Exam 2 Flashcards
1
Q
what is the monomer of a protein?
A
amino acid
2
Q
what is the structure of an amino acid
A
amine group (NH2), carboxyl group (COOH), an R group, all bonded to a central (alpha) carbon
3
Q
All proteins are built from _____ amino acids
A
20
4
Q
how many neutral AA?
A
15
5
Q
why are side chains so important?
A
they enable proteins to perform their functions
6
Q
are nonpolar side chains hydrophobic or hydrophilic?
A
hydrophobic, gather into clusters (oil and water)
7
Q
are polar, basic, and acidic side chains hydrophobic or hydrophilic?
A
hydrophilic, surface of folded proteins impart water solubility of proteins
8
Q
how many AA are chiral?
A
19
9
Q
which AA is achiral?
A
glycine
10
Q
what is the only secondary amine?
A
proline
11
Q
what is the importance of intermolecular forces of proteins?
A
important in determining interactions between amino acids
12
Q
what are the 4 different intermolecular forces in order from strongest to weakest?
A
- ionic + covalent bonds
- hydrogen bonds
- dipole-dipole forces (disulfide bond)
- van der waals forces
13
Q
explain a hydrogen bond b/w AAs
A
side chains can form hydrogen bonds, connecting different parts of a protein molecule
14
Q
explain van der waals forces
A
the overall charge of the molecules brings them together (weak)
15
Q
explain hydrophobic interactions of AA
A
hydrophobic (nonpolar) molecules come together and expel the water between them
16
Q
explain a disulfide bond
A
creates a covalent bond b/w sulfurs
17
Q
what is a peptide bond?
A
an amide bond that links 2 AA together, PLANAR, releases a water molecule
18
Q
how do you name peptides?
A
citing AA residues in order
19
Q
define zitterion
A
a neutral dipolar ion that has one pos charge and one neg charge
20
Q
amino acid net charge
A
0, NH3 is + and COOH is - so cancels = 0
21
Q
define isoelectric point (pi)
A
describes the ph at which a sample of an amino acid has an equal number of + and - charges
(AA each have their own pi due to the side chain)
22
Q
how many essential AA are there?
A
9
23
Q
what are essential AA?
A
amino acids that the human body cannot produce, must be consumed in the diet
24
Q
define metabolism
A
chemical reactions maintaining living state
25
define catabolism
breakdown of molecules to form energy
26
define anabolism
synthesis of compounds needed by cells
27
define a primary structure
sequence of AA in a protein chain (order of the AA)
28
be able to label a primary structure (protein backbone, peptide bonds, and side chains
check notes
29
why is the primary structure important?
primary function is crucial to the function of the protein that the change of even one AA can drastically alter a proteins biological properties
30
define secondary protein structure
spatial arrangement of the polypeptide backbones determines the secondary protein structure
31
what does the alpha helix of the secondary protein structure look like?
coil, stabilized by h bonds along the backbone with r groups positioned on the Purdue of the helix, carbonyl group + amide
32
what does the beta sheet of the secondary protein structure look like?
flat sheet-like structure, adjacent protein chains held together by h bonds along the backbones
33
parallel beta sheet
peptide chains in same direction
34
anti parallel beta sheet
turned around/ladder
35
2 classes of proteins from the secondary structure
- fibrous (tough, insoluble)
- globular (globe shape, water soluble)
36
examples of fibrous proteins
wool, hair, fingernails
37
examples of globular proteins
alcohol dehydrogenase, serum albumin
38
what is collagen?
secondary structure protein, found in skin, cartilage, blood vessels, bone
--> left handed alpha helix
39
what disease is associated with collagen?
scurvy, lack of vitamin C causing alpha helix to destabilize
40
define tertiary protein structure
the way an entire protein chain is coiled and folded into its specific 3D shape (determined by primary structure)
41
define native protein
a protein with the shape in which it functions in living systems
42
define simple protein
composed of only AA residues
43
what are simple proteins?
they can function alone
44
what are conjugated proteins?
aided by a non-amino acid unit
45
define quaternary protein structure
the way in which two or more protein chains aggregate to form large, ordered structures
46
what is hemoglobin?
a protein in a quaternary structure composed of 4 polypeptide chains held together by hydrophobic interactions and 4 heme groups (function: carries O2 around the body and CO2 out of the body)
47
what is protein hydrolysis?
breaking down proteins, peptide bonds hydrolyzed to yield AA (proteases can do this)
48
what is chymotrypsin's function?
hydrolyzes a peptide bond on the carboxyl-terminal side of aromatic AA
49
what is trypsin's function?
hydrolyzes peptide bonds on the carboxyl side of lysine and arginine
50
what is the n-terminal of a peptide?
the AA on the end (left) with amine group on the end
51
what is the c-terminal of a peptide?
the AA on the end (right) with the carboxyl group on the end
52
define denaturation
loss of the secondary, tertiary, and quaternary protein structure
53
agents that cause denaturation
- heat
- mechanical agitation
- detergents
- organic compounds
- ph change
- inorganic salts
54
what is the connection between protein misfolding and neurodegeneration?
neurodegeneration is often attributed to proteins that are not folded the correct way
55
what are some causes of protein misfolding/neurodegeneration?
- head trauma
- genetic mutation
- age
56
what are amyloid fibrils?
stable protein aggregates that form under certain conditions, makes long, stiff fibers of proteins that cause damage to cells and leads to neurodegeneration
57
what causes Alzheimers?
brain tissue formed from the amyloid B peptides
58
how to prevent Alzheimers?
- diet/eating healthy
- exercise
- low doses of aspirin
59
define enzymes
a special class of proteins that act as a catalyst for a biological reaction
60
What is an enzymatic unit?
the time it takes for an enzyme to perform a task
(number of molecules changed from reactant to product per unit of time)
61
How are enzymes named?
most end with -ase
62
How are enzymes catalysts?
- lowers the energy barrier for a reaction
- gives direction to a biochemical reaction
63
Can enzymes be reused?
yes
64
explain specificity with enzymes
the limitation of the activity of an enzyme to a specific substrate or type of reaction
- structure of enzyme
- specific to chiral centers
- relates to rate
65
What is a turnover number?
- measures catabolic activity
- the max number of substate molecules acted upon
- (per enzyme unit time)
66
define active site
pocket with a specific shape and chemical makeup necessary to bind a substrate
67
define substrate
a reactant in an enzyme (catalyzed reaction)
68
How enzymes work, 4 steps written out?
E + S --> ES --> EP --> E +P
- E=enzyme
- S=substrate
- P=product
69
Why are cofactors needed?
the functional groups of proteins are limited to those of the AA side chains, so by combining with cofactors enzymes gain chemically reactive groups that are not available as side chains
70
What are cofactors?
METALS
- get from the diet
- bind to the enzyme
- ex: Cu2+, Fe2+, etc.
71
What are coenzymes?
organic molecules
- NOT BOUND
- ex: NAD
72
How are vitamins and coenzymes related?
vitamins help to build/synthesize coenzymes
73
4 major factors affecting enzyme activity
- substrate concentration
- enzyme concentration
- temperature
- ph
74
How does substrate concentration affect enzyme activity?
- more substrates = higher rate
- less substrates = lower rate
- there is a maximum
(exponential)
75
How does enzyme concentration affect enzyme activity?
more enzymes in a given volume, the quicker the rate will be
(linear)
76
How does temperature affect enzyme activity?
- max is when it reaches the optimal temperature
- too hot, will denature
(bell curve)
77
How does pH affect enzyme activity?
- enzymes vary on optimal ph
- (most enzymes max activity at about 5-)
- most enzymes will denature in extreme ph
(multiple bell curves dependent on enzyme)
78
6 main classes of enzymes
- oxidoreductases
- transferases
- hydrolyses
- isomerases
- lyases
- ligases
79
function of oxidoreductases
- oxidoses --> oxidation of O2 to substrate
- reductases --> reduction of a substrate
- require coenzymes
EXAMPLE: NAD --> NADH
80
function of transferases
- catalyze transfer of a group from one molecule to another
EXAMPLE: ATP --> ADP + PO3^2-
81
function of hydrolases
- breaking down (lipases, proteases, amylases, etc)
- important in digestion
EXAMPLE: polypeptide chain --> AA
82
function of isomerases
- rearrange the bond placement (change chirality)
EXAMPLE: A --> B
83
function of lyases
- addition of simple organic groups (H2O, CO2, NH3) yo a double bond
- no energy required
84
function of ligases
- addition (bonding 2 substrates)
- NEED ENERGY
- proteins and DNA formed
85
enzymes act as catalysts because of:
1. proximity
2. orientation
3. catalytic effect
4. energy effect
5. rate of reaction
86
what are the 2 theories on how a substate fits into an active site?
- lock and key model
- induced fit model
87
what is the lock and key model?
- a substrate will only fit into an enzyme with the correct shape
- flaw = assumes enzymes are static
88
what is the induced fit model?
- enzyme changes shape as substrate fits into active site
89
is the lock and key model or induced fit model more accurate for how an enzyme fits into an active site?
induced fit model because it accounts for the enzyme moving
90
3 general enzyme regulators
- activation
- inhibition
- feedback and allosteric control
91
define an enzyme regulator: activation
any process that starts or increases the action of an enzyme
92
define an enzyme regulator: inhibition
any process the slows or stops the action of an enzyme
93
define an enzyme regulator: feedback control
regulation of an enzymes activity by the product of a reaction later in the pathway
- negative feedback = stops reaction
- positive feedback = continues reaction
94
what is negative feedback?
the product at the end of the pathway stops the reaction
95
what is positive feedback?
the product at the end of the pathway continues the reaction
96
define an enzyme regulator: allosteric control
product binds to enzyme in a place separate from the active site and changes shape of the enzyme/active site
- negative = substrate cannot bind
- positive = substrate can now bind
97
what is negative allosteric control?
the allosteric regulator is bound the the enzyme and the substrate cannot bind
98
what is positive allosteric control?
the allosteric regulator is bound the the enzyme and the substrate can now bind
99
what are the 2 types of inhibition?
1. competitive
2. noncompetitive
100
what is competitive inhibition?
the wrong substate will come in and keep out the actual substate
101
what is noncompetitive inhibition?
an inhibitor binds to a different place and changes the enzymes shape so the substate cannot bind to the active site
102
what is an irreversible inhibitor?
- inhibitor binds to enzyme (covalent) and NEVER COMES OFF
- the enzyme is useless and is destroyed
EXAMPLES: penicillin, aspirin, sarin
103
examples of poisons that are enzyme inhibitors
- venom
- heavy metals (irreversible)
- cyanide (irreversible)
104
examples of enzyme inhibitors that are drugs
- ace inhibitor
- HIV protease inhibitor
- proton pump inhibitor
- cox-2 inhibitors
105
explain the ace inhibitor
inhibitor of angiotensin I converting enzyme
- competitive inhibitor
- brings down blood pressure
106
explain the HIV protease inhibitor
ritonovir, binds to HIV protease active site
- inhibits HIV production
- competitive inhibitor
107
explain the proton pump inhibitor
inhibits the hydrogen potassium ATPase in parietal cells of stomach, inhibiting HCl secretion
- noncompetitive inhibitor
- helps with heart burn
108
explain the COX-2 inhibitor
bind to COX-2 enzyme responsible for inflammation and pain
- ibuprofen! (competitive) and Celebrex
109
define zymogen
enzyme is released as inactive and undergoes a chemical change to be activated
110
explain the genetic control of enzyme regulation
the synthesis of all proteins, including enzymes, are regulated by genes
(example: lactase is not typically synthesized in adults)
111
draw glycine
R chain = H
112
draw alanine
R chain = CH3
113
draw cysteine
R chain = CH2-SH
114
draw aspartate
R chain = CH2-COO-
115
draw lysine
R chain: CH2(x4)-NH2+
116
define vitamin
an organic molecule, essential in trace amounts, that must be obtained in the diet because it is NOT synthesized in the body
117
what are the 2 classifications of vitamins?
- fat soluble
- water soluble
118
what vitamins are fat soluble?
A, D, E, K
119
what vitamins are water soluble?
vitamin b complex and C
120
why can you eat a lot of water soluble vitamins?
because excess can be easily removed in urine
121
vitamin c deficiency and excess
deficiency: scurvy
excess: kidney stones
122
what is vitamin B3 (niacin)
- sources: grains, cheeses, nuts, chicken
- precursor to NAD+ (oxidoreductase coenzyme)
- deficiency: dermatitis, weakness, mental confusion
123
what is vitamin B7 (biotin)
- sources: shampoos, fruits, vegetables, nuts, grains
- benefits: energy support, healthy liver, skin, eyes, hair, nerves, nails, and glucose
124
what is vitamin C used for
need vitamin C to transfer of hydroxyl groups to proline to stabilize alpha helix structure
- left handed helix
125
what is vitamin E
- prevents breakdown of vitamins A and FA (antioxidants)
- source: meat, milk, vegetables
- deficiency: anemia, other
- excess: none
126
what is vitamin K
- essential for liver synthesis of prothrombin and other clotting factors
- source: vegetables, intestinal bacteria
- deficiency: bleeding disorders
- excess: liver disfunction, jaundice
127
define antioxidants
a substance that prevents oxidation by reacting with and oxidizing agent (diffuse free radicals)
128
define free radicals
reactive molecular fragments with unpaired electrons that gain stability by picking up electrons from nearby molecules
129
why are free radicals bad?
- they steal from healthy atoms
- uncontrolled, domino effect of damage, attracted to DNA
130
how do antioxidants diffuse free radicals?
give the electron to the free radical thereby diffusing it
131
What causes free radicals?
- UV damage
- inflammation
- air pollution
- smoking
- ionizing radiation
- metabolism
132
dietary antioxidants
- vitamin C
- vitamin E
- selenium (cofactor)
133
define mineral
an enzyme cofactor, metals in the diet
134
transition metals as minerals
- form positive charge ions
- different ionic states (+1 to +5)
- all combine to enzymes
135
what are macro minerals?
required daily amounts (greater than 100mg/d)
136
examples of macro minerals
Ca, P, Mg, K, Na, Cl, S
137
what are micro minerals?
need less of these (transition elements)
138
examples of micro minerals
transition elements
- chromium, copper, manganese, molybdenum, selenium, zinc
139
Calcium as a macro nutrient: use, source, deficiency, excess
- use: bone formation + muscle contraction
- source: dairy, eggs, beans
- deficient: osteoporosis, muscle cramps
- excess: kidney stones, heart arrhythmias
140
define carbohydrates
a large class of naturally occurring polyhydroxy aldehydes and ketones
141
carbohydrates general formula
CnH2nOn
142
how to name carbohydrates?
- family name ending in -ose
- simple sugars = common names
- number of carbons = prefix (try, treat, pent, hex, hept)
143
define monosaccharide
contain 3-7 carbon atoms and one aldehyde or ketone group
144
naming a monosaccharide
1. identify ketone (ketose) or aldehyde (aldose)\
2. count amount of carbons and determine the prefix
3. combine with -ose
145
name this molecule: aldehyde, 6 carbons
aldohexose
146
what is special about carbohydrate functional groups?
they are involved in reactions with alcohols, lipids, or proteins to form biomolecules
147
are all carbohydrates chiral?
no, proline is achiral
148
D vs L carbohydrate?
chiral carbon atom furthest from the carbonyl group before the last carbon
- D = right
- L = left
149
what are more often seen in nature: D or L carbohydrates?
D
150
how many carbons is in an aldehyde ring?
6
151
how many carbons is in an pentose ring?
5
152
draw glucose
check notes
153
draw fructose
check notes
154
draw sorbitol
check notes
155
What is d-glucose used for in the human body?
dextrose or blood sugar
156
What is the most widely occurring monosaccharide and most important functionally?
glucose
157
what is the most important simple carbohydrate in human metabolism?
glucose
158
what 2 hormones regulate glucose?
insulin and glucagon
159
what is galactose used for?
d-galactose is distributed in plant gums, pectins, and a component in disaccharide lactose
160
what is galactosemia?
galactose deficiency, an inherited (recessive) deficiency of several enzymes needed to metabolize galactose
--> build up causing vomiting, liver failure, brain damage, and cataracts
161
what is fructose used for?
it is a fruit sugar (in honey and many fruits)
162
what is ribose and deoxyribose
both are 5 carbon aldehyde sugars, RNA and DNA
163
what happens when you oxidize a sugar?
it burns fast, very controlled in our body
164
glucose reduces to sorbitol
an addition of H2, aldehyde converted to a ketone
165
what is type 2 diabetes?
- increase of sorbitol buildup in intestines
- higher glucose
166
define glycosidic bond
bond that connects 2 monosaccharides
167
define hydrolysis
adding water to break the bonds
168
define disaccharide structure
- 2 monosaccharides connected by glycosidic bond (alpha or beta)
- create a 1,4 link
169
glucose + fructose
sucrose
170
galactose + glucose
lactose
171
glucose + glucose
maltose
172
explain maltose
- fermenting grains
- alpha 1,4 link
- food sweetener
- digested in the small intestine
173
explain lactose
- milk sugar
- beta 1,4 link
- lactose intolerance
174
explain sucrose
- 1,2 anomeric link
- table sugar (beets and cane)
- sucrase enzyme
175
what are the sweetest sugars?
synthetic sugars
176
how do we taste?
1. molecules are "sensed" by taste cells
2. cells release a signaling compound
3. ion channel conformational channels trigger a neuron to the brain (sweet, salty, bitter, like, don't like)
177
define polysaccharides
polymers of tens, hundreds, or even thousands of monosaccharides linked together through glycosidic bonds
178
examples of polysaccharides
- cellulose (fiber)
- amylose (starch)
- amylopectin (starch)
- glycogen
179
cellulose source
plant -- fiber (structure)
180
cellulose subunit
glucose (1000s)
181
cellulose bond
beta 1,4
182
cellulose structure
compact, dense structure with NO BRANCHES
183
what are some examples of cellulose?
- plants
- wool/cotton
- wood/paper/cardboard
- thickener in food
184
starch examples
- amylose (~20%)
- amylopectin (~80%)
ex: beans, wheat, rice, potatoes
185
starch source
plant
186
starch subunit
glucose
187
what bond does amylose have?
only alpha 1,4, NO BRANCHING
188
what bond does amylopectin have?
alpha 1,4 and 1,6 BECAUSE BRANCHING
189
is cellulose digestible by humans?
NO
190
are starches digestible by humans?
YES
191
what enzyme breaks down starches?
amylase
192
glycogen source
animal (liver and skeletal muscle)
193
glycogen subunit
glucose
194
glycogen bonds
1,4 and 1,6 (branches)
195
what is glycogen storage disease?
- cannot break down glycogen
- continues to store
196
how is glycogen stored in athlete's different than average?
- athletes can train their body to store more glycogen
- rate of consumption is regulated by effort
197
what are the blood types?
- A
- B
- AB
- O
198
what are the differences between blood types?
the differences are based on the presence of 3 different oligosaccharide units = A, B, O
199
why is O blood type the universal donor?
O has a similar composition to A and B so A, B, and AB will lack the antibodies to cell type O
200
why can AB receive all blood types?
has A and B molecules on red cells so it has no antibodies to A, B, or O
201
define energy
can be converted from one form to another but can be neither created or destroyed
202
animal cell respiration formula
food + O2 ---> CO2 + H2O + energy
(oxidation reaction)
203
plant formula
CO2 + H2O ---> C6H12O6 + O2
204
what are our bodies specific requirements for energy?
- must be released from food gradually
- stored in an accessible form
- release must be finely controlled
- just enough energy released for temp
- energy needs to be available to drive chemical reactions that are not favorable at body temp
205
explain Gibbs Free Energy
equation to explain whether a reaction is favorable or not depends on either release to absorption of energy as heat, together with the increase and decrease of disorder
206
Gibbs free energy equation
G= H - T(S)
207
G means (Gibbs free energy)
Gibbs free energy
208
H means (Gibbs free energy)
enthalpy
209
T means (Gibbs free energy)
temperature
210
S means (Gibbs free energy)
entropy
211
what does it mean is Gibbs free energy is negative
exergonic reaction (reaction will spontaneously occur)
212
what does it mean if Gibbs free energy is positive
endergonic reaction (reaction will NOT spontaneously occur)
213
exergonic definition
A spontaneous reaction or process that
releases free energy and has a negative G
214
endergonic definition
A nonspontaneous reaction or process
that absorbs free energy and has a positive G
215
what is a favorable reaction?
exergonic reaction, high reactant energy and low product energy
216
what is an unfavorable reaction?
endergonic reaction, low reactant energy and high product energy
217
does the number size matter in Gibbs free energy?
yes, larger the number the more energy they need
218
what are pathways?
a series of enzyme - catalyzed chemical reactions that are connected by their intermediates, product of first reaction is used in the next reaction and so on
219
define prokaryotic cell
single celled organism (bacteria, blue green algae)
220
define eukaryotic cell
found in single celled yeast and all plants and animals
221
what are the differences between prokaryotic cells and eukaryotic cells?
- eukaryotic are 1000 times larger
- prokaryotic have a cell wall and no membrane bound organelles
222
what are organelles?
small, functional units that perform specific tasks
223
what is a membrane bound nucleus?
stores DNA in eukaryotic cells
224
what is cytoplasm?
region between cells and nuclear membranes
225
what is cytosol?
fluid of cytoplasm (electrolytes, nutrients, enzymes)
226
what is the function of mitochondria?
small molecules are broken down to provide energy (ATP) for an organism
227
structure of the mitochondria
- matrix = citric acid cycle
- inner surface of cell membrane = ETC
- cristae = folds in the inner membrane
- double lipid bilayer
- contains own set of DNA (from the mother)
228
metabolism definition
the sum of all chemical reactions that take place in an organism
229
catabolism definition
breaking down, releasing energy
230
anabolism definition
building larger molecules
231
activation definition
any process that starts or increases the action of an enzyme
232
inhibition definition
Any process that slows or stops the action of an enzyme
233
feedback and allosteric control
two strategies for enzyme regulation
234
3 Types of Metabolic Pathways
- a linear sequence
- a cyclic sequence
- a spiral sequence
235
4 Stages of Metabolism
1. digestion (catabolism)
2. acetyl-coenzyme A production
3. citric acid cycle
4. ATP production
236
what is a derivative of B5?
acetyl-CoA
237
Stage 1: Digestion
enzymes break down molecules
238
Stage 2: Acetyl-Cozenzyme A Production
Acetyl groups are attached to coenzyme A by a bond
between sulfur of the thiol group on coenzyme A and
the carbonyl carbon of the acetyl
(thiol group=the AA cystine)
239
Stage 3: Citric Acid Cycle
break down acetyl CoA to produce energy (NADH and FADH2)
240
Stage 4: ATP Production
NADH and FADH2 are passed through the ETC to produce ATP
