and by buffers Buffers: chemicals that resist large or abrupt changes in pH by acting as acids when pH rises and act as bases when pH drops Strong acids disassociate completely; -weak acids do not 100 HAc • 90 HAc + 10 + 10 Ac

if we add more ions, the H" and Ac" combine to form HAc; equilibrium shifts to the left if we add a base, OH', then more HAc disassociates releasing more H ions which combine

with the hydroxyl ions to form water strong bases disassociate easily and combine with H ions Weak bases like sodium bicarbonate ionize incompletely and can shift left or right Blood pH- see other paper ^

P 43 Organic cmpds; carbon, small, electroneutral, can form chains, rings, and other structures

P 44-46 Carbohydrates include sugars and starches; carbon, hydrogen, oxygen with H and 0 in 2:1 ratio as in water (carbon and hydrate (water)

Classified by size and solubility; larger are usually less soluble Mono Di Poly • , : .

Sugars end in -ose Disaccharides formed by dehydration synthesis Broken by hydrolysis Starch, glycogen Major function = Structural formulas and short version Know glucose and ribose

P 46-48 Lipids: fats and oils, insoluble in water, carbon, hydrogen and oxygen(less oxygen) Triglycerides: 3 fatty acids and a glycerol; stored fuel

Saturated all single bonds Mono or poly unsaturated contain one or more double bonds

Phospholipids- polar "head" and nonpolar "tail"; form cell membranes ^ Steroids-four interlocking hydrocarbon rings; cholesterol-structural formula

P 48-54 Proteins: Structural material and enzymes; carbon, hydrogen, oxygen, and nitrogen; some contain phosphorous or sulfur Made of amino acids; generalized structure of an amino acid: amine group, acid group, R group

Amino acids joined by dehydration synthesis; resulting bond called a peptide bond Dipeptide, polypeptide; proteins—usually hundreds of amino acids

Structural levels in proteins: see Fig 2.18p 51 -:'r^f:

Primary-"strand" of amino acids strung together W ^^^-^ Secondary-for or twist, helix or pleat, because of hydrogen bonds, like a coiled telephone

cord Tertiary- helix or pleat folds in on itself to form a "glob" with a certain 3-D shape Quaternary- two or more polypeptide chains folded with each other

Fibrous and globular proteins Fibrous—like a fiber; collagen, keratin, actin and myosin in muscles; structural Globular—compact, spherical; enzymes, hemoglobin, antibodies; functional

Molecular chaperons—globular proteins that help other proteins fold properly Characteristics of Enzymes: globular proteins that act as biological catalysts to regulate or

. accelerate reaction but are not used up during reaction Coenzyme: vitamin or metallic ions necessary for proper protein function End in -aser, Example: lactase is an enzyme that helps break down the sugar lactose

Mechanism of enzyme activity: recall collision theory and activation energy ( see fig 2.20 p54) 1. enzyme binds with substrate (substance upon which enzyme acts); there is an active

site which is an area on enzyme where substrate fits (lock and key or induced fit model) 2. enzyme-substrate complex rearranges 3. enzyme releases product

P54-57 Nucleic acids: made of carbon, hydrogen, oxygen, nitrogen, and phosphorous Nucleiotides-monomer made of nitrogen base, 5 carbon sugar, and a phosphate group Nitrogen bases: Purines are: adenine, guanine, Pyrimidines are: thymine, cytosine and uracil

DNA: deoxyribonucleic acid; found in nucleus of cell, genetic material, replicates, provides instructions for making proteins, double helix RNA: ribonucleic acid; inside and outside nucleus; carries out instructions in DNA; single strand See table 2.4p 57 -

P57-59 Adenosine triphosphate—ATP; although we rightly say glucose is "fuel" for cells, glucose is broken down during cellular respiration into energy packets the cells can use for reactions; each glucose molecule produces 36 molecules of ATP ADP or adenosine diphosphate is phosphorylated into ATP; wavy line means high energy bond AP~P~P

Chapter 2 review packet: " "

Human blood normally has a pH between 7.35 and 7.45. By comparison, salvia has a pH of 6.6 and stomach juices have a pH from 1-3. A variety of factors affects the acidity or alkalinity(base) of blood such as what is ingested, vomiting, diarrhea, lung function, kidney function and infections.

One way the body controls the blood pH involves the release of carbon dioxide from the lungs. Carbon dioxide is a waste product of cellular respiration (a.complex chemical reaction that releases chemical energy) and is constantly produced by the cells. In the bloodstream, carbon dioxide dissolves in the watery fluid inside the red blood cells forming carbonic acid (H2CO3)

CO2 + H2O _ Waste inside From red blood Cells cells

As more carbon dioxide is produced by cells, more is dissolved in the blood making the blood more acidic, (lower pH)

In the blood, carbonic acid dissociates, or separates, into H ions (hydrogen ions) and HCO3' ions (bicarbonate ions). In the blood, these ions are carried to the lungs. In the lung tissue the hydrogen ions and the bicarbonate ions interact (with the aid of an enzyme) to produce carbon dioxide and water, the reverse of the first equation.

H* + HCO3" • CO2 + H2O

The carbon dioxide passes from the blood to the lungs where it is exhaled. The more carbon dioxide a person exhales, the more CO2 is removed from the blood. This makes the blood less acidic, (higher pH) The pH of the blood increases as breathing becomes faster and deeper. By adjusting the speed and depth of breathing, the brain and the lungs are able to regulate the blood pH from minute to minute.

Acidosis-blood is too acidic. Can be caused by ingestion of certain poisons including too much aspirin; advanced stages of shock or type 1 diabetes; kidney malfunction.

Alkalosis-biood is too basic. Can be caused by rapid, deep breathing (hyperventilating); prolonged vomiting (removes acid from stomach); use of diuretics or some steroids

Both conditions can be life threatening and may require medical attention.

1. Which ion is responsible for acid properties of carbonic acid? . 2. What does dissociate mean? What happens when

carbonic acid dissociates? 3. As you exercise, more CO2 is produced. To rid your body of this your breathing rate

4. One cause of acidosis is 5. One cause of alkalosis is 6. Blood must be kept in a range of pH from to

H2 CO3 carbonic acid

2. Inser t t h e chemical symbol ( t h e chem i s t ' s s h o r t h a n d ) i n the a n s w e r b l a n k s for each o f t h e f o l l o w i n g e l e m e n t s .

1. O x y g e n

2. C a r b o n

3. Po tass ium

4. I o d i n e

5. H y d r o g e n

6. N i t r o g e n

7. C a l c i u m

8. S o d i u m

. 9. P h o s p h o r u s

10. M a g n e s i u m

1 1 . C h l o r i d e

12. I r o n

4. F r o m t h e list b e l o w , select t h e e l e m e n t o r e l emen t s that m a t c h the d e s c r i p t i o n s . Insert the i r c h e m i c a l s y m b o l s i n the a n s w e r b l a n k s .

O x y g e n

C a r l x ) n

Pota.ssium

C a l c i u m

S o d i u m

P h o s p h o r u s

M a g n e s i u m

C h l o r i d e

I r o n

I o d i n e

H y d r o g e n

N i t r o g e n

1. F o u n d as a salt i n b o n e s a n d tee th

2. M a k e u p m o r e t h a n 96% o f the ma.ss o f a l i v i n g ce l l

3. Essent ia l f o r t r a n s p o r t o f o x y g e n i n r e d b l<x )d cel ls

4. Es.sential c a t i ons i n m u s c l e c o n t r a c t i o n

5. Essent ia l for p r o d u c t i o n o f t h y r o i d h o r m o n e s

6. Present i n n u c l e i c ac ids ( i n a d d i t i o n t o C, H , O, a n d N )

7. T h e mos t a b u n d a n t nega t i ve i o n i n ex t r ace l lu l a r Huids

6. F i gure 2.3 i l lustrates f ive w a t e r m o l e c u l e s h e l d t o g e t h e r b y h y d r o g e n b o n d s . First, c o r r e c d y i d en t i f y the o x y g e n a n d h y d r o g e n a t o m s b o t h b y c o l o r a n d b y i n s e r t i n g t h e i r a t o m i c s y m b o l s o n t h e a p p r o p r i a t e c i rc les ( a t o m s ) . T h e n l abe l the f o l l o w i n g s t ruc tures i n t h e f i gu re :

O O x y g e n

Q H y d r o g e n

Q Pos i t i ve p o l e

Q Nega t i v e p o l e

Q H y d r o g e n b o n d s

7. C i rc l e e a c h s t ruc tu ra l f o r m u l a that is l i k e l y t o b e a po l a r c o v a l e n t c o m p o u n d .

C l I

A. Cl - C - C l 1

C l

B. H - C l

H H \

C. N /

H

D . Cl - C l

H \

E. O /

H

i. Use the key cfioices to identity the substances described in the- f o l l ow ing statements. Insert- the appropr iate answers in the answer blanks.

Key Choices

A. Acids B. Bases C. Buffers D. Salts

1- 2. 3. Substances that ionize in water; good electrolytes

4. Proton (H* ) acceptors

5. Substances that dissociate in water to release hydrogen ions and a negative

ion other than hydrox ide (OH~)

6. Substances tha t dissociate in water to release ions other than H * and O H "

7. Substances formed w h e n an acid and a base are combined

8. Substances such as l emon juice and vinegar

9. Substances that prevent rapid o r large swings- in pH

10. Substances such as ammonia and mi lk o f magnesia

4. Define pH.

5. Using the key choices, ful ly characterize weak and strong acids.

Key Choices

A. Ionize completely in water E. Ionize at high pH

B. Ionize incompletely in water F. Ionize at l ow p H

C. Act as part of a buffer system G. Ionize at p H 7

D. When placed in water, always act to change the p H

Weak acid; , Strong acid:

Organic Compounds

1. Match the terms in Co lumn B w i t h the descriptions in Co lumn A. Enter the correct letters in the answer blanks.

C o l u m n A Coiurnn B

1. Bu i ld ing blocks o f carbohydrates A. Amino acids

2- Bu i ld ing blocks o f fat B. Carbohydrates

3. Bu i ld ing blocks o f protein C. Lipids (fats)

4. Bu i ld ing blocks o f nucleic acids D. Fatty acids

• 5. Cellular cytoplasm is pr imar i ly composed o f this substance

E. Glycerol

6. The single most important fuel source for body cells

F.

G.

Nucleotides

Monosaccharides

7. Not soluble in water H . Proteins

8. Contains C, H, and O in the ratio C H j O

9- Contain C, H , and O, but have relatively small amounts o f oxygen

11. These bui ld ing blocks contain N in addit ion to C, H, and O

,12. Contain P in addi t ion to C, H , O, and N

.13. Used to insulate the body and found in all cell niembranes

_14. Primary components o f meat and cheese

,15 . Primary components o f bread and lo l l ipops

.16 . Primary components o f egg yo lk and peanut o i l

_17. Includes col lagen and hemog lob in

_18 . Class that usually includes cholesterol

36 Chapter 2 Chemi.stry Comes Alive

2. For each o f the fo l lowing statements that is true, insert T in the answer blank. For each false statement, correct the underl ined word(s ) and insen your cor­rect ion in the answer blank.

\. Phospholipids are polarized molecules.

2. Steroids are the major form in wh i ch Ixx ly fat is stored.

'. 3. Water is the most abundant c ompound in the body.

4. Nonpolar molecules are generally soluble in water.

_ ^ 5. The bases o f RNA are A, G, C, and U.

. 6. The universal energy currency o f l iv ing cells is RNA.

7. RNA is single-stranded.

8. The bond type l ink ing the subunits o f proteins together is commonly called the hydrogen bond .

9. The external fuel o f choice used by cells as a ready source o f energy is stargh-

j _ ' \ 0 . The nucleotide base complementary to G is Q.

^ 11. The backbone o f a nucleic acid molecule consists o f sugar and base units.

3. Five s impl i f ied diagrams o f the structures of five biochemical molecules are shown in Figure 2.4.

First, identify (he molecules and insert their correct names in the answer blanks on the figure (A through E).

Second, select a different color for each type o f molecule listed be l ow and use it to color the coding circle and the corresponding molecular structure in the i l lustrat ion.

O O Nucleotide Q Monosaccharide

O Funct ional prote in Q Polysaccharide

Th i rd , answer the questions relating to these diagrams by insert ing your answers in the blanks be low the figure.

A. B.

C.

^ o / W \ / \ D.

O II

- P -I

o E. .

F i g u r e 2 .4

1. Give an example o f a biochemical having a structure l ike diagram C.

2. Wh ich t w o diagrams illustrate structures o f monomers ( bu i l d ing blocks)?

3. Name the level o f structure il lustrated in diagram B.

4. Wh i ch two diagrams illustrate mplecules used for energy storage?

5. Wh ich diagram shows a structure that most looks l ike a molecule o f ATP?

4. I f any of the fo l lowing statements about enzymes is true, wr i te T in the answer blank. I f a statement is false, correct the underi ined w o r d and wr i te the correction in the answer blank.

1. All enzymes are proteins.

2. The substances on wh ich enzymes act are called cofactors.

3. The name o f an enzyme usually ends in the suffix -ide.

4. Coenzymes are vitamins that assist the chemical action of enzymes.

5. Enzymes increase the activation energy of biochemical reactions.

6. The active site of an enzyme is the location of substrate attachment.

7. Changes in p H or temperature decrease enzyme aa iv i ty because bonds break and the enzyme returns to its tertiary simcture.

F. A n s w e r the f o l l ow ing ques t i ons by wr i t ing y o u r a n s w e r s in the a n s w e r b l anks .

1. Name the Ixsnds that help ho ld the two D N A

strands together.

2. Name the three-dimensional shape of the DNA

molecule.

PART II: BIOCHEMISTRY

1. Use a n X t o des ignate w h i c h o f t h e f o l l o w i n g are o r gan i c c o m p o u n d s .

1. C a r b o n d i o x i d e 3. Fats 5. P ro t e ins 7. H2O

2. O x y g e n 4. K C l 6. G l u c o s e 8. D N A

Inorganic Compounds 1. C o m p l e t e the f o l l o w i n g s ta tements c o n c e r n i n g t h e p r o p e r t i e s a n d b i o l o g i c a l

i m p o r t a n c e o f water .

1.

2.

3.

4.

5.

6.

7.

T h e ab i l i t y o f w a t e r t o m a i n t a i n a r e l a t i v e l y c ons tan t t e rhpera -tu r e a n d t h u s p r e v e n t s u d d e n changes is because o f its h i g h

(1) . B i o c h e m i c a l r eac t i ons i n the b o d y m u s t o c c u r i n (2)

A b o u t (3) % o f t h e v o l u m e o f a l i v i n g c e l l is wa te r . Water mo l e cu l e s are b o n d e d t o o t h e r w a t e r m o l e c u l e s because o f the p resence o f (4) b o n d s . T h e c o o l i n g ef fect o f p e r sp i r a ­t i o n as it e v apo ra t e s f r o m the s k i n is t h e resu l t o f the h i g h •

(5) o f wa t e r . Water , as H * a n d O H " i o ns , is essent ia l i n b i o c h e m i c a l r eac t i ons s u c h as (6) a n d (7) r eac t i ons .

ravorable p H

10. T w o diagrams, A and B, are shown in Figure 2.8. These represent the stylized structures o f ATP and cyclic AMP. Select a different color for each t e rm w i t h a color-coding circle and color the structures. Identify each biochemical by inserting its name in blanks A and B below. Label all high-energy bonds w i t h corresponding colored arrows o n the diagrams.

O Phosphate Q Ribose Q Adenine Q High-energy bond

F i g u r e 2 .8