1
Q
the sharing of electrons between atoms
A
covalent bonds
2
Q
when the electronegativity difference is <0.5, the electrons are shared equally between atoms, and no dipole is formed (eg. C-H bond has a difference of 0.4, so it is BLANK)
A
nonpolar covalent bonds
3
Q
when the electronegativity difference is >0.5 but <1.6, the electrons are shared unequally between atoms, and a dipole is formed (e.g. O-H bond has a difference of 1.3, so it is BLANK; C-O bond has a difference of 0.9)
A
polar covalent bond
4
Q
random electron cloud movement that creates a temporary induced dipole
-increased surface area for interaction increases the melting point, boiling point, and surface tension
A
london dispersion forces
5
Q
the S- of the more electronegative atom in a polar covalent bond is attracted to the S+ of the less electronegative atom in a different polar covalent bond
A
dipole-dipole interactions
6
Q
strong dipole-dipole generated by S+ hydrogen bonded covalently to S-F, O, or N that creates a unique very strong dipole
- S+ hydrogen acts as a H bond donor
- S- atom (either F, O, or N) or any other atom with a lone pair of electrons can act as an H bond acceptor
A
hydrogen bonding
7
Q
driven by entropy (the system wanting to move towards disorder or lack of organization), hydrophobic groups draw away from water/polar solutions into the interior
-while this may seem to be “ordered,” when the hydrophobic groups are all together excluding water they can actually move more randomly as they do not have the repulsion of the polar groups
A
hydrophobic interactions
8
Q
there are multiple ways to create ions (+ or - charged), including ionic bonds, acid/base reactions, and redox reactions. However, the ions are created, once made the + charges will attract to the - charges, and like charges will repel away from each other
A
electrostatic or ionic interactions
9
Q
these amino acids orient themselves outward to be close to water
A
hydrophilic interactions
10
Q
positively charged side groups bond to negatively charged ones
A
ionic bonds
11
Q
cysteine forms a bond with another cysteine through its side group
A
disulfide bonds
12
Q
these amino acids orient themselves towards the center of the polypeptide to avoid water
A
hydrophobic interactions
13
Q
is the key solvent for all biochemical reactions within cells. BLANK is able to form hydrogen bonds in solution
A
Water
14
Q
is a shell of solvent surrounding a solute. When water is the solvent, the shell is referred to as a hydration sphere or hydration shell
A
solvation solute
15
Q
dissolve in water
A
hydrophillic molecules
16
Q
aggregate away from water
A
hydrophobic molecules
17
Q
molecules with hydrophillic polar head groups and hydrophobic non-polar tail groups
A
amphipathic lipids
18
Q
use H20 to cut a bond
A
hydrolysis
19
Q
water is used to break apart macromolecules
A
catabolic reactions
20
Q
are different than the other classes of macromolecules because they are classified by their hydrophobicity and by their structure. They can have either an energy storage function, a structural function, or a role in signaling
A
lipids
21
Q
-energy storage function
-a structural function
-a role in signaling
A
lipids
22
Q
includes, fats, sterols, waxes, and vitamins. They do not have repeating monomers, but are instead defined by the fact that they are insoluble in water
A
lipids
23
Q
what are the six major classifications of lipids?
A
triacylglycerols, fatty acids, phospholipids, glycolipids, steroids, and the terpenes
24
Q
are made up of carbon chains with a carboxyl group at the end. The carbon chains can be either saturated or unsaturated
A
fatty acids
25
meaning they only have single carbon-carbon bonds
- free rotation
saturated bond
26
meaning they have some carbon-carbon double bonds. Double bonds in the fatty acid tail gives it a "kink" which can affect the fluidity and permeability of cell membranes
- no free rotation
- kink
- take up more space
unsaturated bond
27
prefer to store saturated fats and prefer to use
unsaturated fats
28
are composed of a glycerol backbone bound to three fatty acid chains through an ester linkage. Synthesis of BLANK happens through a dehydration reaction
triglycerides
29
are used for long term storage in fat cells and for thermoregulation
triglycerides
30
what is this
glycerol
31
what is this?
triglycerides
32
are similar to phospholipids, in that they are amphipathic with a 3 carbon backbone with at least one fat chain. However, carbon 2 has a nitrogen group and the fat chain is NOT attached through a ester linkage
sphingolipids
33
is 18 carbons long. BLANK play important roles in tissue development as well as cell adhesion and recognition
sphingosine
34
derived from cholesterol, using enzymes in a biochemical pathway (e.g. cortisol, testosterone, progesterone, estrogen, aldosterone, and vitamin D) and have characteristic four-ringed structures
steroids
35
are made of a five-carbon isoprene unit that repeats in the structure, with 10-40 carbons and a high degree of conjugation often present. Are a very diverse chemical group of naturally occuring compounds, with a variety of functions
terpenes
36
tell the neighbor molecules what to do
paracrine
36
are derived from fatty acids, and have a role in paracrine signaling
eicosanoids
37
are found in both plants and animals, and used for protection against water loss and pathogen invasion. Are characterized as hydrocarbons that are connected through ester linkages
waxes
38
Triglycerides and cholesterol are hydrophobic and therefore insoluble in blood. They are transported throughout the body as
lipoproteins
39
consist of a lipid hydrophobic core (triacylglycerols and cholesterol) surrounded by phospholipids and apoproteins
lipoproteins
40
the four major classes of lipoproteins in order of decreasing side and ratio of lipid to protein are:
1. Chylomicrons: fatty acids absorbed from the diet
2. very low-density lipoproteins (VLDL)
3. low density lipoproteins (LDL)
4. High density lipoproteins (HDL)
**transport fats from cell to cell
41
fatty acids absorbed from the diet
Chylomicrons
42
very low-density lipoproteins
VLDL
43
low density lipoproteins
LDL
44
High density lipoproteins
HDL
45
in healthy individuals, 30% of blood cholesterol is carried by BLANK, commonly called "good" cholesterol
HDLs
46
or polypeptides, are built from a chain of amino acid residues lined together by a peptide bond that forms during a translation at a cytosolic/ RER ribosome
proteins
47
pH
protonated
48
pH> pka
deprotonated
49
dipolar ion that s overall netural; a molecule with both positively and negatively charged groups. When an amino acids carries both a positive charge on the amino group and a negative charge on the carboxylic acid group, it has an overall neutral charge and is called a
zwitterion
50
in highly acidic environments (low pH values), amino acids tend to be
positively charged
51
in highly alkaline environments (high pH values), amino acids tend to be
negatively charged
52
is the pH at which amino acid carries no net electrical charge. Amino acids will have a net positive below the pI, and a net negative charge above the pI
isoelectric point (pI)
53
neutral molecule pI equation
pI= (pka1 + pka 2) / 2
carboxyl group + amino group
54
acidic amino acids and cysteine
pI= (pka1 + pKR / 2)
- carboxyl group is designated pKa1
55
basic amino acids
pI = (pKR + pKa2 / 2)
- amino group is designated pKa 2
56
four different groups to the central atom
chiral
57
when BLANK, rotate light and have optical activity (plane-polarized light)
chiral
58
which amino acid is not chiral
glycine
59
which amino acid forms disulfide bonds and has and R configuration
cysteine
60
imidiazole ring
61
The MCAT prefers to use anion names (ex. apartate and glutamate) instead of acid names (eg aspartic acid and glutamic acid) because most amino acids in cells exist in the deprotonated form. In biology, the amino acids in proteins and peptides are L-amino acids
important to know
62
of a protein is its sequence of amino acids connected in a polypeptide: a peptide bond is formed between the amino group of one amino acid and the carboxyl group of the adjoining amino acid, via a dehydration reaction
primary structure
63
refers to localized folding in regions of the polypeptide chain. It results from hydrogen bonding between the carbonyl oxygen of one peptide group and the hydrogen of the amine of another peptide group. The R groups are not involved in determining THIS structure
secondary structure
64
two common secondary structures are
alpha helix and beta pleated sheets
65
amino acids in a backbone structure are always BLANK amino acids apart
4
66
(also called the final conformation/3D shape) results from R-group interactions, including:
1. Hydrophobic interactions
2. Covalent disulfide bonds between cysteines
3. ionic interactions
4. hydrogen bonds
5. van der waals
tertiary structure
67
when two thiol groups bond together what happens like when two disulfide bonds occur
lose electrons and oxidation happens
68
is a folded structure that facilitates a particular function of the protein, such as DNA binding. However, if the sequence is isolated from the protein it would not fold into that shape, and is dependent on the regions around it to hold its shape
motifs
69
proteins made up of more than one polypeptide chain also have a BLANK where each chain is a subunit.
quaternary structure
70
a protein with two identical subunits
homodimer
71
while a protein with two non-identical subunits
heterodimer
72
when the native configuration of a protein is disrupted, the protein is said to be
denatured
- the primary structure is the only structure out of the 4 that will not be affected by this
73
denaturing agents include:
1. Heat: disrupts all forces
2. Salt: disrupts electrostatic bonds
3. pH change: disrupts electrostatic bonds
4. Urea: disrupts H bonds
5. Mercaptoethanol: disrupts disulfide bonds
6. Organic solvents: disrupts hydrophobic interactions
74
carbohydrate groups attached to protein. These are components of cellular plasma concentrations
glycoproteins
75
consist of more than 50% carbohydrates and some protein. These are components of the extracellular matrix
proteoglycans
76
proteins that have a covalently attached prosthetic group which are necessary to function.
Hemoglobin and cytochromes of the electron transport chain are common examples
cytochromes
77
there are two main groups of proteins
non-enzyme and enzyme
78
are capable of binding to their targets, but do not catalyze reactions.
non-enzyme proteins
79
Common examples of non-enzyme proteins are
-membrane channels and receptors
-transport proteins
-antibodies
-motor proteins
80
are made from carbon and water and have the empirical formula CH2O. The most common is glucose
carbohydrate
81
are stereoisomers of cyclic saccharides that differ in their configuration at the anomeric carbon
anomers
82
what are the two anomers called
alpha and beta
83
D sugar on a fischer projection is on the
right
- on the last chiral carbon in the chain
84
alpha =
opposite
for anomeric carbon
85
beta =
same
for anomeric carbon
86
how do we find the anomeric carbon in the linear fischer projection?
it is the carbonyl carbon, which is a carbon double bonded to oxygen (c=o). the end of the chain is closest to this carbon is where we start numbering the chain from
87
how do you find the anomeric carbon in a ring
it is the carbon bound to two oxygens. the end of the chain is closest to this carbon where we start numbering the chain from
88
is a branched glucose polymer that consists of a (trans) linkages in alpha (1-4) and alpha (1-6) pattern
glycogen
89
contains beta-linkages (b (1-4))
cellulose
90
an enzyme that will break these beta-glycosidic linkages
cellulase
91
alpha linkages with branching
glycogen
92
alpha linkages with minimal branching
starch
93
beta linkages with no branching
cellulose
94
single sugar molecule (glucose, galactose, and fructose)
monosaccharide
95
two sugar molecules (lactose, sucrose, maltose)
disaccharide
96
three or more sugar molecules (glycogen, amplyose, amylopectin, and cellulose)
polysaccharide
97
what is this
lactose
98
what is this
sucrose
99
what is this
maltose
100
are proteins that function to increase the rate of biological processes
enzymes
101
- enzymes are neither consumed nor permanently altered during any reaction
-enzymes do not change delta G of the reaction (free energy gained or released)
-enzymes do not change the equilibrium of the reaction (net forward and reverse reaction balance)
what enzymes are not!
102
the substrate fits exactly into the active site of the enzyme
lock and key theory
103
the active site of the enzyme changes shape as the substrate bonds
induced-fit theory
104
are non-protein components required for the enzyme to function as a catalyst
cofactors
ex. NADH and CoA
105
a cofactor is a co-enzyme covalently bound to the enzyme is called
a prosthetic group
106
fat-soluble vitamins
ADEK
107
a complete, catalytically active enzyme together with its bound coenzyme and/or metal ion is called
holoenzyme
107
the protein part of the enzyme is called
the apoenzyme
108
enzyme reaction rate is closely associated with
pH
[H+] in solution
109
enzyme reaction rate is closely associated with
temperature
110
enzyme reaction rate is closely associated with
substrate concentration
111
as the concentration of substrate increases, the rate of the reaction also increases (but to a lesser degree) until a maximum rate, Vmax has been achieved
saturation kinetics
112
is proportional to enzyme concentration
vmax
if more enzyme is added, the vmax will rise
113
michaelis constant = the substrate concentration where the reaction rate is 1/2 Vmax
Km
114
is inversely proportional to enzyme-substrate affinity
Km
higher Km says lower affinity
115
is independent of enzyme concentration... if double enzyme, same Km
Km
116
how fast one enzyme works when there is no substrate deficiency
kcat
vmax = Kcat[Etotal]
-the higher the Kcat, the faster the reaction at higher substrate concentrations
117
how good an enzyme is using a specific amount of substrate
catalytic enzyme
*probably pretty low [s] concentration
118
are derived from the Michaelis-Menten equation
lineweaver-burk plots
- the slope line is equal to Km/Vmax
- the x-intercept is equal to -1/Km
- is equal to 1/Vmax
119
what is this
catalysis
120
what is this
inhibition
121
often resemble the substrate and reversibly bind to the enzyme's active site, thereby blocking the substrate front binding
competitive inhibitors
122
bind at a site other than the active site (allosteric site). They do not bind to the enzyme until it has formed the enzyme-substrate complex. Adding more substrate does not increase the reaction rate. lowers both the vmax and km
uncompetitive inhibitors
123
bind the enzymes at an allosteric site and change the 3-D conformation so the the substrate can still bind to the active site with the same affinity as before. The enzyme, however, is no longer in the optimal configuration to stabilize the transition state of the reaction, therefore the reaction will not occur
non-competitive inhibitors
124
bind at a site other than the active site. However, they can bind to either the enzyme alone, or to the enzyme-substrate complex, which indicates their effect on Km and Vmax. All lower vmax
mixed inhibitors
125
lower the substrate affinity, increasing the Km. They do not affect vmax. They will change the x-intercept but not the y-intercept
competitive inhibitors
126
increase the vmax and the substrate affinity, lowering the Km. On the graph, the lines for the inhibited and uninhibited reactions will be parallel
uncompetitive inhibitors
127
decrease the vmax and usually decrease the substrate affinity, increasing the km
mixed inhibitors
128
decrease the vmax but do not affect the substrate affinity and so do not change the Km. They will change the y-intercept but do not affect the x-intercept
non-competitive inhibitors
129
what is this?
competitive inhibition
130
what is this?
non-competitive inhibition
131
what is this?
mixed inhibition
132
what is this?
uncompetitive inhibition
133
km = increase
vmax = no change
competitive inhibitors
134
km = decrease
vmax = decrease
uncompetitive inhibitors
135
km = increase or decrease
vmax = decrease
mixed inhibitors
136
km = no change
vmax = decrease
noncompetitive
137
inactive enzymes are irreversibly activated by proteolytic cleavage
proteolytic cleavage
138
enzyme activation often via a modifier
reversible covalent modification
139
control proteins or protein subunits associate with enzymes to activate or inhibit their activity
control proteins
140
modify enzyme configuration and activity by binding to specific sites on the enzymes.
allosteric interactions
141
catalyzes transfer of electrons
oxidoreductase
142
transfer functional groups
transferases
143
hydrolyze bonds
hydrolases
144
breaks and forms new bonds
lyases
145
isomerizes molecules
isomerases
146
joins molecules together using ATP
ligases/synthetases
147
that phosphorylate a substrate (add a phosphate)
kinase
148
that dephosphorylate a substrate (remove a phosphate)
phosphatases
149
occurs when products downstream in a reaction series comes back and inhibits the enzymatic activity of an earlier step
negative feedback
150
occurs when one of the products downstream in a reaction series comes back and increases the enzymatic activity of an earlier step
positive feedback
ex. childbirth
151
What processes occur in the cytosol?
All anaerobic metabolic pathways generate some energy.
152
What is glycolysis?
An anaerobic, catabolic process that cuts glucose in half to produce 2 ATP, 2 NADH, and 2 pyruvate.
## Footnote
It is a 10-step pathway regulated at steps 1, 3, and 10.
153
What is fermentation?
A redox reaction that transfers electrons from NADH to pyruvate to regenerate NAD+ as a glycolysis substrate when no O2 is present.
## Footnote
This occurs when there is no ETC activity.
154
What is gluconeogenesis?
An anabolic process that takes 3C substrates to produce glucose in the liver, reversing glycolysis with new enzymes at steps 1, 3, and 10.
155
What is glycogenesis?
An anabolic process that uses g-1-p from g-6-p to make glucose polymer, catalyzed by glycogen synthase.
## Footnote
Occurs in the liver and muscles for short-term energy storage in a FED state.
156
What is glycogenolysis?
A catabolic process where glucose is released as g-1-p that becomes g-6-p for gluconeogenesis or glycolysis, catalyzed by glycogen phosphorylase.
## Footnote
Occurs in an UNFED state (fasting) with low blood sugar.
157
What is the Pentose Phosphate Pathway?
A redox reaction for NADPH production; carbon can be used for nucleotide synthesis or re-enter as glycolysis intermediates.
## Footnote
Converts g-6-p to ribulose-5-p, generating 2 NADPH and losing CO2.
158
What is fatty acid synthesis?
An anabolic process that uses NADPH and ATP to make malonyl CoA from acetyl CoA, generating fatty acids by adding 2C groups repeatedly.
## Footnote
Catalyzed by fatty acid synthase.
159
What is protein anabolism?
The process of assembling proteins in the RER by peptide bonds in a FED/post-prandial state.
160
What is protein catabolism?
The deamination (loss of NH2) of amino acids in the liver during an UNFED state.
## Footnote
This is not an ideal use of amino acids.
161
What is the function of Smooth ER?
Smooth ER is involved in lipogenesis, building triglycerides (glycerol + 3 fatty acids) and packaging them in lipoproteins (LDL, HDL).
162
What is the role of mitochondria in cellular respiration?
Mitochondria are essential for aerobic metabolism, utilizing pyruvate and generating ATP through processes like the Kreb's cycle.
163
What is the significance of the H+ gradient in mitochondria?
The H+ gradient serves as an energy source for ATP synthesis.
164
What are the stages of aerobic metabolism?
Aerobic metabolism includes pyruvate oxidation (decarboxylation) and the Kreb's cycle (citric acid cycle), which produces ATP and electron carriers (NADH, FADH2).
165
What occurs during anaerobic metabolism?
In anaerobic metabolism, B-oxidation breaks down fatty acids into acetyl CoA, FADH2, and NADH, and ketogenesis builds ketones as an alternative fuel.
166
What is pyruvate dehydrogenase complex (PDC)?
PDC is a multisubunit regulated enzyme that catalyzes the conversion of pyruvate to acetyl CoA.
167
What is ketogenesis?
Ketogenesis is an anabolic process that builds ketones from glucose, occurring in the unfed state.
168
What is cellular metabolism?
Metabolism consists of all cellular chemical reactions that are either anabolic (molecular synthesis) or catabolic (molecular degradation).
169
What are anabolic reactions?
Anabolic reactions synthesize complex molecules from simpler molecules. These are energy storing reactions that require energy and are therefore endergonic.
170
What are catabolic reactions?
Catabolic reactions break down complex molecules into simpler ones. These reactions release energy and are therefore exergonic.
171
What does glucose catabolism consist of?
Glucose catabolism typically consists of glycogen degradation (glycogenolysis), glycolysis, the Kreb's cycle, and the Electron Transport Chain.
172
What is glycolysis?
Glycolysis is an anaerobic process that breaks down glucose in the cytosol of cells.
173
What are the energy-acquiring stages of cellular respiration?
The energy-acquiring stages are glycolysis, the Kreb's Cycle, and the Electron Transport Chain.
174
What is ATP?
ATP (adenosine triphosphate) is the most abundant energy carrier in the cell.
175
What happens during the hydrolysis of ATP?
The hydrolysis of ATP → ADP + Pi is exergonic and releases a significant amount of energy that can be used to drive endergonic reactions.
176
How does ATP transfer energy?
ATP can transfer energy by donating a phosphate group (phosphorylating) another molecule, creating a new covalent bond.
177
178
179
What is NADH?
NADH (nicotinamide adenine dinucleotide) is a reducing agent, meaning it can donate an electron to another molecule.
180
How many ATP can each NADH molecule produce?
Each NADH molecule can donate two electrons to the electron transport chain, producing 3 ATP.
181
What are other electron carriers besides NADH?
Other electron carriers include NADPH and FADH2.
182
What are redox reactions?
Redox reactions are central to metabolic pathways and involve two reactions: reduction and oxidation.
183
What happens during a redox reaction?
Electrons are transferred from an electron donor to an acceptor.
184
What does RIG stand for?
RIG stands for Reduction Is Gain.
185
What does GER stand for?
GER stands for Gain of Electrons Reduction.
186
What does LEO stand for?
LEO stands for Loss of Electrons Oxidation.
187
What is oxidation?
Oxidation is losing electrons and increases the oxidation state.
188
What is reduction?
Reduction is gaining electrons and decreases the oxidation state.
189
Provide an example of reduction.
NAD* + H+ + 2 electrons → NADH
190
Provide an example of oxidation.
NADH → NAD+ + H+ + 2 electrons
191
What is the role of ATP in metabolic reactions?
During metabolic reactions in the cell, ATP is an energy carrier.
192
What is the role of NADH in metabolic reactions?
During metabolic reactions in the cell, NADH is an electron carrier.
193
Pic
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194
What is glycolysis?
Glycolysis is the first stage of both anaerobic and aerobic respiration, occurring in the cell cytosol and producing two pyruvate molecules from one glucose molecule.
195
What type of transport is used for glucose entry into the cell?
Glucose enters a cell through GLUT transporters using facilitated diffusion.
196
What are the products of glycolysis?
Glycolysis produces two pyruvate (3-carbon) molecules and a net gain of two ATP.
197
Is carbon dioxide released during glycolysis?
No carbon dioxide is released during glycolysis; only one C-C bond is cleaved.
198
How many ATP are consumed and produced during glycolysis?
Two ATP are consumed during the first five steps and four ATP are produced in the later five steps, resulting in a net gain of two ATP.
199
Can all living organisms perform glycolysis?
Yes, all living organisms can perform glycolysis as it is anaerobic metabolism that evolved prior to the oxygen environment.
200
What is the role of hexokinase in glycolysis?
Hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate.
201
What is the significance of phosphofructokinase-1 (PFK-1)?
PFK-1 is a key regulatory enzyme in glycolysis that catalyzes the conversion of fructose 6-phosphate to fructose 1,6-bisphosphate.
202
What is NADH and its role in glycolysis?
NADH is produced during glycolysis and is important for the transfer of electrons in cellular respiration.
203
What are the two types of reactions in glycolysis?
There are irreversible reactions and reversible reactions in glycolysis.
204
What is the Pentose Phosphate Pathway?
A metabolic pathway parallel to glycolysis that generates NADPH and ribose 5-phosphate for nucleotide synthesis.
205
What is allosteric activation?
A process where molecules change the shape of an enzyme to increase its activity.
206
What are examples of allosteric activators for PFK-1?
ADP, AMP, and inorganic phosphate (Pi).
207
What are allosteric inhibitors?
Molecules that decrease enzyme activity, such as ATP and citrate.
208
What is the role of Phosphofructokinase-1 (PFK-1)?
It is a key regulatory enzyme in glycolysis that converts fructose 6-phosphate to fructose 1,6-bisphosphate.
209
What is the significance of ATP in glycolysis?
ATP is both a substrate and an allosteric inhibitor for PFK-1.
210
What does Phosphoglucose isomerase do?
It converts glucose 6-phosphate to fructose 6-phosphate in a reversible reaction.
211
What is the net equation for glycolysis?
1 Glucose + 2 NAD+ + 2 ADP + 2 Pi → 2 pyruvate + 2 NADH + 2 H+ + 2 ATP.
212
What is the role of Glyceraldehyde 3-phosphate (G3P)?
It is produced from glyceraldehyde and is a key intermediate in glycolysis.
213
What is 1,3-Bisphosphoglycerate (1,3 BPG)?
An intermediate in glycolysis that can donate a phosphate group to ADP to form ATP.
214
What does Enolase do in glycolysis?
It converts 2-phosphoglycerate to phosphoenolpyruvate (PEP).
215
What is the function of Pyruvate kinase?
It catalyzes the conversion of phosphoenolpyruvate to pyruvate, producing ATP.
216
Pic
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217
Where does aerobic respiration occur in eukaryotes?
Aerobic respiration occurs within the mitochondria.
218
What are the two main components of mitochondria?
Mitochondria have an outer membrane and an inner membrane.
219
What is the matrix in mitochondria?
The matrix is the inside of the mitochondria where the Kreb's cycle takes place.
220
What is the role of the electron transport chain?
The electron transport chain is organized on the inner membrane of the mitochondria.
221
What is the permeability of the outer membrane of mitochondria?
The outer membrane is permeable to small molecules such as pyruvate and NADH.
222
What happens to pyruvate when it enters the mitochondria?
Pyruvate is converted into acetyl CoA, producing CO2 and reducing NAD+ to NADH.
223
What are the four possible metabolic fates of acetyl CoA?
1. Energy production using Kreb's cycle
2. Amino acid production using Kreb's cycle intermediates
3. Fatty acid synthesis via citrate shuttle
4. Ketogenesis in the liver during low blood glucose
224
What initiates the Kreb's cycle?
Acetyl CoA combines with oxaloacetate (four carbons).
225
What are the products of each turn of the Kreb's cycle?
1 ATP, 3 NADH, and 1 FADH2 are produced.
## Footnote
Additionally, two CO2 molecules are produced as a by-product.
226
What is the net result from one glucose molecule in the Kreb's cycle?
2 ATP, 6 NADH, and 2 FADH2 are produced from two cycles.
227
What is the mnemonic for the substrates of the citric acid cycle?
"O Canada Is A Super Song For Me" helps remember:
- Oxaloacetate
- Citrate
- Isocitrate
- a-ketoglutarate
- Succinyl-CoA
- Succinate
- Fumarate
- Malate
228
What are flavoproteins?
Proteins that contain derivatives of riboflavin, produced by gut bacteria, acting as electron acceptors and donors.
229
What roles do FAD and FMN play?
FAD is involved in cellular respiration, while FMN has a role in complex I of the electron transport chain.
230
Example
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231
What is the Electron Transport Chain (ETC)?
The Electron Transport Chain (ETC) is a series of proteins (cytochromes) and a lipid carrier called Coenzyme Q (ubiquinone) embedded within the inner membrane of the mitochondria.
232
How are electron carriers arranged in the ETC?
These electron carriers are arranged in order of increasing electronegativity.
233
What happens to energy during the movement of electrons through the ETC?
Energy is transferred from the movement of electrons from reduced coenzymes NADH and FADH2 through the ETC, which is used to pump protons across the mitochondrial inner membrane into the intermembrane space.
234
What is the effect of increased proton concentration in the intermembrane space?
An increased proton concentration results in a decreased pH in the intermembrane space when the electron transport chain is active.
235
What does the redox process in the ETC establish?
The redox process establishes an electrochemical gradient of protons across the inner membrane.
236
What drives ATP synthase in the ETC?
The resulting proton-motive force drives ATP synthase, which manufactures ATP from ADP + Pi by oxidative phosphorylation.
237
What is chemiosmotic coupling?
Chemiosmotic coupling is the idea that the proton gradient created via electrons passing through the ETC provides the energy to bond phosphates for the creation of ATP.
238
What is the overall reaction of the electron transport chain?
Overall, the electron transport chain is a reduction-oxidation reaction: NADH loses electrons (oxidation) to become NAD+, and oxygen gains electrons (reduction) to form water.
239
Why is the process known as oxidative phosphorylation?
The process is known as oxidative phosphorylation because it involves the donation of electrons into the ETC (NADH, FADH2) and the addition of phosphate to ADP as protons move through ATP synthase.
240
What is the Electron Transport Chain (ETC)?
The Electron Transport Chain (ETC) is a series of proteins (cytochromes) and a lipid carrier called Coenzyme Q (ubiquinone) embedded within the inner membrane of the mitochondria.
241
How are electron carriers arranged in the ETC?
These electron carriers are arranged in order of increasing electronegativity.
242
What happens to energy during the movement of electrons through the ETC?
Energy is transferred from the movement of electrons from reduced coenzymes NADH and FADH2 through the ETC, which is used to pump protons across the mitochondrial inner membrane into the intermembrane space.
243
What is the effect of increased proton concentration in the intermembrane space?
An increased proton concentration results in a decreased pH in the intermembrane space when the electron transport chain is active.
244
What does the redox process in the ETC establish?
The redox process establishes an electrochemical gradient of protons across the inner membrane.
245
What drives ATP synthase in the ETC?
The resulting proton-motive force drives ATP synthase, which manufactures ATP from ADP + Pi by oxidative phosphorylation.
246
What is chemiosmotic coupling?
Chemiosmotic coupling is the idea that the proton gradient created via electrons passing through the ETC provides the energy to bond phosphates for the creation of ATP.
247
What is the overall reaction of the electron transport chain?
Overall, the electron transport chain is a reduction-oxidation reaction: NADH loses electrons (oxidation) to become NAD+, and oxygen gains electrons (reduction) to form water.
248
Why is the process known as oxidative phosphorylation?
The process is known as oxidative phosphorylation because it involves the donation of electrons into the ETC (NADH, FADH2) and the addition of phosphate to ADP as protons move through ATP synthase.
249
Example
<>
250
What are the net reactants and products of aerobic respiration?
Glucose + O2 → CO2 + H2O, a combustion reaction!
251
What is the role of NADH in the electron transport chain?
NADH donates electrons and moves 10 H+ into the intermembrane space.
252
How many ATP are produced from each NADH?
Each NADH through the ETC pumps 10 H+ into the intermembrane space, generating 3 ATP.
## Footnote
(10H+/3 = 3 ATP)
253
What is the transport cost for NADH produced in glycolysis?
NADH produced in glycolysis generates a net of 2 ATP due to transport costs.
254
What is the ATP yield from FADH2?
Each FADH2 pumps 6 H+ across the membrane during electron transport to generate 2 ATP.
255
What are the components of the electron transport chain?
1. NADH:ubiquinone oxidoreductase
2. Succinate dehydrogenase
3. Coenzyme Q
4. Ubiquinol-cytochrome c oxidoreductase
5. Cytochrome C
6. Cytochrome c oxidase
7. ATP synthase
256
What is the function of ATP synthase?
Synthesizes ATP from ADP and Pi while pumping H+ into the intermembrane space.
257
What is the role of cytochrome C?
Transfers electrons from complex III to complex IV.
258
What is the total H+ pumped into the intermembrane space by NADH?
NADH pumps 10 H+ into the intermembrane space.
259
What is the total H+ pumped into the intermembrane space by FADH2?
FADH2 pumps 6 H+ into the intermembrane space.
260
Ex
<>
261
What is the net ATP produced from one glucose molecule through glycolysis?
2 NADH and 2 ATP produced.
## Footnote
Followed by oxidative phosphorylation (O.P.) producing 6 ATP within the electron transport chain (E.T.C.).
262
What are the products of pyruvate oxidation?
2 Acetyl CoA and 2 NADH produced.
## Footnote
This includes the reduction of 2 NAD+ to 2 NADH.
263
What is produced during two turns of the Kreb's cycle?
2 ATP, 6 NADH, and 2 FADH2.
## Footnote
ATP produced by substrate level phosphorylation.
264
How much ATP is generated from one pyruvate molecule?
15 ATP per pyruvate.
## Footnote
This includes 12 ATP from NADH, 2 ATP from substrate level phosphorylation, and 1 ATP from FADH2.
265
What is the total potential ATP produced from one glucose molecule?
Net potential ATP produced is 30 ATP.
## Footnote
This includes contributions from glycolysis, Kreb's cycle, and oxidative phosphorylation.
266
Ex
<>
267
What is the pentose phosphate pathway (PPP)?
A pathway that branches off glycolysis, functioning to create NADPH and certain five carbon sugars (e.g., ribose).
268
Where is the pentose phosphate pathway mainly employed?
Mainly in the liver and adipocytes for lipid synthesis.
269
What can glucose-6-phosphate enter instead of glycolysis?
The pentose phosphate pathway (PPP).
270
What can ribulose 5-phosphate be converted back into?
Glycolysis intermediates, specifically fructose 6-phosphate and glyceraldehyde-3-phosphate.
271
What is generated in the oxidative branch of the PPP?
NADPH, which is essential for fatty acid synthesis.
272
What does the non-oxidative branch of the PPP create?
Five carbon sugars, such as ribose for making nucleotides for DNA and RNA.
273
What is the main difference between NADPH and NADH?
NADH is used in catabolic reactions, while NADPH is used in fat biosynthesis, the immune system, and preventing oxidative damage.
274
What is glycogenesis?
Glycogenesis is the process of synthesizing glycogen.
275
What happens when glucose intake exceeds the body's immediate energy needs?
The excess glucose can be stored as glycogen.
276
What is glycogen?
Glycogen is a multibranched polysaccharide made up of many glucose molecules.
277
Where is glycogen primarily stored?
Glycogen is primarily stored in liver and skeletal muscle cells.
278
What is the first step in glycogenesis?
The first step involves converting glucose to glucose-6-phosphate, catalyzed by hexokinase.
279
What does the addition of a phosphate group to glucose do?
It traps the glucose within the cell.
280
What is formed after the transfer of the phosphate from carbon 6 to carbon 1?
Glucose-1-phosphate is formed.
281
What energy source is used to cleave the phosphate off during glycogenesis?
The energy from UTP (uridine triphosphate) hydrolysis is used.
282
How are glucose monomers added to glycogen?
They are added onto an existing glycogen polymer via an a-1,4-glycosidic linkage.
283
What does the branching enzyme do in glycogenesis?
It cuts a 6 residue-long chain and attaches it via an a-1,6-glycosidic linkage when a glycogen polymer has 10+ glucose residues.
284
What happens when high blood glucose is present?
There is no need to break down energy stores; cells can take up glucose for catabolism.
285
What triggers glucose uptake by cells?
Insulin is released from the pancreas, facilitating glucose uptake by triggering glucose transporters (GLUTs) to move to the cell membrane.
286
What occurs when blood glucose is high?
Pancreas B-cells increase insulin secretion; muscle, adipose tissues, and liver perform glycogenesis.
287
What happens when blood glucose is low?
The body draws from storage glucose for metabolism; glucagon is released from the pancreas.
288
What is glycogenolysis?
The process where the liver breaks down glycogen into glucose 1-phosphate (G1P) using glycogen phosphorylase.
289
What does glucose 1-phosphate (G1P) convert into?
G1P is converted into glucose 6-phosphate (G6P), which can be utilized for glycolysis, gluconeogenesis, or pentose phosphate pathway.
290
What does the liver do when low blood glucose exists?
The liver increases gluconeogenesis and ketogenesis to release energy molecules into the blood.
291
What occurs when glucose is needed for catabolism?
Pancreas a-cells increase glucagon secretion; the liver performs glycogenolysis.
292
What hormones primarily regulate blood glucose?
Insulin and glucagon are the primary hormones that regulate blood glucose levels.
293
Which other hormones are involved in blood glucose regulation?
Epinephrine and cortisol also play a role in blood glucose regulation.
294
What is the role of epinephrine in glycogenolysis?
Epinephrine activates glycogen phosphorylase in liver cells, leading to glycogen breakdown.
295
How does cortisol affect blood sugar levels?
Cortisol increases glycogen storage and gluconeogenesis in the liver, but decreases glycogen storage and inhibits glucose uptake in muscle.
296
What is the relationship between cortisol and insulin?
Cortisol inhibits insulin secretion, affecting blood sugar and carbohydrate metabolism.
297
Which tissues continue to absorb glucose in the absence of insulin?
Only the nervous system (including the brain) and the liver continue to absorb glucose without insulin.
298
What is glycogenolysis?
Glycogenolysis is the process of breaking down glycogen into glucose.
299
What is gluconeogenesis?
Gluconeogenesis is the synthesis of glucose from non-carbohydrate sources.
300
What is lipolysis?
Lipolysis is the breakdown of fats into fatty acids and glycerol.
301
What is proteolysis?
Proteolysis is the breakdown of proteins into amino acids.
302
What is gluconeogenesis?
Gluconeogenesis is a metabolic process that generates glucose from non-carbohydrate carbon substrates such as lactate, glycerol, pyruvate, glycolysis intermediates, Kreb's cycle intermediates, and certain amino acids.
303
How is gluconeogenesis related to glycolysis?
Gluconeogenesis is almost identical to glycolysis in reverse, but unique enzymes are required at the ATP-consuming steps of glycolysis.
304
What enzyme replaces the first step of glycolysis in gluconeogenesis?
Step 1 is replaced with glucose-6-phosphatase, which removes a phosphate from glucose-6-phosphate to make glucose.
305
What enzyme replaces the third step of glycolysis in gluconeogenesis?
Step 3 is replaced with fructose 1,6-bisphosphatase, which removes a phosphate from fructose 1,6-bisphosphate.
306
What are the two steps that replace the tenth step of glycolysis in gluconeogenesis?
Step 10 is replaced by two steps: first, pyruvate carboxylase adds a CO2 to pyruvate to make oxaloacetate; second, PEP carboxykinase adds a phosphate and removes a CO2 to produce PEP.
307
What is the cost of producing PEP from pyruvate/lactate/oxaloacetate?
The production of PEP costs a GTP per PEP formed.
308
What is required for a molecule to be a substrate for gluconeogenesis?
The molecule must have a three-carbon backbone.
309
Why can't fatty acids or acetyl CoA be used to make new glucose molecules?
Fatty acids are catabolized in β-oxidation into acetyl CoA, which is a two-carbon group.
310
What processes are crucial for maintaining blood glucose levels?
The combination of glycogenolysis and gluconeogenesis is crucial for maintaining blood glucose levels.
311
What common intermediate do glycolysis, gluconeogenesis, glycogenolysis, and glycogenesis intersect at?
They all intersect at the common intermediate: glucose 6-phosphate.
312
What are fatty acids essential for?
Fatty acids are essential membrane components (phospholipids, sphingolipids) and storage components (triglycerides).
313
Where are fatty acids generated?
Fatty acids are generated in the cytosol using NADPH, acetyl CoA, and ATP.
314
What is the enzyme complex responsible for fatty acid synthesis?
The enzyme complex that synthesizes fatty acids is called fatty acid synthase.
315
How are fatty acids constructed?
Fatty acids are constructed through the sequential addition of two-carbon acetyl groups.
316
What is required to produce malonyl CoA?
The production of malonyl CoA requires the addition of a CO2.
317
What is the role of malonyl CoA in fatty acid synthesis?
Malonyl CoA (3C) is a temporary intermediate step that allows the addition of acetyl CoA (2C) to the growing chain.
318
What is acyl CoA?
Acyl CoA is a fatty acid that has been activated by the addition of a CoA group, allowing it to enter the mitochondria for ß-oxidation.
319
What is the primary function of fatty acids in triglycerides?
Fatty acids in triglycerides store energy in adipose tissue.
320
How do unsaturated fats compare to saturated fats in energy storage?
Unsaturated fats store less energy and take up more space than saturated fats.
321
How can fatty acids be released into the bloodstream?
Fatty acids can be released through dietary uptake or lipolysis.
322
What happens to fatty acids after they diffuse into organs?
They are turned into acetyl-CoA via ß-oxidation.
323
What can acetyl-CoA be converted into?
Acetyl-CoA can be converted into a ketone body, catabolized for energy in the Kreb's cycle, or utilized for fatty acid synthesis.
324
How do fatty acids travel in the blood?
Fatty acids travel in blood via albumin and lipoproteins.
325
What is the process of ß-oxidation?
ß-oxidation is the process where acyl-CoA is oxidized two carbons at a time in the mitochondria.
326
What is the ATP cost for converting fatty acids to acyl-CoA?
The conversion costs 1 ATP.
327
What are the two steps of ß-oxidation?
1. Fatty acids → acyl-CoA (costs 1 ATP) along the outer membrane of the mitochondrion. 2. Acyl-CoA is cleaved two carbons at a time into acetyl-CoA in the mitochondrial matrix.
328
What happens to odd-numbered fatty acid chains during ß-oxidation?
The last three carbons are used as a substrate for gluconeogenesis.
329
What happens to fatty acids during starvation?
The liver breaks down fatty acids into acetyl CoA.
330
What occurs to acetyl CoA in the absence of insulin?
Some acetyl CoA gets converted into ketones in the mitochondria of liver cells.
331
What are ketones also known as?
Ketone bodies.
332
What is the primary function of ketone bodies?
They provide an alternative source of energy for tissues other than red blood cells (RBCs).
333
Can ketone bodies be used for gluconeogenesis?
No, ketone bodies cannot be used as substrates for gluconeogenesis.
334
What are the three primary ketone bodies produced in humans?
Acetone, acetoacetic acid, and B-hydroxybutyrate.
335
What structural feature do all ketones have?
A carbonyl group, which is very polar and allows them to dissolve in blood.
336
What is the smell associated with acetone?
Acetone smells fruity, which is why nail polish remover smells that way.
337
What is a sign that a person is in ketosis?
Their breath will have a sweet smell due to ketones.
338
When does ketogenesis occur?
Ketogenesis occurs in the mitochondria and is associated with low insulin levels.
339
What was the keto diet originally called?
The Atkins diet.
340
What is the principle behind the keto diet?
It advocates for low carbohydrate consumption to 'trick' the body into believing it is starving.
341
What is a potential downside of the keto diet?
It can result in nutrient deficiencies due to the removal of most plant-based foods.
342
What happens to weight after resuming carbohydrate consumption post-keto diet?
Many people will regain the weight once they begin consuming carbohydrates again.
343
What is protein metabolism?
Protein metabolism involves the synthesis (anabolism) and breakdown (catabolism) of proteins in cells.
344
When does protein formation (anabolism) occur?
Protein formation occurs mainly during the fed state and is associated with glycolysis, glycogenesis, and lipid storage.
345
When does protein breakdown (catabolism) occur?
Protein breakdown occurs mainly during the fasting state and is associated with gluconeogenesis, glycogenolysis, B-oxidation, and ketogenesis.
346
How does protein breakdown begin?
Protein breakdown begins with the hydrolysis of amino acid peptide bonds by enzymes in the gastrointestinal tract.
347
What enzymes are involved in protein breakdown?
Enzymes involved include brush-border enzymes (amino-peptidase) and pancreatic enzymes (trypsin, chymotrypsin, and carboxypeptidase).
348
What happens during amino acid breakdown?
Amino acid breakdown begins with the removal of the nitrogen group, producing ammonia and a carbon chain.
349
What happens to ammonia produced during amino acid breakdown?
The ammonia is fed into the liver urea cycle.
350
What other roles do amino acids have in the body?
Amino acids can be used as building blocks for neurotransmitters, hormones, or heme groups.
351
Can amino acids be used in metabolic pathways?
Yes, some amino acids can be used as substrates for Kreb's cycle, gluconeogenesis, ketogenesis, or synthesizing other amino acids.
352
How many amino acids are essential?
9 of the 20 amino acids are essential and must be obtained from the diet.
353
What does BMI stand for?
Body Mass Index
354
How is BMI calculated?
BMI = weight (kg) / height² (m²)
355
What is the BMI range for underweight individuals?
Underweight = <18.5
356
What is the BMI range for healthy individuals?
Healthy = 18.5-25
357
What is the BMI range for overweight individuals?
Overweight = 25-30
358
What is the BMI classification for obese individuals?
Obese = >30
359
What percentage of adults in North America are considered obese?
35%
360
What health risks are associated with obesity?
Increased risks of heart disease, stroke, diabetes, and many cancers.
361
What factors influence the risk of developing obesity?
Genetics, environment, caloric intake, and hormones.
362
What are inborn errors of metabolism?
A class of genetic disorders characterized by mutations that impair the processing of biomolecules.
363
What types of metabolism can be affected by inborn errors?
Disorders of carbohydrates, amino acids, organic acids, and lysosomal storage diseases.
364
How are many inborn errors of metabolism detected?
They are screened for as part of Newborn Screening.
365
What is the rate-limiting enzyme for Glycolysis?
Phosphofructokinase-1
366
What is the rate-limiting enzyme for Fermentation?
Lactate dehydrogenase
367
What is the rate-limiting enzyme for Glycogenesis?
Glycogen synthase
368
What is the rate-limiting enzyme for Glycogenolysis?
Glycogen phosphorylase
369
What is the rate-limiting enzyme for Gluconeogenesis?
Fructose-1,6-bisphosphate
370
What is the rate-limiting enzyme for the Pentose Phosphate Pathway?
Glucose-6-phosphate dehydrogenase
371
What compound is important for the bouquet of wine?
Acetoin
372
What are the two compounds closely related to acetoin?
2,3-butanediol and diacetyl
373
What is the threshold value for diacetyl in wine?
8 mg/litre
374
How is acetoin formed during fermentation?
By the microbial activity of lactic acid bacteria and yeasts
375
Why is the study of acetoin in wine important?
It investigates the influence of microorganisms on the composition and quality of wine
376
What is the mitotic spindle made from?
The mitotic spindle is made from polar microtubules produced by the centrosome.
377
What connects to kinetochore microtubules during mitosis?
The mitotic spindle connects to kinetochore microtubules at the centromere of each chromosome.
378
What is the centrosome commonly referred to as?
The centrosome is commonly referred to as the microtubule organizing center (MTOC).
379
What initiates microtubule polymerization?
Microtubule polymerization starts at the MTOC, where 13 gamma tubulin molecules are first added in a circular shape.
380
What are the components added to microtubules during growth?
Growth of the microtubule occurs with the addition of alternating alpha/beta tubulin dimers each bound to GTP.
381
What is the role of beta-tubulin in microtubule stability?
Only beta-tubulin can hydrolyze GTP and change microtubule stability.
382
What are protofilaments?
Protofilaments are the building blocks of microtubules, consisting of 13 subunits.
383
What is the structure of cilia and flagella?
Cilia and flagella are composed of microtubule doublets and triplets.
384
What are basal bodies?
Basal bodies are structures that anchor cilia and flagella.
385
Sensation
Sensation is the process by which we receive information from the outside world.
386
Psychophysics
Psychophysics is the study of physical stimuli and the sensations and perceptions that result.
387
Viruses
Viruses are tiny infectious agents that consist of genetic material (DNA or RNA) surrounded by a protein coat (or capsid).
388
Virus envelope
The protein coat of a virus may also be surrounded by a lipid-rich envelope derived from the host cell membrane. This envelope typically contains some virus-specific proteins and helps the virus re-infect a new host cell. An example is HIV, which is surrounded by an envelope made up of a lipid bilayer. The envelope is embedded with 'spike' proteins that help the virus enter host cells.
389
Characteristics of viruses
Viruses lack organelles and a nucleus, are substantially smaller than bacteria and eukaryotic cells, and are not classified as living organisms.
390
Size comparison of viruses
In terms of size, viruses are on average about 150x smaller than bacteria, and roughly 300x smaller than eukaryotic cells.
391
Subviral Particles
Subviral particles are infectious agents related to viruses that include viroids and prions.
392
Viroids
Viroids are small rings of naked RNA with no capsids, and they only infect plants.
393
Prions
Prions are naked proteins capable of self-replication without DNA or RNA that only infect animals.
394
Virus-like particles
There are virus-like particles that are smaller and simpler than viruses.
395
Viroids structure
Viroids are naked, single-stranded pieces of circular RNA that infect plants. They do not have a capsid and so do not fit the definition of a virus.
396
Viroids replication
During infection, viroids replicate in the nucleus or chloroplast then travel through the plasmodesmata and phloem.
397
Prions structure
Prions are naked, misfolded Prp proteins capable of self-replicating without DNA or RNA.
398
Prions infection
Prions only infect animals and will induce other proteins to misfold.
399
Prions effects
The misfolded proteins will aggregate in the brain, damaging it and causing symptoms of dementia and difficulty with movement.
400
Brain tissue in prion infection
The brain tissue will look spongy with many little holes.
401
Bacteriophages
The bacteriophage (or phage) is a virus that infects bacteria.
402
Bacteriophage structure
A bacteriophage consists of an outer protein capsid enclosing genetic material (called the head), a tail, and fibers used to attach the virus to the surface of a bacterium.
403
Bacteriophage example
This is just one example of a virus; viral structures can vary wildly.
404
Generalized Viral Life Cycles
Viruses are self-replicating biological units yet must reproduce within a specific host cell. The generalized phage and animal virus life cycle is as follows: Attachment to the host cell, penetration of the cell membrane or cell wall, and entry of viral material.
405
Bacteriophages
Bacteriophages infect bacterial cells by injecting genetic material through the plasma membrane. This occurs in a hypodermic syringe-like motion.
406
Bacteria replicate, transcribe and translate the viral DNA
New virions are assembled within the host and the phages are released by cell lysis, extrusion or budding.
407
Key Concept
Most viruses that infect animals do not leave capsids outside the cell, but rather enter the cell through receptor-mediated endocytosis.
408
Generalized Viral Life Cycles
Viruses are self-replicating biological units yet must reproduce within a specific host cell. The generalized phage and animal virus life cycle is as follows: Attachment to the host cell, penetration of the cell membrane or cell wall, and entry of viral material.
409
Bacteriophages
Bacteriophages infect bacterial cells by injecting genetic material through the plasma membrane. This occurs in a hypodermic syringe-like motion.
410
Bacteria replicate, transcribe and translate the viral DNA
New virions are assembled within the host and the phages are released by cell lysis, extrusion or budding.
411
Key Concept
Most viruses that infect animals do not leave capsids outside the cell, but rather enter the cell through receptor-mediated endocytosis.
412
Animal viruses
Animal viruses have a nucleic acid genome packaged within a protein shell called a capsid. Their genome can be either a single-stranded or double-stranded RNA or DNA. They may also have a lipid envelope, derived from the host cell plasma membrane.
413
Spike proteins
The virus has proteins it expresses on its surface that allow it to bind to receptors on the host cell membrane. These proteins, called the spike proteins, are inserted into the envelope. Once the spike proteins bind to the receptor, the virus is either (1) endocytosed into the host cell, or (2) inserts its genome into the host cell by fusing the envelope with the host cell membrane.
414
Animal viruses infection process
Similar to other viruses, animal viruses must infect the host cell then direct the host cell's metabolic machinery to synthesize new virus enzymes and particles. Once the new virus particles are formed, they either: (1) bud off from the host cell using the host cell membrane to make the envelope, or (2) build up in the infected cell until the cell bursts. (lysis)
415
Phagocytosis
Cell plasma membrane engulfs virus.
416
Viral genomes
Viral genomes are very diverse. The nucleic acid can be either DNA or RNA, and either single-stranded or double-stranded.
417
RNA viruses
RNA viruses are able to replicate in the cytosol. Most RNA viruses will carry a gene for RNA-dependent RNA polymerase, which is used to replicate the viral RNA genome. Double-stranded RNA viruses will use this polymerase to replicate positive-sense RNA.
418
positive sense single-stranded RNA
If the genome is a positive sense single-stranded RNA, it can act as an mRNA intermediate and be translated into protein.
419
negative-sense RNA
If it is a negative-sense RNA, the strand must first be transcribed into a positive-sense RNA before it can be translated.
420
DNA viruses
Similar to the host genome, most DNA viruses will replicate in the nucleus. A single-stranded DNA virus will hijack the host enzymes to make a complementary DNA strand and form double-stranded DNA.
421
Hepatitis C virus (HCV)
Hepatitis C virus (HCV) is a + strand RNA genome in an enveloped animal virus that after binding to receptors on the cell membrane is brought into the cell through receptor-mediated endocytosis.
422
HCV RNA
When the + strand RNA is released into the cell, it can immediately begin translation into protein for new viral assembly.
423
Mode of + Sense RNA (SSRNA) Enveloped Virus Infection in Animal Systems
With +strand RNA viruses, the genetic information is released into the animal cell and immediately can be utilized to code for proteins.
424
Retrovirus Life Cycle
Retroviruses contain RNA and the enzyme reverse transcriptase. They enter a host cell by fusion and use reverse transcriptase to form DNA from their RNA template. The DNA is then integrated into the host's genome, which transcribes, translates, and assembles new retroviruses. the nay retroviruses exit the host by budding, mature, and then reinfect new dEDNA geneme.
425
MCAT Tip
In the lab, Reverse Transcriptase is used to reverse transcribe mRNA into complementary DNA, called CDNA.
426
HIV
HIV is caused by a unique retrovirus that targets CD4* T cells in humans.
427
Lytic Cycle
In the lytic cycle, the virus' genetic material directs the cell's metabolism to produce viral components, including viral proteins and genetic material. Virus particles are synthesized and released when the cell lyses, allowing them to infect other host cells.
428
Lysogenic Cycle
In the lysogenic cycle, viral DNA inserts itself into the host cell chromosome, allowing it to be replicated along with the host cell's DNA. The virus is said to be dormant and is called a provirus (prophage if it is a bacteriophage). The provirus will separate from the host chromosome upon exposure to stress, such as UV or carcinogens, and re-enter the lytic cycle.
429
Key MCAT Message
Temperate viruses follow either a lysogenic cycle (no symptoms) or lytic cycle. Virulent viruses have lytic life cycles (symptoms).
430
Lytic and lysogenic cycles
431
Classification of Organisms
All organisms (including bacteria) can be classified by how they acquire carbon and energy. The first prefix (chemo/photo) refers to the organism's energy source and the second prefix refers to the organism's carbon source (auto/hetero).
432
Chemoautotroph
Energy from oxidization of inorganic matter? Yes
433
Chemoheterotroph
Energy from oxidization of inorganic or organic matter? No
434
MCAT Tip
Autotrophs are producers capable of fixing CO2. Heterotrophs rely on autotrophs to synthesize organic compounds.
435
Prokaryotes
Prokaryotes are split into Bacteria and Archaea domains.
436
Archaea
Archaea are singled celled microorganisms with no cell nucleus, no organelles and are placed in a phylogenetic clade distinct from prokaryotes and eukaryotes. They generally have extreme habitats, such as super hot, freezing, alkaline, acidic, salty, or high exposure to radiation. These organisms reproduce asexually and are more closely related to eukaryotes than bacteria.
437
Bacteria
Bacteria are a large group of single-celled microorganisms, typically a few micrometers in length. They have a wide range of shapes and habitats and can be classified by shape.
438
Spirilli
spiral
439
Bacilli
rod
440
Cocci
spherical
441
Streptococcus
round / Spherical
442
Classification of Organisms
All organisms (including bacteria) can be classified by how they acquire carbon and energy. The first prefix (chemo/photo) refers to the organism's energy source and the second prefix refers to the organism's carbon source (auto/hetero).
443
Chemoautotroph
Energy from oxidization of inorganic matter? Yes
444
Chemoheterotroph
Energy from oxidization of inorganic or organic matter? No
445
MCAT Tip
Autotrophs are producers capable of fixing CO2. Heterotrophs rely on autotrophs to synthesize organic compounds.
446
Prokaryotes
Prokaryotes are split into Bacteria and Archaea domains.
447
Archaea
Archaea are singled celled microorganisms with no cell nucleus, no organelles and are placed in a phylogenetic clade distinct from prokaryotes and eukaryotes. They generally have extreme habitats, such as super hot, freezing, alkaline, acidic, salty, or high exposure to radiation. These organisms reproduce asexually and are more closely related to eukaryotes than bacteria.
448
Bacteria
Bacteria are a large group of single-celled microorganisms, typically a few micrometers in length. They have a wide range of shapes and habitats and can be classified by shape.
449
Spirilli
spiral
450
Bacilli
rod
451
Cocci
spherical
452
Streptococcus
round / Spherical
453
Key Features of Bacteria
A lipid membrane, or cell membrane, which encloses the contents of the cell and acts as a barrier to hold nutrients, proteins, and other components of the cytoplasm. A cell wall is also present sometimes.
454
No membrane-bound organelles
(e.g., nucleus, mitochondria, Golgi apparatus, or endoplasmic reticulum).
455
Bacteria may be either anaerobic or aerobic
(e-transport chain in cell membrane).
456
A single, circular chromosome of double-stranded DNA
With no membrane-bound nucleus, this genetic material is localized in an irregularly shaped nucleoid region.
457
Bacteria possess plasmids
which are small extra-chromosomal DNA molecules that may contain genes for antibiotic resistance (R factors) or virulence factors.
458
Bacterial DNA
10-100 per cell.
459
Plasmids
~5 million bp, replicate independently, ~5000 genes of genome (~5000 proteins).
460
Few genes (2-3 genes)
must help bacteria survive.
461
Bacteria possess ribosomes for translation
which are smaller than eukaryotic ribosomes.
462
Bacteria grow to a fixed size and then reproduce
through binary fission, a form of asexual reproduction.
463
Bacteria move using their flagella
which are made from long, hollow, rigid, helical cylinders of the globular protein flagellin.
464
Flagellar propulsion
allows bacteria to move toward signals from substances, which is known as chemotaxis.
465
Flagella
convergent evolution; 2 unrelated organisms that develop a similar structure in similar environments (selected for) not by common ancestor.
466
Example of convergent evolution
birds fly, insects... they are not closely related.
467
Eukaryotes also have flagella
made of different proteins (microtubules).
468
Flagella movement
Whips back and forth.
469
features of Bacteria
A cell membrane, or cell membrane, which encloses the contents of the cell and acts as a barrier to hold nutrients, proteins, and other components of the cytoplasm. A cell wall is present sometimes.
470
membrane-bound organelles
(e.g., nucleus, mitochondria, Golgi apparatus, or endoplasmic reticulum).
471
glycolysis + Fermentation
Bacteria may be either anaerobic or aerobic (e-transport chain in cell membrane).
472
Bacterial DNA
A single, circular chromosome of double-stranded DNA in the membrane. In the nucleus, this genetic material is localized in an irregularly shaped nucleoid region.
473
Plasmids
Bacteria possess plasmids, which are small extra-chromosomal DNA molecules that may (not always) contain genes for antibiotic resistance (R factors) or virulence factors.
474
Bacteria possess ribosomes
for translation, which are smaller than eukaryotic ribosomes.
475
Bacteria grow
to a fixed size and then reproduce through binary fission, a form of asexual reproduction.
476
Bacteria move
using their flagella, which are made from long, hollow, rigid, helical cylinders of the globular protein flagellin. Flagellar propulsion allows bacteria to move toward signals from substances, which is known as chemotaxis.
477
protoplast
The bacterial plasma membrane and everything inside it is called the protoplast.
478
bacterial envelope
Surrounding the protoplast is the bacterial envelope.
479
bacterial envelope
The bacterial envelope can be thought of as both the plasma membrane and the cell wall of a bacterium.
480
outer capsule
Sometimes, bacteria possess an outer capsule which, if present, is part of the bacterial envelope.
481
cell wall
The cell wall, which may or may not have an adjacent capsule, prevents the protoplast from bursting.
482
cytosol
The cytosol of a bacterium is hypertonic to its surroundings, so water flows into the cell until hydrostatic pressure equals osmotic pressure.
483
hypertonic
higher than
484
isotonic
equal
485
hypotonic
lower than
486
hypertonic cell
high solute inside compared to environment.
487
hypotonic environment
low solute in environment.
488
Classification of bacteria
Classification of bacteria is often based on gram staining.
489
In gram-positive bacteria
In gram-positive bacteria, a thick peptidoglycan cell wall prevents the Gram stain from leaking out resulting in a purple appearance.
490
In gram-negative bacteria
In gram-negative bacteria, a thin peptidoglycan cell wall allows most of the Gram stain to be washed out resulting in a pink appearance.
491
Outer membrane leaflet
Gram-negative bacteria also have an outer membrane leaflet that contains lipopolysaccharide (LPS), which can trigger an immune response.
492
Peptidoglycan cell wall
The peptidoglycan cell wall is a series of disaccharide polymer chains crossed-linked with amino acids.
493
Function of peptidoglycan cell wall
It allows for elastic movement of the bacteria, transfer of large molecules, and is a frequent target for antibiotics.
494
Key Concept
In gram-positive bacteria, there is a lot of peptidoglycan on the outside of the cell vs in gram-negative bacteria, there is less peptidoglycan and it's located between two membranes.
495
Symbiosis or Mutualism
is where the relationship is mutually beneficial for both (e.g., natural enteric flora/bacteria in gut help us digest food while they get some nutrients).
496
Parasitic
is where the relationship is beneficial only to the bacteria, and often entails the bacteria growing and reproducing at the expense of the other organism (e.g., Yersinia living in human gut → Gl upset).
497
Commensalism
is where the relationship is beneficial to one species but does not impact the other species (e.g., the human skin has many bacteria that live on it, which derive benefit but do not impact humans).
498
Amensalism
is where the relationship is harmful to one species and the other species is unaffected (e.g., when one species is killed by another species chemical secretion, and the species secreting is unharmed. For example, penicillin from fungi that is an antibiotic to bacteria).
PREP101 MCAT
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