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Midterm Review
Components of the Cytoskeleton
• Three main types of fibers make up the
cytoskeleton:
– Microtubules are the thickest of the three
components of the cytoskeleton
– Microfilaments, also called actin filaments, are the
thinnest components
– Intermediate filaments are fibers with diameters in a
middle range
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
3 Types of Cytoskeleton Fibers:
Microtubules
•
•
•
•
Protein = tubulin
Largest fibers
Shape/support cell
Track for organelle
movement
• Forms spindle for
mitosis/meiosis
• Component of
cilia/flagella
• Plant & animal
cells
Microfilaments
• Protein = actin
• Smallest fibers
• Support cell on
smaller scale
• Cell movement
• Eg. ameboid
movement,
cytoplasmic
streaming, muscle
cell contraction
• Plant & animal
cells
Intermediate
Filaments
• Intermediate size
• Permanent fixtures
• Maintain shape of
cell
• Fix position of
organelles
• Only in some
animal cells
Water Potential
• What is the water potential equation?
Water Potential
• What is the water potential equation?
Water potential equation:
ψ = ψS + ψP
• Water potential (ψ) = free energy of water
• Solute potential (ψS) = solute concentration (osmotic
potential)
• Pressure potential (ψP) = physical pressure on solution
Water Potential
• How do you calculate Solute Potential?
Water Potential
• How do you calculate Solute Potential?
ψS = -iCRT
•
•
•
•
i = ionization constant (# particles made in water)
C = molar concentration
R = pressure constant (0.0831 liter bars/mole-K)
T = temperature in K (273 + °C)
• The addition of solute to water lowers the solute
potential (more negative) and therefore
decreases the water potential.
Water Potential
Water Potential
Water Potential
What is the water potential of a cell with a solute potential of -0.67 kPa and a pressure
potential of 0.43 kPa?
Macromolecules
• List the 4 macromolecules, their monomers,
polymers, and types of bonds.
Macromolecules
• List the 4 macromolecules, their monomers,
polymers, and types of bonds.
– Carbs: monosaccharides, polysaccharides,
glycosidic linkage
– Lipids: fatty acids and glycerol, triglycerides, ester
linkage
– Proteins: amino acids, polypeptides, peptide
bonds
– Nucleic Acids: nucleotides, nucleic acids,
phosphodiester bonds
Macromolecules
• Describe the basic structure of an amino acid.
Amino Acid
• R group = side chains
• Properties:
• hydrophobic
• hydrophilic
• ionic (acids & bases)
• “amino” : -NH2
• “acid” : -COOH
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Macromolecules
• What are the 4 levels of protein structure and
describe them.
Four Levels of Protein Structure
1. Primary
– Amino acid (AA) sequence
– 20 different AA’s
– peptide bonds link AA’s
Four Levels of Protein Structure (continued)
2.Secondary
– Gains 3-D shape (folds, coils) by H-bonding
– Alpha (α) helix, Beta (β) pleated sheet
Four Levels of Protein Structure (continued)
3.Tertiary
– Bonding between side chains (R groups) of amino acids
– H bonds, ionic bonds, disulfide bridges, van der Waals
interactions
Four Levels of Protein Structure (continued)
4.Quaternary
– 2+ polypeptides bond together
– R groups of polypeptide chains held together with H bonds, ionic
bonds, disulfide bridges, van der Waals interactions
Natural Killer (NK) cells perforate cells
• All cells in the body (except red blood cells) have a
class 1 MHC protein on their surface
• Cancerous or infected cells no longer express this
protein; NK attack these damaged cells
– release perforin protein into membrane of target cell
– forms pore allowing fluid to
natural killer cell
flow in & out of cell
– cell ruptures (lysis)
cell
– granzymes also released
to induce
membrane
perforin
apoptosis
cell
membrane
virus-infected cell
Helper T Cells: A Response to Nearly All Antigens
• CD4 binds the class II MHC molecule
– keeps the helper T cell joined to the antigenpresenting cell while activation occurs
• Activated helper T cells secrete cytokines that stimulate
other lymphocytes
Antigenpresenting
cell
Peptide antigen
Bacterium
Class II MHC molecule
CD4
TCR (T cell receptor)
Helper T cell
Humoral
immunity
(secretion of
antibodies by
plasma cells)
Cytokines
+
B cell
+
+
+
Cytotoxic T cell
Cell-mediated
immunity
(attack on
infected cells)
Fig. 43-18-3
Released cytotoxic T cell
Cytotoxic T cell
Perforin
Granzymes
CD8
TCR
Class I MHC
molecule
Target
cell
Dying target cell
Pore
Peptide
antigen
Fig. 43-19
Humoral Immunity
Antigen-presenting cell
Bacterium
Peptide
antigen
B cell
Class II MHC
molecule
TCR
Clone of plasma cells
+
CD4
Cytokines
Secreted
antibody
molecules
Endoplasmic
reticulum of
plasma cell
Helper T cell
Activated
helper T cell
Clone of memory
B cells
2 µm
The Role of Antibodies in Immunity
• Neutralization - pathogen can’t infect host because it’s bound to
antibody
• Opsonization - antibodies bound to antigens increase phagocytosis
• Antibodies together with proteins of the complement system
generate a membrane attack complex and cell lysis
Viral neutralization
Opsonization
Activation of complement system and pore formation
Bacterium
Complement proteins
Virus
Formation of
membrane
attack complex
Flow of water
and ions
Macrophage
Pore
Foreign cell
Evolution
• Allopatric and Sympatric Speciation
Two main modes of speciation:
Allopatric Speciation
Sympatric Speciation
“other” “homeland”
“together” “homeland”
Geographically isolated
populations
Overlapping populations within
home range
• Caused by geologic events
or processes
• Evolves by natural selection
& genetic drift
Gene flow between
subpopulations blocked by:
• polyploidy
• sexual selection
• habitat differentiation
Eg. Squirrels on N/S rims of
Grand Canyon
Eg. polyploidy in crops (oats,
cotton, potatoes, wheat)
Fig. 24-14-4
• Incomplete reproductive barriers
• Possible outcomes: reinforcement, fusion, stability
Isolated population
diverges
Possible
outcomes:
Hybrid
zone
Reinforcement
OR
Fusion
Gene flow
Hybrid
Population
(five individuals
are shown)
OR
Barrier to
gene flow
Stability
Evolution – Hybrid Zones
Evolution
• Draw a phylogenetic tree to correspond to the
following data.
Species
1
2
3
4
5
1
-
2
1
-
3
8
8
-
4
19
20
19
-
5
7
9
2
18
-
Evolution
Species
1
2
3
4
5
1
-
2
1
-
3
8
8
-
4
19
20
19
-
• Species 1 & 2 – only 1 difference
• Species 3 & 5 – only 2 differences
• Species 4 compared to 1, 2, 3, & 5 – most
differences  outgroup
5
7
9
2
18
-
Evolution
Species
1
2
3
4
5
1
-
2
1
-
3
8
8
-
4
19
20
19
-
5
7
9
2
18
-
Membrane Transport
• What is the difference between hypertonic,
hypotonic, and isotonic?
Membrane Transport
• What is the difference between hypertonic,
hypotonic, and isotonic?
– Isotonic solution: Solute concentration is the
same as that inside the cell; no net water
movement across the plasma membrane
– Hypertonic solution: Solute concentration is
greater than that inside the cell; cell loses water
– Hypotonic solution: Solute concentration is less
than that inside the cell; cell gains water
Fig. 7-13
Hypotonic solution
H2O
Isotonic solution
H2O
H2O
Hypertonic solution
H2O
(a) Animal
cell
Lysed
Normal
Shriveled
Hypotonic solution
H2O
Isotonic solution
H2O
H2O
Hypertonic solution
H2O
(b) Plant
cell
Turgid (normal)
Flaccid
Plasmolyzed
Fig. 7-UN3
“Cell”
0.03 M sucrose
0.02 M glucose
Environment:
0.01 M sucrose
0.01 M glucose
0.01 M fructose
Fig. 7-UN4
Membrane Transport
• Side A in a U-tube has 5M sucrose and 3M
glucose. Side B has 2M sucrose and 1M
glucose. The membrane is permeable to
glucose and water only. What happens to
each side?
Membrane Transport
• Side A in a U-tube has 3M sucrose and 1M
glucose. Side B has 1M sucrose and 3M
glucose. The membrane is permeable to
glucose and water only. What happens to
each side?
Photosynthesis
• What are the 2 main steps of Photosynthesis?
– Light Reactions
– Calvin Cycle
Fig. 10-5-4
CO2
H2O
Light
NADP+
ADP
+ P
i
Light
Reactions
Calvin
Cycle
ATP
NADPH
Chloroplast
O2
[CH2O]
(sugar)
Fig. 10-13-5
4
Primary
acceptor
2
H+
+
1/ O
2
2
H2O
e–
2
Primary
acceptor
e–
Pq
Cytochrome
complex
e–
e–
3
8
P700
5
Light
ATP synthase
6
ATP
Pigment
molecules
PS I
NADP+
+ H+
NADPH
Pc
e–
P680
PS II
Fd
NADP+
reductase
e–
1 Light
7
Fig. 10-17
STROMA
(low H+ concentration)
Cytochrome
Photosystem I
complex
Light
Photosystem II
Light
Fd
NADP+
reductase
3
NADP+ + H+
4 H+
NADPH
Pq
–
H2O
THYLAKOID SPACE
(high H+ concentration)
e– e
1
1/
Pc
2
2
O2
+2 H+
4 H+
To
Calvin
Cycle
Thylakoid
membrane
STROMA
(low H+ concentration)
ATP
synthase
ADP
+
P
i
ATP
H+
Fig. 10-18-3
Input 3
(Entering one
at a time)
CO2
Phase 1: Carbon fixation
Rubisco
3 P
Short-lived
intermediate
P
6
P
3-Phosphoglycerate
3P
P
Ribulose bisphosphate
(RuBP)
6
ATP
6 ADP
3 ADP
3
Calvin
Cycle
6 P
P
1,3-Bisphosphoglycerate
ATP
6 NADPH
Phase 3:
Regeneration of
the CO2 acceptor
(RuBP)
6 NADP+
6 Pi
P
5
G3P
6
P
Glyceraldehyde-3-phosphate
(G3P)
1
Output
P
G3P
(a sugar)
Glucose and
other organic
compounds
Phase 2:
Reduction
Cotransport: membrane protein enables “downhill”
diffusion of one solute to drive “uphill” transport of other
Eg. sucrose-H+ cotransporter (sugar-loading in plants)
Point Mutations
• A point mutation is a change in one base in a gene
• Effects can vary:
– Mutations in noncoding regions  often harmless
– Mutations in gene might not affect protein production
b/c of redundancy in genetic code
– Mutations that result in change in protein production
are often harmful, but can sometimes increase the fit
between organism and environment
Evolution
• Orthologous and Paralogous genes
Fig. 26-18
Ancestral gene
Ancestral species
Speciation with
divergence of gene
Species A
Orthologous genes
Species B
(a) Orthologous genes
Species A
Gene duplication and divergence
Paralogous genes
Species A after many generations
(b) Paralogous genes
Thermodynamics
• What is the Gibb’s Free Energy equation?
Thermodynamics
• What is the Gibb’s Free Energy equation?
– ∆G = ∆H – T∆S
– ∆G = change in free energy
– ∆H = change in total energy
– ∆S = change in entropy
– T = temperature in Kelvin
Thermodynamics
• What is the Gibb’s Free Energy equation?
– ∆G = ∆H – T∆S
– In a reaction that occurs at 25°C, the enthalpy is
52.78 kJ and the entropy is 0.21 kJ/K. Calculate
the ∆G.
Thermodynamics
• What is the Gibb’s Free Energy equation?
– ∆G = ∆H – T∆S
– In a reaction that occurs at 25°C, the enthalpy is
52.78 kJ and the entropy is 0.21 kJ/K. Calculate
the ∆G.
– ∆G = (52.78) – (25 + 273)(0.21)
– ∆G = (52.78) – (298)(0.21)
– ∆G = (52.78) – (62.58)
– ∆G = -9.8 kJ
Evolution
• What is the difference between the Founder
Effect and the Bottleneck Effect?
Evolution
Evolution
• What are the 4 observations and 2 inferences
that Darwin developed?
Evolution
• What are the 4 observations and 2 inferences
that Darwin developed?
– Members of a population vary greatly in their traits
– Traits are inherited from parents to offspring
– All species are capable of producing more offspring
than the environment can support
– Many offspring doe not survive
– Individuals whose inherited traits give them a higher
probability of surviving and reproducing in a given
environment tend to leave more offspring than other
individuals
– This unequal ability of individuals to survive and
reproduce will lead to the accumulation of favorable
traits in the population over generations
Fig. 26-11
Evolution
Tuna
Leopard
TAXA
Vertebral column
(backbone)
0
1
1
1
1
1
Hinged jaws
0
0
1
1
1
1
Four walking legs
0
0
0
1
1
1
Amniotic (shelled) egg
0
0
0
0
1
1
Hair
0
0
0
0
0
1
(a) Character table
From this data, create
a phylogenetic tree
Fig. 26-11
Evolution
Lancelet
(outgroup)
Lamprey
Tuna
Vertebral
column
Salamander
Hinged jaws
Turtle
Four walking legs
Amniotic egg
Leopard
Hair
(b) Phylogenetic tree
Evolution
• What are the 2 Hardy-Weinberg equations?
And what does each symbol represent?
Evolution
• What are the 2 Hardy-Weinberg equations? And
what does each symbol represent?
–
–
–
–
–
p2 + 2pq + q2 = 1
p+q=1
p = frequency of the dominant allele
q = frequency of the recessive allele
p2 = frequency of the homozygous dominant
genotype
– q2 = frequency of the homozygous recessive genotype
– 2pq = frequency of the heterozygous genotype
Evolution
• What are the five conditions necessary for a
population to be in Hardy-Weinberg
equilibrium?
Evolution
• What are the five conditions necessary for a
population to be in Hardy-Weinberg
equilibrium?
– No mutations
– Random mating
– No natural selection
– Extremely large population size
– No gene flow
Evolution
• What are the differences between directional
selection, disruptive selection, and stabilizing
selection?
Fig. 23-13
Original population
Original
Evolved
population population
(a) Directional selection
Phenotypes (fur color)
(b) Disruptive selection
(c) Stabilizing
selection
Evolution
• What are the steps to producing the first cells
on earth?
Evolution
• What are the steps to producing the first cells
on earth?
– Abiotic synthesis of small organic molecules
– Joining of those small molecules into
macromolecules
– Packaging molecules into “protobionts”
– Formation of self-replication molecules
Cells
• What are the functions of the following cell
parts?
– Nucleus
– Ribosomes
– Smooth ER
– Rough ER
– Golgi
Cells
• What are the functions of the following cell
parts?
– Nucleus: contains cell DNA
– Ribosomes: make proteins
– Smooth ER: makes lipids, stores calcium,
detoxification, breaks down carbs
– Rough ER: secretes glycoproteins, distributes
vesicles
– Golgi: makes macromolecules, modifies proteins,
packages proteins
Cells
• Which organelles are part of the
endomembrane system and how do they work
together?
Cells
• Which organelles are part of the
endomembrane system and how do they work
together?
– Nuclear envelope
– Endoplasmic reticulum
– Golgi apparatus
– Lysosomes
– Vacuoles
– Plasma membrane
Fig. 6-16-3
Nucleus
Rough ER
Smooth ER
cis Golgi
trans Golgi
Plasma
membrane
Membrane Transport
• Label the parts of the plasma membrane
Fig. 7-7
Fibers of
extracellular
matrix (ECM)
Glycoprotein
Carbohydrate
Glycolipid
EXTRACELLULAR
SIDE OF
MEMBRANE
Cholesterol
Microfilaments
of cytoskeleton
Peripheral
proteins
Integral
protein
CYTOPLASMIC SIDE
OF MEMBRANE
Cell Respiration
• What are the 3-4 main steps of Cellular
Respiration?
Cell Respiration
• What are the 3-4 main steps of Cellular
Respiration?
– Glycolysis
– Intermediate Step/Link Reaction
– Krebs Cycle/Citric Acid Cycle
– Oxidative Phosphorylation
Fig. 9-6-3
Electrons carried
via NADH and
FADH2
Electrons
carried
via NADH
Citric
acid
cycle
Glycolysis
Pyruvate
Glucose
Oxidative
phosphorylation:
electron transport
and
chemiosmosis
Mitochondrion
Cytosol
ATP
ATP
ATP
Substrate-level
phosphorylation
Substrate-level
phosphorylation
Oxidative
phosphorylation
Fig. 9-8
Energy investment phase
Glucose
2 ADP + 2 P
2 ATP
used
4 ATP
formed
Energy payoff phase
4 ADP + 4 P
2 NAD+ + 4 e– + 4 H+
2 NADH + 2 H+
2 Pyruvate + 2 H2O
Net
Glucose
4 ATP formed – 2 ATP used
2 NAD+ + 4 e– + 4 H+
2 Pyruvate + 2 H2O
2 ATP
2 NADH + 2 H+
CYTOSOL
MITOCHONDRION
NAD+
Transport protein
1
Pyruvate
NADH + H+
2
3
CO2
Coenzyme A
Acetyl CoA
Fig. 9-11
Pyruvate
CO2
NAD+
CoA
NADH
+ H+
Acetyl CoA
CoA
CoA
Citric
acid
cycle
FADH2
2 CO2
3 NAD+
3 NADH
FAD
+ 3 H+
ADP + P i
ATP
NADH
50
2 e–
NAD+
FADH2
2 e–
40

FMN
FAD
Multiprotein
complexes
FAD
Fe•S 
Fe•S
Q

Cyt b
30
Fe•S
Cyt c1
IV
Cyt c
Cyt a
Cyt a3
20
10
2 e–
(from NADH
or FADH2)
0
2 H+ + 1/2 O2
H 2O
Cell Respiration
• What are the 2 types of anaerobic respiration?
– Alcoholic fermentation
– Lactic Acid fermentation
• In alcohol fermentation, pyruvate is converted
to ethanol in two steps, with the first releasing
CO2
• Alcohol fermentation by yeast is used in
brewing, winemaking, and baking
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
• In lactic acid fermentation, pyruvate is reduced
by NADH, forming lactate as an end product,
with no release of CO2
• Lactic acid fermentation by some fungi and
bacteria is used to make cheese and yogurt
• Human muscle cells use lactic acid fermentation
to generate ATP when O2 is scarce
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Photosynthesis
• What are the 2 main steps of Photosynthesis?
Thermodynamics
• What are the 2 laws of thermodynamics?
Thermodynamics
• What are the 2 laws of thermodynamics?
– First law of thermodynamics: the energy of the
universe is constant:
– Energy can be transferred and transformed,
but it cannot be created or destroyed
– Second law of thermodynamics:
– Every energy transfer or transformation
increases the entropy (disorder/randomness) of
the universe
Enzymes
• What is the difference between a competitive
and noncompetitive inhibitor?
Enzymes
• What is the difference between a competitive
and noncompetitive inhibitor?
– Competitive inhibitors bind to the active site of
an enzyme, competing with the substrate
– Noncompetitive inhibitors bind to another part of
an enzyme, causing the enzyme to change shape
and making the active site less effective
Fig. 8-19
Substrate
Active site
Competitive
inhibitor
Enzyme
Noncompetitive inhibitor
(a) Normal binding
(b) Competitive inhibition
(c) Noncompetitive inhibition
Enzymes
• What is end product inhibition?
Enzymes
• What is end product inhibition?
– the end product of a metabolic pathway shuts
down the pathway
– Feedback inhibition (negative feedback) prevents
a cell from wasting chemical resources by
synthesizing more product than is needed
Fig. 8-22
Initial substrate
(threonine)
Active site
available
Isoleucine
used up by
cell
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Intermediate A
Feedback
inhibition
Isoleucine
binds to
allosteric
site
Enzyme 2
Active site of
enzyme 1 no
longer binds Intermediate B
threonine;
pathway is
Enzyme 3
switched off.
Intermediate C
Enzyme 4
Intermediate D
Enzyme 5
End product
(isoleucine)