,/

/ 'Name: S;J
p _____ _____ ___ Student#:
nl, I

- Unit 1: The Chemistry of Life

Topics
1.1 Structure of Water & Hydrogen Bonding
1.2 Elements of life 1.4 Properties of Biological Macromolecules
1.5 Structure & Function of Biological Macromolecules
1.3 Introduction to Biological Macromolecules
1.6 Nucleic Acids
Textbook Chapters to Read:
Ch. 1: The science of AP Biology_ review
Ch. 2: The nature of molecules and properties of water
Ch. 3: The chemical building blocks of life
Terms for Conceptual Understanding: (Not a list to memorize, identify and focus on key terms)
Protein Hydrolysis reaction RNA Amine Group
Carbohydrate Dehydration reaction Ribose 3' & 5'
Lipid Covalent Bonds Deoxyribose Saturated fats
Nucleic Acid Ionic Bonds Unsaturated fats
Anti parallel
Hydrogen Bond Nucleotides Primary Structure
Alpha-helix
Cohesion Amino Acids Monomer
Beta-sheet
_Adhesion Carboxyl Group Polymer
Secondary Structure
Surface Tension R-group Tertiary Structure Hydrophobic
Polarity DNA Quaternary Structure Hydrophilic

Objective Checklist: {I can ... )

• 1.1: Explain how the properties of water resulting from its polarity & hydrogen bonding affect its biological function:
o Including the subcomponents of biological molecules & their sequence determine the properties of that molecule.
o Living systems depend on properties of water that result from its polarity & hydrogen bonding.
o The hydrogen bonds between water & molecules result in cohesion, adhesion & surface tension.

• 1.2: Describe the compositions of macromolecules required by living organisms:

o Organisms must exchange matter with the environment to grow, reproduce, & maintain organization.
o Atoms & molecules from the environment are necessary to build new molecules:

• Carbon is used to build biomolecules like carbohydrates, proteins, lipids, and nucleic acids.

• Carbon is also used in storage compounds & the formation of cells in all organisms.

• Nitrogen is used to build proteins & nucleic acids.

• Phosphorus is used to build nucleic acids & some lipids

• 1.3: Describe the properties of the monomers & the type of bonds that connect the monomers in biological molecules.
o Hydrolysis & dehydration synthesis reactions are used to cleave & form covalent bonds between monomers.
• DO NOT NEED TO KNOW ➔ specific structures of amino acids, nucleotides, carbohydrate polymers.

• 1.4: Describe the properties of the monomers & the type of bonds that connect the monomers in biological molecules.
o Structure & function of polymers are derived from the way their monomers ar~ assembled:

• Nucleic acids ➔ biological information is encoded in sequences of nucleotide monomers, each containing a

(f 5-carbon sugar, a phosphate, & a nitrogen base (adenine, guanine, cytosine, & thymine). DNA & RNA differ in
structure & function.

Created by: Sarah Berlinger, 2020 Source: College Board AP Biology CED and Trey Bell, 2020.
 Proteins ➔ specific order of amino acids in a polypep
tide (prim ary structure) dete rmin
es the overall shape of
the protein.
• Amino acids have directionality: .
an amino (NH2) term inus , & a
carboxyl (COOH) term inus .

• The amino acid's R-group can be

categorized by chemical propertie

' ionic. The interactions of these s like hydrophilic, hydrophobic

R-groups dete rmin e the structur , or
e & func tion of tha t region of
protein. the

• Complex Carbohydrates ➔ com

prise sugar monomers whose structur
es dete rmin e the prop ertie s & func
of the molecules. tion s

• Lipids ➔ are nonpolar macrom

olecules :
• Differences in saturation dete rmin
e the structure & func tion of lipid
• Phospholipids contain polar regio s.
ns that inte ract with othe r pola
r molecules. Such as water, and
nonpolar regions that are ofte n with
hydrophobic.
• DO NOT NEED TO KNOW ➔ spec
ific structures of lipids
• 1.5: Explain how a change in the
subunits of a poly mer may lead
to changes in structure or func
o Directionality of the subcompone tion of the macromolecule:
nts influences structure & func
tion of the polymer:
• Nucleic acids have a linear sequ
ence of nucleotides with ends
defined by the 3' hydroxyl and
the sugar in the nucleotide. Duri 5' phosphates of
ng DNA & RNA synthesis, nucleot
strand, resulting in the form atio ides are add ed to the 3' end of the grow ing
n of a covalent bond between
nucleotides.
DNA is structured as an antipara
llel double helix, with each stra
nd running in opposite 5' to 3'
Adenine nucleotides pair with orie ntat ion.
thym ine nucleotides with TWO
Guanine nucleotides with THREE hydr oge n bon ds. Cyto sine nucleotides pair with
hydrogen bonds.

•
Proteins comprise linear chains
of amino acids, connected by the
form atio n of covalent bonds at
term inus of the growing peptide the carboxyl
chain.
• Proteins have 4 elements of prot
ein structure that will dete rmin
e its function.
• Primary structure determined
by the sequence order of amino
• acids
Secondary structure tha t arise
s through local folding of the ami
alpha-helix or beta-sheets. no acid chain into structures like
the
• Tertiary structure is the overall
30 shape of the prot ein and mini
• mizes free energy.
Quaternary stru ctur e arises from
interactions·between mul tiple
peptide units.
• Carbohydrates comprise line ar
chains of sugar monomers conn
ected by covalent bonds. Carb
polymers may be linear or bran ohydrate
ched.

• 1.6. Describe the stru ctur al simi

larities and differences betw een
DNA & RNA:
o DNA and RNA molecules
have structural similarities and
differences related to thei r func
tion "
• Both DNA and RNA have thre e
com pon ents -sug ar, a phosph
ate group, and a nitrogenous bas
nuc leot ide unit s that are connec e-th at form
ted by covalent bonds to form
a line ar molecule with 5' and 3'
nitrogenous bases perpendicula ends, with the
r to the sugar-phosphate back
bone.
• Basic stru ctur al differences betw
een RNA & DNA include:
• DNA contains deoxyribose and
RNA contains ribose.
• RNA contains uracil and DNA cont
ains thym ine.
• DNA is usually dou ble strande
d; RNA is usually single strande
• The two DNA strands in double- d.

•
stranded DNA are antiparallel
in directionality.

Created by: Sarah Ber ling er,

202 0 Source: College Boa rd 202 0
AP Biol ogy CED and Trey Bel/1 •
p 1/
-

Review of basic chemistry

1. Wher e is the energy nound withi

. .n a molecule (what part or location)7
~
El\4 )'( i~ " ~ ~ c:v>r- i~ ~rC AI ~c,l,6L o ~ tk. Cl,~

2. Wha t determines interactions between atoms?

1k o.ww ~ o-1, ~ ~-

3. Explain why covalent bonds are stronger than ionic bond

s. . -»v ~ _s"..yt

lo\f<l-\e---~ ~ )'f-n,"1-'" . lie. ~ ""~~ is

W~ )l.t-17 Wt e,- t.i~\ \7 (N

+k. ~~7. &Nfftu,h-c)I\ ~ C),-~

• 4. Why is water considered_ a polar molecule? 1J,\

W"'+-,..-
Ji~~~'htlr\
i) ~L,..
JC,
k. -4+ ~ ti.. s\i'-f' ·1

to wate r while others do not?

5. Why do some substances "get wet" when exposed
~ ~ \,J~ v- ..-oleJ,,;, ~ ~l~ ~
~~~ -r~t CJI"' ~v- ~ ~
~o ti._ oU.... e,,f.,- .;J..J., v~"'t tk ~• "' l,.,,t--
- -1- ,-.l - ~J of- (<>I,.,-

I
 Review of the Properties of Water
bonds with water are said to be hydrophilic ~
1. Compounds that have the capacity to form hydrog~~ ( ter fearing). Is the molecule on the below ~~
loving). Those without this capacity are hydropho ~c wa answer consider drawing on the image. \
• ? HINT· Think water Explain your '
hydrophilic or hydrophobic• • • ~ ~ j,4- I) Afa./
'- ~ ~ ch ,,k~1 '- r.,.
TL,~ ~\e,(-11~ I
1 I

"1"' p..:R.,.. ~l ~ ~.

. . . h dr • • s (H30+ often described

2. In addition to being polar, water molecules can dissociate mto Y omum to~ . ' . _7
simply as H+) and hydroxide ions (OHl The concentration of each of thes~ 10~ m pure water ts lO •
Another way to say this is that the concentration of hydronium ions, or H+ tons, ts one out of every 10
million molecules. Similarly, the concentration of OH_ ions is one in 10 million molecules.

a. The H+ ion concentration of a solution can be represented as its pH value. The pH of a solution is
defined as the negative log10 of the hydrogen ion concentration. What is the pH of pure water?

lo-1
=. I~ tl-1,z. (2) r
b. Refer to the diagram of the molecule of acetic acid in question 1. The COOH group can ionize to
release a H+ ion into solution. If you add acetic acid to water and raise the concentration of H+
ions to 104 , what is the pH of this solution?

3. Life as we know it could not exist without water. All the chemical reactions of life occur in aqueous
solution. Water molecules are polar and are capable of forming hydrogen bonds with other polar or
charged molecules. As a result, water has the following properties:
A. H20 molecules are cohesive; they form hydrogen bonds with each other.
B. H20 molecules are adhesive; they form hydrogen bonds with polar surfaces.
C. Water is a liquid at normal physiological (or body) temperatures.
D. Water has a high specific heat.
E. Water has a high heat of vaporization.
F. Water's greatest density occurs at 4°C.
 Expla in how these r . M than one
p P operties of water ar I pheno mena described in parts a-h below . ore
roperty may be used to ex I • . e re ated to the
p am a given phenomenon.

• a. During the winter, air te

however th fi h
.
mperatures m the northe
' e s and other arum·als livmg • •
1~,:, ,:, 4't. -b ~ be,~ ~'rV ~ ~ (ji.,ti .
I. _ 1
rn United States
m the lakes survive.
can

;~~ ~
remai n

~
below O

rt.~"
o
C

'
for

'4~
mon

~
1
th ·
s,
I ~ ~k k,
()

+k ..,.,J.,.. ~~ "'' "' lrv,;t 1i-~

solve quickly in wate\l,v
b. Many subst ances -for example, salt (NaCl) and sucro se-dis
lcJD.-kr ~
o.lkfi~ a~ i+ fo ,J-tzd·J, 1v -tk, rol-v-~~ {)+- a

J~>~4 a· ~v-l1.
a meniscus forms at the top of the water col~ . ~k l
c. When you pour water into a 25-mL graduated cylinder,
1k,, \\ Lc.. +,
.,i..,\-,-,- b..'if +-
c.J,k,.\L.. -1-L ._,,.i.,., .-,Ho .~, f)... {"/,, j}klJ
~~ wJv. ~ ~, .fk- :,lw ~+- +k, ~J.

e help reduce a human's body temperature. ~ t'k-

d. Sweating and the evaporatioy of sweat from the body surfac
heJ' .,i, ~~ if- t-et,,v~:> i~J> o4- ~ ~ \/'-f\Ml
(,f' <..- +k. ~r. \,.I
W~~ ~ ()..
~ ~ it u94/b
-ti., ,~ ~ ~ ~ a L ~ (). JA- c,f
4,, ~rk +k b.J. .

• e. A bottle contains a liquid mixture of equal parts water and

l I,. L ~,,
Wv~ r \> o-
\ L I
~~ o..r M.()\Uvlt. ~
I ~
mineral oil. You shake the bottle vigorously
and then set it on the table. Although the law of entropy favors
separates into layers of oil over water.
maximum randomness, this mixture
, "-I I I
0 r i , . ~c.,\.. hi~ ll1'" "'-1,\-,.-vt."'f'" ~ ~~.

Water drops that fall on a surface tend to form rounded drops

or bead~., IJ i I I
j
f.
11\~ a ~.) +k ~+v - i\> l"C.)\\V 1'~
We;.. ~ 1,. ~~~ ~~ J h-~.. h..,h,J- ..w,l ~v~
S ~ · 4-kc w;..te.r" ;l ~J~>'-1-e i~· ~ i't- c.(V'
t,u.. al, ~rt o---.l ~~" (/'- nw,1 ~~
I>- ~ r
~ ~\.t.1r <ilr~ '>·
J --
c)r';l,l ""

more after you polish (or wax) the car than

g. Water drops that fall on your car tend to bead or round up
befqre you polished it.
()"~ l~~ 1~k-~ ~ .. ~~,,G,,\J.e- ih
~ I) ~~ ~ ~L;k > ~rL -- ~~l- <>, w~ I~°'" +tf£-
W4tr • l i , ~ ~ "Ji)~ ~
~k
tt--,r-·......, ~ ~1tnv-1',~ r..r,j.J,., -tk
wE1\,( .

the water will move up into (or be

h. If you touch the edge of a paper towel to a drop of colored water,
absorbed by) the towel.
h1~ f" b-,,._.\..i w,-~ ~ vk1 kk ~
rlor
\A_jl:l)W ~ ~41)- e. ~o v~ ~ i,1'1'
f'"r- ~~\J"""'L, 4tt .l yh J.JIY W.
r
Biochemistry Basics
What concepts from chemistry are helpful in studying biology?

Why?
\
is because everything
Typically chemistry is a prerequisite course for advanced biology courses. This
The structures and
in your body, everything in a plant, everything in a virus, etc. is made of atoms.
and properties of the organism. Which
properties of the molecules in an organism determine the features
ies, which have basic prop-
m~lecules are polar, which are nonpolar? Which molecules have acidic propert
course will help you to
emes? A quick review of these concepts at the beginning of your advanced biology
understand the molecular basis for life.

Model I - Molecular Drawings

Ball-and-stick model of Lewis structure of 1-pentanol Line drawing of 1-pentanol
1-pentanol

H H H H H
I I I I I ~OH
H-C- C-C- C-C- 0--H H3C
I I I I I
H H H H H

Ball-and-stick model of glucose Lewis structure of glucose Line drawing of glucose

H
\ OH
C-OH
w--,
,.,....c--o
H\/ \/H

Ho/\? H VC\OH
c--c OH
I I
H OH

Ball-and-stick model of Lewis structure of unsaturated Line drawing of unsaturated

unsaturated fatty acid fatty acid fatty acid

OH

I. Name the three molecules that are illustrated in Model I.

n I l lvlOk ~J ~s'---1-.-rQ.t-ul .fu.++t
~
~~
1-e,..Tri.Nl , ~
Model 1.
2. Name the three types of drawings that are used to illustrate the molecules in
Qwtl - ~ - ~t.lL M,Ow I lewa i1nlc+J ~I , ~ 4~~

Biochemistry Basics
 3. How many bonds are 'call

• 4.
Carb on

Which
~

types •
of drawmg
typi Y formed by each of the following atoms:
H dr
J ogen
1
Oxygen
2,
uleil
• Model I provide more accurate images ofth e sh ape Of a molec •
. s m
Justify your reasoning.
Tk ~,,~ -<t~ "vk. ~~l ~ ~ e~~ re-r ~-\J -tk, e \ ~ + (Ml~ ~J
"~ C\t'G~ ;,.. +k j-j) ~
5 • Refer to Model I.
the line drawings?
a. Symbols or atoms of what element(s) are missing from
(vi~ o--i k~o ~ ~ ¾-
SfW~J.-. ~~~
C4"~ .r.,,. ~ c~ ~J, ~//{
st
of these elements are in the ruc-
b. In reading a line drawing, how do you know where atoms
ture if they are missing from the drawing?
++- W~ ~ ~ It '-"-r ~ ~~ t~ o~\1 l-~ ~ ~ b~. 'l ~
~..,.
~ ~,~ ~
,tv~t--f
-1~ '"'"' o-.i1,,$c. ~~t ~~ ~~ ~i~ wj H +o ot-t~ t.

drawing of isoleucine shown below and draw

6. Locate the carbon and hydrogen atoms in the line
them in as if the drawing were a Lewis structure.

•
OH

Isoleucine

an -OH group attached to the midd le carbo n

7. Isopropyl alcohol is a three-carbon molecule with
ngs.
atom. Draw this molecule using all three types of drawi

y
one of the comp ound s in Model 1, which
8. If you were asked to write the chemical formula for
type of the drawing would be the easiest to use? Justif
y your reasoning.

-rb l;~ ~~ ~~ o.i.-u tk

CC4'-~~" O\I~ WI~ tll
V?.J e~ Jkllr .

drawing rather than a ball-and-stick mode l or

9. What is rhe advantage to a scientist in using a line

, Lewis structure?

-t ~
ot o-
},t,~ +~\-
~ fewlt.
eu., L /fie~ •U.;,.c,..t-- uovJ J....e , ,t\or<.._ ~ ~ ,htc.t ~
POG ILrn Activities for AP* Biology
2
 Model 2 - Properties of Biological Molecules
Polar Molecules Nonpolar Molecules
(hydrophilic) (hydrophobic)
Acidic Acidic
H,C~OH

OH
Lactic acid Fatty acid
Neutral Neutral
CH3 0

H,C~OH
NH2

Valine (amino acid)

HO
Cholesterol

H OH
Glucose
OH

HO
OH
,1----0 OH
OH n
H OH
Vitamin A
H OH
Lactose

Basic
OH
HO

HO
Adrenaline

H~NH,
Testosterone
HO
Dopamine
NH2

(0 NH N

Adenine

Biochemistry Basics 3

-
■
 10. Conside r the I I

• '
po ar mo ecules in Model 2.
a. In general the

c~1,t\
f
presence o atoms of what element(s) makes a molecule polar?
b.J~ ft,i~ ~ Jo ~ . ,
o..J ,.,~
M,i n...l.,,, ~~~ ~
-rv r.11
1
.

b. What property do atoms of these elements have chat helps make the molecules they are in
polar? -' k
' °' ~k v l
1
hQo.t. """1 ~~~'ff ,~J J..i)h ,....,1., f:>['- ~+ W.>·
~ ~~ lw~l ~->•

c. Can nonpolar molecules also have atoms of these elements? If yes, what distinguishes a non-
/
polar molecule from a polar molecule?
~~ +k-t J,.;'t-- W t\!,v'G.

, Nn.fi>~ Mo~ ~ Gt,l-.o ~ oJ-o~ c,1.. 4~ c fc,-«- "-.1

~ fV'- 4L. i ~ ',Ml(-- ~~ ~ k. ~pe,-,'h7-- ~~ ~ tt:ci.Ah i'f'- O
+ + v-.1. - e, ..,J

tk ~l~.
dissolve
11. In chemistry there is a saying "like dissolves like," which means things will mix with or
into each ocher best when their polarities are similar.
a. Is water polar or nonpolar?
fO\.,,--

b. Is oil polar or nonpolar?

~F~
c. Which of the substances in Model 2 would dissolve well in water? Justify your reasoning.

rk ~ ~ ""u t,,,•..., 4 k -iJ.., •wte. r1-1 CA,\a. .. ~

Ji~~rb..,h~ •
d. Which of the substances in Model 2 are more likely to dissolve well in oil? Justify your reasoning.
,+ll .}k Mlt~/.,,t 4"'/a.1~ ~ 01 l ,1 "'~ ~-r.Jlc..-1

e. Which class of substances in Model 2, polar or nonpolar, is more likely to be found in high
concentrations in the bloodstream of a vertebrate? Justify your reasoning.
1k wr,J ..J,~ bco-~ ~ k- tk- ~ e\-t. 0o ~~lj ~~ ::> '1'f~ h,

cJ. G ~ ,"'- f\i. c.iN\. w"""~ 41~--L.CN\ (""o-kil'-).

12. Refer to Model 2.

a. What is another term for a polar molecule?
hy~~- c..
b. What is another term for a nonpolar molecule?
h1/.o~Ltt-
, c. Give the literal translation for the terms you gave in parts a and b above.
~ w~ ~""! t '-" ~j, c,,(_ lv.Yt'v-ll
POGILTM Activities for AP* Biology
4
 · 1 ical molecules. Describe the carboxyl func-
· b10
s m ogh . n
13. Functional groups are key groups of atom ave m comm o •
molecules in Mode l 2
tional group that both acidic

a~ -- L=.O
ed in chemistry. Explain how the reaction below
14. Recall the definition of an acid that you learn
illustrates the acidic properties of lactic acid.

H,C00H + H,O ► H,C 0 0 - +

OH OH
Lactate ion J- J)»l""l. ~I).

v\\'\ ~ ~ '\-4."d. tkr.;. ~ ~

Lactic acid
i-ln fQ.~+~°" i~~ 1()£,+~ Ol(,,\1

~ t- ~k- ~ ~ ~ W\~ ~l\lc.-C'AV'\ Ni- 1-'> ""~\L.. ,~~ t\'., ilM1.'L

~-,~ ,ri.t 4~t J1vQ) vf Ht- iJ~>.

e group, that the basic molecules in Mod el 2 all

15. Describe the functional group, called an amin
have in common?

ed in chemistry. Explain how the reaction below il-

16. Recall the definition of a base that you learn
lustrates the basic properties of adrenaline.

OH H H
N
I +IN-C H3
HO
HO
"-cH3
+ H2O . k + OI-r
HO

Adrenaline
i<A +l~ ~>L; ~q.~ ,~ -i

~ ~ ,j ~ 0c,1'J..z. ~

7 or pH < 7) of fairly conc entra ted aqueous solu-

17. Predict the approximate pH (pH = 7, pH >
2.
tions of the following comp ound s from Mod el
Lactic acid Dopa mine \0
Amin o acid lf Lactose

5
Biochemistry Basics
 18. In chemistry 1 olecular bond. They occu r
betw you earned that covalent bonds are one type of intram f•
nonmetal atoms ma molecule. You may have also learned about a type O mter mo-
•
I uI eenb
s are weak attractive forces between polar
ec I arul ond called a hydrogen bond. Hydrogen bond
mo ec es • • th or H-E
conrammg every polar bonds such as H-0, H-N

.
H
\
0-H

a. Label at least two covalent bonds in the diagr

am above.
.
b. Label at least one hydrogen bond in the diagram above
hydrogen bonds with itself (that is, othe r mol-
19. Whic h of the molecules in Model 2 would form
in a solution?
ecules of the sa,rie type) or with water molecules if
*
uJcJ..v1 Maiec--lt. wl~ QI>'\ w."llu:> ~c,.-,o~ Lo- t~tl (j ...6'1f·

6 POGIL Activities for AP* Bio.logy

lM
Exten sion Ques tions
20 Alth h • 'd
• oug ammo ac1 s have "ac1'd".m the1r
• name some are acidic in water solutions, some are
,
ase on the structures
· . b d
• ~ th·15 observation
b as1c, and others are neutral. Propose an explananon or
and descriptions of the amino acids below.
Neutral amino acids
0

HOYOH
NH2

Acidic amino acid Basic amino acid

0
0

OH
N~ N~
tt, i) .i.,.. -to -ii_ """""" a,;JJ lu,,,,'o' J . ~ '2."'a"'-'f,. If- V¥\ ""'-.11. ""4l.
l~rM f I~ (}&ll~1'<..-- c,y k4~t.. ~fl t-k.. ~~ Ms,u .,.J;~,l k-~ hcy--or-
~1.

21. The structure shown below is a line drawing of noncyclic AMP,

ecule in molecular communication systems.
an import ant messenger mol-
N42..
r
a. Draw the missing carbon and hydrogen atoms on the molecule.
/
. W--. C./ C~
•oll. ~ f! ll ~\
0
II
-o-p -o -;> I
.

I
\ / \
~ o-.. ~ - 9 -L- -'1 trc 1/'.• //c\. N
\i
I
-o
o- \ c_/0-........_
:\l _" /~
OH OH \ l
O'd
b. Write the chemical formula for a molecule of noncyclic AMP.

f
Biochemistry Basics
7

I
 22. The phosphate fu nctional . th
hydrogens." group m e noncyclic AMI' fQ • 21 contains "ac1·d·1c
molecule o uesuon •
a. Explain what th' h
1k
IS P rase means.
n,;-. ~
t_
p;:;rte ' I
-tk, ~ 1 i)'\ --JP 0v
·!r- eon ~"!\) -2t1ni fl (.{,+OIi\)

~~~

b. Draw the noncyclic AMP molecule after it has

~I~~
disso lved in water. /

0 Al
\I / --ri /~
I
0- ~ f -o -
/V
C. \µ / c '-.. N /?' (."-._
I .• I / ()'----.) \1
o- (_"-.
I \ \-I
L-(.

\ \
0~ ~

8 POGILTM Activities for AP* Biology

 Pr ote in St ru ctu re
?
ctur e and wha t role do fun ctio nal gro ups play
Wh at are the levels of pro tein stru

Why?
reactions, pro vid ing stru~ture~ and
tasks such as facilitating chemical
Prote_ins ~ccomplish man y cellular coils up and folds dete rmm es its
co another. Ho w a pro tein cha in oth er molecules and thu s
carrym~ mfo~macion from one cell turn , dete rmi ne how it interacts wit h
sha pe. Its sha pe will, in
three-dimens1onal
per form s its fun ctio n in the cell.

de Bo nd
Mo de l 1 - Formation of a Pepti
Am ino acid 1 Am ino acid 2
CH3

H" j ~o
+ N -- c- -c

ref l \-H

+ r
Dipep tide

Mo del 1.
1. Exa min e the ami no acids in
diagram.
a. Cir cle an ami ne gro up in the
lic acid (car boxyl) group.
b. Dra w a tria ngl e aro und a carboxy
ilar to one another?
2. Ho w are the am ino acids sim
CL C °"" ~ (, ~ ~¾
,-~ ~ k t~ OJ \- ~ M -.tn ,o~ ~ . vJ ~

6'\ <&h.i't\J ~,., ~) u- ~~x 1 l ON'~ "-~~

eren t from one ano ther ?

3. Ho w are the am ino acids diff

1
Pro tein Str uct ure
 4. Bow rnan .
y anuno acids .
are Involved in th .
e reaction to mak cli
2. ea pept1.der~
5. In Model 1 th ..
dipeptid c original arnino acids ar b. d th
e. e com Inc: rough a condensation reaction to make the
a. What does T? re .
.. '1 present In the dipeptide?

b. What does
R2
~ II,. _'Pf J .fie, t't\.\- ~ ...;!
represent the dipeptide?
In

6. Puc a box around the .

1k R ~"' '1' ~ i 'JJOd- (»,,·~ C],cI~-
reactio • M d atoms m the amino acids that become the H O molecule produced by the
n 1n O el 1. 2

7. A peptide bond is a al b d 1· ki .
cov enc on m ng two amino acids together in a pepude.
a. Circle the peptide bond in Model 1.

b. Between which two atoms in the dipeptide is the peptide bond located?

~L~N
c. Between what two functional groups is the peptide bond located?

8. There are 22 different amino acids found in nature. Two were shown in Model 1. Additional
examples are shown below. With your group, write one. or two grammatically correct sentences
to describe how these amino acids are similar and how they are different. Use the terms R-group,
amine group, and carboxyl group in your description.

I
H N-C-COOH
i
H

I
IH2SH

H N-C-COOH
H2C

I
H N-C-COOH
TI
/c,
NH2
H2
D
1
H N-C-COOH
H
i I 2 I z I
H H H
Glycine Cysteine Asparagine Phenylalanine
(Gly) (Cys) (Asn) (Phe)

All .Jk e~·~ qe

~ ~ ~e. (A ~4'..\ (P.f b-~ ~ 1o W\ (M'~r,""a

'roJf 4i..J ~ _,w-bot\ J~➔ ,11 -\.~Y ~~~"'{'')

2 POGieM Activities for AP* Biology

r

Model 2 - Protein Structure (Part A)

Primary Structure Gl
. . h "-'
Ammo acid sequence: Ser - Tyr -Ala - P e - vai
- CY
s - Tsyr - Asp - Cys - y

Peptide structure:
OH
OH

H
I
,,
cI z HI CH H
Q
I "-:::

CH
H,c, /H,
H clH H <;:Hz SH H
¢
CH 2 HI
L,I
o2-

¥ I
rn,sH H
I
I zI 3
I I I I I
I I_ -N-c-c-N-c-c-N-CH2-co2H
N-c-c N-c-c-N-c-c-N-c-c-N-C-c-N-T ell I II II
I II I 11, I II I II HI II H O H O 0
HO H 0\ HO HO 0

Secondary Structure

¢ OH

-r--~'""' &,c,~ Hydrogen bon

d

CH 20H CH 2 H CH 3 CH 2 H I o
H 2N-J-c-N-b-c-J-b-c-N-c-c-~-c-_ll
I II
HOH
I I 11
Ho
I
H
II I I
oHH O
II
•
H
I c\
•• NH
•
SH •
•
I .. CH-CH SH
H O CH2 0 H • H / 2

H02C-CH -~-~-l-Z-~-l-Z-~-l-Z
2 I I --c I
H CH \\
H C 2 0
21

CO 2

OH

9. Locate the primary structure of the polypeptide in Model 2.

a. Draw an arrow to two different peptide bonds in the diagram.

b. Circle three separate amino acids that were joined together to make the polypeptide.

Protein Structure 3
•
 10. The first fi . · d
. ve ammo acids in th· I .
ali
v ne, 1n that d S is po ypepade are serine, tyrosine alanine, phenylalanme, an
or er( er-T,yr-Ala-Phe-Val). If the amino acids were' changed or rearranged("1.e.,
to Val-Phe-Al -S T,
group, Use th'a. e:- yr),_ the polypeptide would have a different name and identity. With your
•
. of the primary structure of a protem.
• a d efin"mon
1 I~-
ts tnrormatton t0 wnte

~ J_ ~\> ~cl_, l1t\~1 ih ~ 8~._ SLtvdltil..

. structure in Model 2.
l l. Locate the secondary protein

a. What types of bonds are holding the secondary structure in place?

H1~ ~i.-s
b. What groups on the amino acids are always involved in these bonds?
1k ;- G.,-~.t-•!1 ~ !+ ~~ ~~~

st
12- Draw a rectangle around two different R groups on the amino acids in the secondary ructure in
Model 2.
13. Is there any interaction between R groups in the secondary structure in Model 2?

ltb
14. Secondary protein structure can take the form of an alpha(a)-helix or a beta(~)-pleated sheet, as
illustrated below.
a. Which drawing represents an a-helix, Molecule 1 or Molecule 2? Explain your reasoning.
r¼>k v-'le 2 ~ ;-,. +.,,{*.J ~c,~ M-rb ~ "'~~.}.b~..
b. Which drawing represents a ~-pleated sheet? Explain your reasoning. /
. \ -- l ~ 11 , ~Lk, 1 ~s ~ o- ~t~ eb..~ ,-kc.A- ~c."~ n .Jil)✓j fk
') ......,,,- ~'&.6 ~~ Jk·h. Molecule 2
Molecule 1

Amino----1►-
acids rR'f~~►...-. . .~

the secondary
~15. With your group, write a grammatically correct sentence that summarizes how
protein structure is formed from the primary structure.
J~ >u-4,Jt-'( Strv~ ~ ~ hkci"" l..,,.J. k~ el/yt (erl-i a,1'00

(
•
4
OM1,

POGILn, Activities for AP* Biology

Mod el 3 - Prot ein Stru ctur e (Part B)
Terti ary Struc ture

H--- o-CH 2

CH-
I
0--- H
I
2

~Jrocy~ CH-S
2 -S- CH2

l
(CH2)4-NH ;_,,
L o~c -cH
fl ~~~At~
2
\o-.~ Br~~
~

•
Quat erna ry Struc ture

Three polypeptide chains

Protein Structure 5
•
 16.
Exarnine th
ture in pla e teftiahr
~ J strurt-.. _ .
ce. - ..'1.1-e in Model 3
a. Four types f b and note the interactions that hold chis level of struc-
o onds or.
Disulfi de b . Interactions are shown . .
l-I I ridge • Label them with the followmg terms.
Ydrophobic intera . Hydrogen bond
b D Ctlons
• escribe the . Ionic bond
Part of the amino acid th . .
1k R-~I\JJf~ at part1c1pates in these interactions.

c. Howd0
es your answer in ar b d' a:
P t Iuer from the bonds that stabilize the secondary structure?
lfrLJ-k ~ ~ 1V\Je~t ~i,,. fhvf\ tk ~~ ~
uv-bt t I jr",Jr,
17• Whit type
of functi al
ho d" on groups or atoms would need to be present in the R-groups for hydrogen
n tng to occur betw • 'ds ·
een two ammo ac1 m a protein chain?

L-o.r~ ~'I n .... \ r,~ ....

' V, ·o v--'""' J ""J \ ~

18. What type of functional groups or atoms would need to be present in the R-groups
for hydro-
phobic interactions to occur between two amino acids in a protein chain?

19. How many polypeptide chains are shown in the tertiary protein structure in
Model 3?

20. Many proteins, but not all, have a fourth level of structure termed quatern
ary structure.
a. How many polypeptide chains are shown in the quaternary structure of the protein in
Model 3?
s
b. What types of bonds and interactions hold the quaternary structure in place?

6 POGIL™ Activities for AP* Biology

f\.21. With your group, using grammatically correct sentences, define the following.
a. Tertiary protein str:/cture. I 1 1. . 1• _ d,tw, ~-it , b,{J ~ ) ; Oii\ C. b.J,,
ik ~ ,µ-uy 1
"1~fno~ 0 ,Mtlr'7t )
(i;,\~ ~1~ w. 11'4, lv.... \1\~ \,,,iv'
I),,,<, \kfl l!Wa<--) +k pf'llei• ~
J-11~ ~ C&:·h,,/1' t.,>f (I\ ~ ~· 0 .v~. ,
~ tb~ P)tft!-P\;k
b. Quaternary protein structure.
,\. f,~\ le.el J s~t-« 1
I L \ oJe~
i-'
11\fl~ ~u +1 r- I / I
J11i~.

tf'O'J" )\Jot\t) <> '

22. Imagine a protein chain

that includes the following amino acids among several others.

CH 20H
TI
/c, ~
~
I IH2SH H2y NH2 H C
2
H N-C-C OOH
2 I H2N-T- COOH
I
H N-C-CO H N-C-CO OH
I
OH
H 2 I 2 I
H
H H
Serine Cysteine Asparagine Phenylalanine
a. Which of the amino acids could form a hydrogen bond with another amino
acid in the chain
to stabilize the secondary structure of a ~-pleated sheet?

A~r-u..j;~ J Sen~

b. Which of the amino acids could form disulfide bonds with another amino acid
in the chain
to stabilize the tertiary structure of the protein?
l1sj..e ~

c. Which of the amino acids could participate in hydrophobic interactions with another amino
acid in the chain to stabilize the tertiary structure of the protein?

d. What types of bonds or interactions could asparagine form with another amino acid in the
chain in order to form a quaternary structure with another protein chain?

tt,~ H

Protein Structure 7
 .
23. Fill in the follow·ing chart usmg wh
re Structure
at you've 1earned from Models 1 3.
Bond(s) or interaCti·ons
h0 lding the structure
Number of
polypeptide
Short description
together chains .involved

A ~b"' h4- ~~

Primary Ffh~~ Ac-i!l 6o,JJ ~

1

~--. ·.·
'~~ i'<t '-)
l,t-iuc-t I .v..l ~ ~r"
Secondary k1J'°r w~ u W' rk-AI'- ~ ,/,JtJ
I

d.u.J-or " 4ht

D~~~Jt ~:.J~1 io,.'1, ti\ ~t:' ok) kf.w W\

~Ql\h, kt~," h1tlrer t,~~ a? e. I

Tertiary
1~o" -\, ~ ~Amt' ~"f S tt+- ~;,.o "'~.S
b .~l)

~l+ i~ M~tiJe.
~ t(_fJ~ -wJe "

Quaternary w..,J~ " b..ii J.1'14.~ ~ ~p k 2 or more

rni~"' .

•
Read This! res or
to disrupt the shape of a protein. High temperatu
Heating and changing pH levels are two ways s, ionic bonds,
nt of the protein will break hydrogen bond
pH levels that vary from the natural environme ed. This
Covalent bonds will usually remain undi sturb
disulfide bridges, and hydrophobic interactions.
called denaturing.
process of destroying the shape of a protein is

is maintained after denaturing? Explain your

24. Which of the fo~r levels of protein structure

~ke;''"""f .>m.<,f.re- is ~ ~ (JJ,Jk , -#.t.) ,, sfu;/,.,., a,c, { ff fv1JJ..-. br ~1/ Ja_

b~.,, ~Lr~ QIC, ~ ¼c- 4 ~+ ~~ .

8 POGIL Activities for AP* Biology

TM
 ~2 5. Proteins carry out a var
iety of functions, and their fun
structure and shape. Enzymes ction is critically dependent up
are proteins. What would hap on th~ir
pen to the str uct ure an
an enzyme that was exposed to
heat or a drastic chan~e in pH
d function of ~
1 k tNtz."(1+4- w.,,1,l
~~~~~~l(A,it :~,vt- buu~
b...... W v, J "" ,.,,
?
~i;.,c.
t.A7
jJ, .,L.._ , JI _
""""'('· . ko ~
/__JL I ,-
il-- ~ t b~l _io o1 ~J,~+..k. "'-''"-l.-
,
26. When people get their hai
r chemically straightened, one
disulfide bonds that give the hai chemical is pu t on the hair to
r strands their shape (curled) break the
reform the disulfide bonds to and a second chemical is use
hold the hair in a new positio d to
n (straight).
a. What level(s) of protein stru
cture is/are affected by these pro
cesses?
lk +~11~ il\rvc,!we

b. Why doesn't the hair stay stra

ight forever after this treatment?
'TL li r ~l<l'f- ""7 s-/ri.r/J L.1 r11 - ,J-k_ ~~;,,_ ~ ~ Ji, wl ,re
r,.w....,~ k~.

(f

Pro tein Str uct ure

----------------
__J
 Extension Questions
27. If am •
Utat1on in the DN
a polar R-group with A of an organism results i . . .
ture of the pr . another amino a •d . n the replacement of an amino acid contammg
otein be affi c1 containi
answer. ected? Address th .
k ng a nonpolar R-group, how might the struc-
e unpact on all levels of the protein structure in your

T ~ ~+- ...ni .l...,tQ,J\-, J...,.,,t. k.'4.t)o. ~'1 .,n,,,ul-- """- ~

+l ~~ii\ ,k, G~ ell; ~ 1 ~~"""""""'·

28.
~gg ~hites ~e primarily composed of the protein albumin. One familiar example of the denatur-
~~ 0 proteins is the difference between the albumin structure in a raw egg versus a cooked egg.
s~g what _you know about the levels of structure in proteins, propose an explanation of chang-
es in albwrun (and other proteins) that occur during cooking.
LJl"' "'"~"ir, 4.. f'°J.;\,. > 0/lr~ ,tc, bji i-,6 &\-- 1....-t--1 u'"' '-'6 .tk.. r-:Je."- +. d-+-.
1~~ a;w~ 4J... ~ "" +It,,~ f. C,~ kc~ ~, ,;) pt~\.le... ~!J J/o.y ,~
{""'+-

29. Predict what would happen to the egg white if a raw egg were placed in vinegar. Explain your
thinking.

tk ~ ~~ ..J.l ~~ ~•.c. ,i.k ,_.,k.... ...,,11 l. ltfllid. -J, Wf

wrK ~a-- fk r,.,1,,.-.. ' '

.f..J--f.... ..~ ch,~

En21...._ J,.,,~ l<h v-u--r ~

°""'~ r:,xJ,'1»1 +~
Ja--> ...~'d...a." f+ +;,,µ- (,M}f
.\'11 ~st,w ~"- (A, ~ ,J, ~t._ r~ CY (Ii e,.s1f ~-l,...~J to b,o,4, 4,J,
~Vw\ >olso ~.·
:,

LO POGIL'l.1 Activities for AP* Biology

 Application Problems for
Biochemi stry of Proteins, Levels of
Structure, No n- Covalent
Fort~\
These are very difficult quest
ions. You are being asked to
apply content in a new way.
1. You hav e discovered a new Do your best.
enzyme, enzyme E, which bre
bo nd s after tyrosine or phenyl aks do wn proteins by cleaving peptide
alanine.
a. Enzyme E is the product
of gene G that encodes a pro
kilodaltons (50 kD). Wh en tein wi th the mo lec ula r we igh
yo u purify enzyme E, yo u ob t of 50
50 kD. However, active enz tain a single typ e of polypept
yme E has a molecular weigh ide of
50 kD. t of2 50 kiloclaltons (250 kD
), no t

...
111. Is the primary structure of the
50 kD protein the same or dif
structurr of the 250 kD protein ferent fro m the primary

•
? Ex
. ~~ '1\.- ~ ~.. ~ 4\...., ~plain briefly.
~- -r \V' ~I /'~ ~ ~ ~ r •
,J~

1v. Is the tertiary structure of the

50 kD protein the same or dif
structure of the 250 kD protein ferent from the tertiary
? Explain briefly
•

v. ls the quaternary structure of

the 50 kD protein the same
quaternary structure of the 250 or different from the
~~ o, ~~ u- r'1 ~~
kD \Jrotein? Ee ai n briefly.

1) , ~\) trctr61"'-' ,wJd\~ ,,.J..ln

f3 cl,~t.rM "-"~•) "~~~ ~ ~o 'Q r"'~
~ f'~ (k, ~L g I
~ t~
b. Yo u tes t enz ym e E activi
ty on a large protein substra
E. Yo u the n tre at the substr te. This substrate is not cleave
ate wi th DT T (a compound d by enzyme
enz ym e E activity again. Th that disrupts disulfide bonds)
is time the substrate is cleave and test the
abl e to cleave the pro tei n sub d by enzyme E. Why was enz
strate only after the substrate yme E
Gt--.. -,~,1,:,a.\\-1 t\..
.t.l\"L-1"'- ~ 1111- ~ ~ ~ ~~
was treated with DTT?
~ c;.,.b )~~ ~
.\o
.l ,\ )~ - 'ti -M r, ~
f ~ ~ .Jntnu)e. ~~ h-k "-r t ~
d..'!'fA1 1 ~ +k, ~,._.____
vlfuv,"'( if- io :tt'f- -fo ~ U ,~ .
 1.w een dru
protem that exists only- -inv\.,
th g resistant fun •
substrates that you hop ·ue ~g
resista
e Wt bind t . nt funoi !" and drug sensitive fun01 you
b"• 1 ou named thi
th R . b", hav di
o It. , • . _· . . , e sco
s e es1st protein and designvered a

~- .. > ·~tei
.·;
·J,!- --... !{"

~;~ q~
~- Al.ii
. .

~~rU:::!~~ fue ~dstronhgest intermolecular int~r:;:n ~~:~

·.t . •,•• .

' :li~~t!pr~teih· .

a. •
~ o ac1 s own on the Res· t
ionic bond, cov substrate 1 as shown and the side
al t b d, h 18 protem• (th h
Hint· Lo k e~ on . ydrogen bond, and hyd ere s ould be 4, one for each). Choos
0 th rophob icity. e from
• at e side cham on the resist protein .
and hypothesize what bond/force cou
ld be formed.

You make the followin additional

substrates.

b. What is the strongest interaction

that now
Val exists between the Ala of the Resist
protein and substrate 2?

J\L1

:~ ~ •__:~~#sipr~teu,i: -.· '.•

c. What is the strongest interaction

that now
exists between the Glu of the Resist
protein
and substrate 3?

er
tr d. Which substrate would you exp
ect to bind the most tightly to the Re
or substrate 3 and explain why you sist protein? (substrate 1, substrate
made this choice. 2

• <o cna Irey 8PII ~- I IX