Advanced Biology Name:
Biochemistry Notes
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1. Contrast the terms atom and element.
2. State six elements essential to life that make up 95% of living matter.
3. Describe the structure of an atom - label the diagram below and defne the terms that you label.
4. Contrast the terms atomic mass and atomic number.
5. What is the diference between the terms atomic mass and atomic weight?
6. Given the atomic number and mass number of an atom, how would you determine the number of
neutrons?
7. What is an isotope and what is special about radioactive isotopes?
8. What determines interactions between atoms? How are valence electrons important? Look at
Figure 2.1 and predict the number of covalent bonds each atoms is capable of forming. Explain
WHY in terms of the octet rule.
9. Distinguish ionic and covalent bonds.
10. Defne electronegativity and explain how it infuences the formation of chemical bonds.
11. Distinguish among nonpolar covalent and polar covalent bonds.
12. What is the diference between a structural and molecular formula?
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13. What are some types of structural models used to represent the bonding/shape of a molecule?
14. Explain how the type of bonding involved afects the fnal shape of the molecule.
15. Describe the formation of a hydrogen bond and explain how it difers from a covalent or ionic bond.
16. Distinguish between the terms hydrophilic and hydrophobic. What determines is a molecule will be
hydrophilic or hydrophobic overall?
17. Compare and contrast van der Waals interactions with other types of chemical bonding.
18. Rank the types of chemical bonding in terms of energy, from least to greatest.
19. Based on the reading, what is an example, in a living system, of how molecular shape is critical.
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20. Why is water considered a polar molecule?
21. Draw two water molecules in a way that illustrates a hydrogen bond.
22. Distinguish between heat and temperature.
23. Defne: (you may need to use another source for these terms)
a.Calorie
b.Specifc heat (heat capacity)
c.Heat of vaporization
d.Heat of fusion
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24. Below is a heating/cooling curve for water.
Label the points at which water would be a gas,
liquid, and solid. Also indicate the transition
points and which corresponds to the heat of
vaporization and heat of fusion). What is so
special about the curve during phase transition?
25. For each of the properties of water, briefy defne the property and then explain how waters polar
nature and polar covalent bonds contribute to the special property. Include an example in nature of
each property also.
a.High heat capacity
b.High heat of vaporization/fusion
c.Evaporative cooling
d.Cohesion
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e. Adhesion
f. Surface tension
26. What is secia! a"out #ater and densit$%
27. &efine the fo!!o#ing ter's(
a. So!ute
". So!)ent
c. A*ueous so!ution
d. +$drohi!ic
e. +$droho"ic
f. +$dration she!!
28. ,a"e! the diagra' "e!o# to de'onstrate the dissociation of the #ater 'o!ecu!e and then re!ate this
diagra' to + -"e sure to gi)e the e*uation for +..
29. What defines an acid and a "ase%
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30. &istinguish "et#een a strong acid/"ase and a #ea0 acid/"ase.
31. What are the co'onents of a "uffer% Write and e1!ain the car"onic acid "uffer s$ste' in hu'an
"!ood. 2ou #i!! see this e*uation again3
32. +o# do "uffers i!!ustrate the !a# of 'ass action%
33. Wh$ are aarent!$ s'a!! changes in + so i'ortant in "io!og$%
34. Compare and contrast inorganic and organic molecules
35. What is special about carbon that makes it the central atom in the chemistry of life?
36. Create a table below. After each functional group - draw the structure, name the compound,
write an example, and note the functional properties. (Doesnt this look like great exam material?)
a. Hydroxyl
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b. Carbonyl (aldehyde and ketone)
c. Carboxyl
d. Amino
e. Sulfhydryl
f. Phosphate
37. With each of the a"o)e functiona! grous4 #hat t$e of "onding interactions cou!d each one ta0e
art in%
38. Which functiona! grous ha)e the a"i!it$ to function as acids or "ases%
39. What are the four 'a5or c!asses of 'acro'o!ecu!es in ce!!s%
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40. What t$e of che'ica! reactions are used to 'a0e/"rea0 'acro'o!ecu!es% &iagra' each
reaction "e!o#.
CARBOHYDRATES
41. What is the genera! for'u!a for a car"oh$drate%
42. What are the 'a5or ro!es of car"oh$drates%
43. &escri"e the structure of a t$ica! 'onosaccharide such as g!ucose.
44. &ifferentiate "et#een he1ose and entose sugars.
45. &escri"e the structure of a t$ica! disaccharide such as sucrose. Write out a condensation
reaction "et#een g!ucose 'o!ecu!es4 and e1!ain h$dro!$sis. -What t$e of !in0age is for'ed%.
46. &efine the roerties/co'osition of the four 'a5or o!$saccharides found in ce!!s.
g. Starch / 6!$cogen
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h. 7e!!u!ose
47. +o# does the orientation of the !in0age differ "et#een starch -'a!tose. and ce!!u!ose
-ce!!o"iose.% -see 8igure 2.10.
LIPIDS
48. A fatt$ acid is technica!!$ co'osed of 74 +4 and 94 5ust !i0e car"oh$drates : ho#e)er the$ ha)e
*uite different che'ica! and h$sica! roerties. ;1!ain #h$.
49. What are the )arious ro!es of !iids%
50. &iagra' the s$nthesis of a trig!$ceride and a hosho!iid 'o!ecu!e. 7irc!e and !a"e! a!! the
functiona! grous in)o!)ed in this rocess : #hat t$e of !in0age is for'ed% Point out the o!ar and
nono!ar ends of the hosho!iids : a!so identif$ the h$droho"ic and h$drohi!ic ends of this
'o!ecu!e.
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51. ;1!ain the difference "et#een a saturated and unsaturated fatt$ acid. ,ist so'e uni*ue
e'ergent roerties that are a conse*uence of these structura! differences.
52. &ifferentiate "et#een a fatt$ acid4 trig!$ceride and hosho!iid.
53. S0etch a hosho!iid "e!o#. What is the significance of a o!ar head and non<o!ar tai!s in a
hosho!iids% -=se the ter' a'hiathic..
54. What is the "asic structure of a steroid% ,ist the three steroids descri"ed in $our te1t and their
function-s..
CHAPTER 3.1 -- NUCLEIC ACIDS
55. &iagra' an indi)idua! nuc!eotide4 identif$ the 5<car"on sugar4 the hoshate grou and the
nitrogenous "ase. &escri"e ho# these 'ono'ers are !in0ed together to for' a nuc!eic acid.
What t$e of !in0age is this%
56. &istinguish "et#een a $ri'idine and a urine. +o# do urines and $ri'idines air u in
co'!e'entar$ "ase airing%
57. Su''ari>e the functions of nuc!eic acids.
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58. &istinguish "et#een ?@A and &@A -"oth in ter's of structure and function..
59. ,ist the functions of nuc!eotides !i0e AAP4 6AP4 and cABP.
60. What is so secia! a"out the trihoshate grou on AAP%
CHAPTER 3.2 PROTEINS
61. Cdentif$ the a!ha<car"on4 the car"o1$! grou4 the a'ino grou4 and the ? grou of an a'ino
acid.
62. ;1!ain ho# a'ino acids 'a$ "e groued according to the h$sica! and che'ica! roerties of
the side chains. De sure to e1!ain the significance of the fo!!o#ing a'ino acids( c$steine4
g!uta'ic acid4 !$sine4 arginine4 asartic acid4 and histidine.
63. Cdentif$ a etide "ond and e1!ain ho# it is for'ed.
64. ;1!ain #hat deter'ines rotein confor'ation and #h$ it is i'ortant.
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65. &efine ri'ar$ structure.
66. &escri"e the t#o t$es of secondar$ rotein structure4 and e1!ain the ro!e of h$drogen "onds in
'aintaining the structure.
67. &efine tertiar$ structure. ;1!ain ho# #ea0 interactions and disu!fide "ridges contri"ute to
tertiar$ rotein structure.
68. =sing he'og!o"in as an e1a'!e4 descri"e *uaternar$ rotein structure.
69. &efine denaturation and e1!ain ho# roteins 'a$ "e denatured. -Wh$ are roteins so
sensiti)e to changes in te'erature and +..
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70. Su''ari>e the t$es of che'ica! "onding in)o!)ed in each !e)e! of rotein structure.
71. &iscuss se)era! en)iron'enta! conditions that 'a$ affect rotein structure. What is the secific
effect of each on "onding interactions that genera!!$ 'aintain rotein structure%
SECTION 2.5 CHEMICAL REACTIONS AND ENERGY
72. Explain what happens when a chemical reaction occurs.
73. &efine the fo!!o#ing ter's(
a. ;nerg$
". Einetic energ$
c. Potentia! energ$
74. &efine(
d. Beta"o!is'
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e. Ana"o!is'
f. 7ata"o!is'
75. Wh$ are cata"o!ic and ana"o!ic reactions often !in0ed in !i)ing organis's%
State the Laws ! The"#$%&a#'(s)
8irst ,a# Second ,a#
76. What is free energ$%
77. 9rganis's cannot use heat energ$ to dri)e their energ$<re*uiring rocesses. &oes this 'ean
that the heat re!eased "$ 'eta"o!is' is of no use to the'%
78. De!o# is the 6i""s free energ$ e*uation(
6 F + < AS #here + F entha!$ -the heat of the s$ste'.
A F te'erature
S F entro$
79. Cf a reaction gains heat it is an endother'ic reaction. Cf the reaction gi)es off heat4 it is an
e1other'ic reaction. Ahis a!one &9;S @9A deter'ine the sontaneit$ of a reaction4 what
actually determines if a reaction is sontaneous in ter's of 6%
80. Cn the e*uation 6 F + : AS4 #hich art of the e*uation reresents(
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a. 7hange in entha!$%
". 7hange in tota! energ$%
c. 7hange in free energ$%
d. ;ndother'ic reaction%
e. ;1other'ic reaction%
f. 7hange in entro$%
81. &efine in ter's of 6(
g. ;1ergonic reaction
h. ;ndergonic reaction
82. What is re*uired for an endergonic reaction to occur%
83. What does it 'ean for a che'ica! reaction to "e sontaneous%
84. =sing the concet of entro$4 state #hen a reaction #i!! occur sontaneous!$.
85. ;1!ain #h$ high!$ ordered !i)ing organis's do not )io!ate the Second ,a# of Aher'od$na'ics.
86. Cf a che'ica! reaction is re)ersi"!e4 e1!ain ho# the concentration of su"strates and roducts
inf!uences che'ica! e*ui!i"riu'.
87. 7o'!ete the fo!!o#ing chart(
G"a*h A G"a*h B
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Cs 6 ositi)e or
negati)e
;1ergonic or
endergonic
Sontaneous
2es or @o
=hi!! or &o#nhi!!
?eaction
Products ha)e
'ore or !ess
energ$ than
reactants
SECTIONS 3.3 + 3.,
88. What is an en>$'e%
89. Ao the right is an e1a'!e of a
reaction cur)e. ,a"e! the a1es4 the
energ$ of acti)ation4 energ$ of
su"strates4 and energ$ of roducts.
i. Which !ine reresents an
uncata!$>ed che'ica!
reaction%
5. Which !ine reresents an
en>$'e<cata!$>ed che'ica!
reaction%
90. ;1!ain ho# the energ$ of acti)ation is re!ated to the ?AA; of a che'ica! reaction.
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2
1
91. +o# does an en>$'e enhance the ?AA; of a che'ica! reaction% Cdentif$ the reaction cur)e for
an en>$'e<cata!$>ed reaction on the cur)e a"o)e. What arts of this reaction does an en>$'e
@9A a!ter%
92. What is the ri'ar$ #a$ that en>$'e !o#ers the energ$ of acti)ation%
93. &efine(
0. Acti)e site
!. Cnduced fit 'ode! of en>$'e action
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94. &escri"e #hat is occurring at each ste in the cata!$tic c$c!e of an en>$'e.
95. Sho#n is a rogress cur)e for an en>$'e<cata!$>ed reaction. Ahe oint at #hich su"strate #as
added to an en>$'e so!ution is indicated #ith an arro#. &escri"e #hat this grah is te!!ing $ou :
descri"e the a1es and #hat the s!oe of the !ine 'eans during the initia! hase -A.4 !inear hase
-D. and the !ateau -7.. &iscuss in ter's of "oth the ?AA; of roduct for'ation and ho# each
of these hases re!ate to the en>$'e c$c!e diagra'ed a"o)e.
96. Wh$ is the for'ation of the en>$'e<su"strate co'!e1 i'ortant in seeding u the reaction%
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e&-%#e
a(t'.e s'te
e&-%#e
T'#e
/ P "
$
0 ( t
1
A
B
C
97. What t$es of a'ino acids do $ou thin0 $ou 'ight find in an en>$'e acti)e site%
98. +o# does the acti)e site dictate the secificit$ of an en>$'e% -"oth in the su"strates it acts on
and the roduct it he!s for'.
99. &escri"e ho# each factor affects the ?AA; of an en>$'e<cata!$>ed reaction4 diagra' the
reaction cur)e and e1!ain each diagra'(
a. Su"strate concentration
". ;n>$'e concentration
c. Ae'erature
d. +
100. ;1!ain the ro!e of cofactors and coen>$'es.
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101. Wh$ is it i'ortant that 'eta"o!ic ath#a$s are regu!ated%
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102. &escri"e ho# each of these scenarios can inhi"it en>$'e acti)it$(
a. 7o'etiti)e inhi"ition
". @onco'etiti)e inhi"ition
c. 8eed"ac0 -a!so ca!!ed roduct. inhi"ition
d. A!!osteric inhi"ition
103. Bost of the ti'e4 inhi"ition is re)ersi"!e. What haens if an inhi"itor is irre)ersi"!e%
6i)e so'e e1a'!es of irre)ersi"!e en>$'e inhi"itors.
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