Download Bio9A Quiz 1 Study Guide

Bio9A Quiz 1 Study Guide
Chapter 1 – The Science of Biology
A. Evolutionary Principles
a. Evolution is change over time. Evolutionary relationships can be described using
phylogenies or “trees”. (Fig 1.10)
b. Evolution of Cells
i. All organisms made from cells (Fig 1.11)
1. Prokaryotic – simple, no membrane-bound organelles
2. Eukaryotic – complex, has membrane-bound organelles
ii. DNA exists in all cells. They may be packaged differently.
iii. Membranes are all the same
c. Unity and Diversity
i. Homologous structures – different function/structure but common ancestor (Fig
1.9)
ii. Changes in DNA explain diversity. Genetic code of DNA is the same in all
organisms
iii. Energy usage is virtually the same in all organisms. Breaking ATP releases
energy
B. Biological Information
a. Genetic information is stored in nucleic acids
i. DNA bases are A, T, G, C. Their sequence provides information
b. Information flow in a cell
i. The “Central Dogma” states information is expressed by being passed from DNA
 RNA  Protein. Protein is the functional part of this information
c. Heredity
i. Genetic information is passed down to the next generation of cells. DNA
replication allows this. DNA has evolved to be a great molecule for this.
C. Scientific Inquiry: Practicing Science
a. Scientific Method: Question (Observation)  Hypothesis  Experiment  Conclusion
(Fig 1.3)
i. Hypothesis is an answer or prediction to the question. It must be falsifiable.
ii. Experiment includes: design, data collection, and evaluation.
1. Controls (control variables) – factors held constant for verification of
results.
2. Independent variable – factor manipulated by researcher.
3. Dependent variable – what is measured by researcher.
iii. Conclusion accepts or rejects hypothesis.
b. Reductionism vs. systems approach.
i. Reductionism – break down mechanism to simplest components
ii. Systems – looks at relationship of components with the whole organism.
Bioinformatics with computers allows this approach today.
c. Social Context: the use of powerful technologies, ethics, social responsibility
Chapter 4 – The Cell
A. Overview of the Cell
a. Cell Theory
i. All living things are made up of cells.
ii. The smallest living thing is a cell and cells may make up multicellular organisms.
iii. Cells arise from preexisting cells.
b. General features
i. Plasma membrane – allows isolation of cell contents, regulation of materials into
and out of cells, interaction with other cells.
ii. DNA as genetic material.
iii. Cytoplasm – fluid portion in the cell.
iv. Organization and size permit homeostasis.
1. Cells are generally small to allow greater surface area to volume ratio
(Fig 4.1)
2. Different shapes and sizes depending on function (Fig 4.2)
c. Prokaryotes vs. Eukaryotes
i. Prokaryotes are small, lack organelles. They have cell walls, nucleoids,
ribosomes. Some have fimbriae, flagella, capsules. (Fig 4.3)
ii. Eukaryotes are bigger, contain organelles, and are more complex (Fig. 4.6, 4.7).
B. Eukaryotic Organelles
a. Differences between plants and animals – plants have a cell wall, plastids, central
vacuole. Animals have centrioles.
b. Nucleus – “control center” (Fig 4.8)
i. Holds DNA in form of chromatin (DNA + protein). Chromosomes are the DNA
part.
ii. Nucleolus is center for ribosome assembly.
iii. Nuclear envelope is a double membrane. Nuclear lamina is meshwork. Nuclear
pores allow RNA to exit.
c. Ribosomes – “protein making machine” (Fig 4.9)
i. Made from RNA and proteins.
ii. Found in cytosol, nuclear envelope, and rough ER.
d. Endomembrane System (Fig 4.12)
i. Endoplasmic Reticulum – “manufacturing center” (Fig 4.10)
1. Membranes form flattened tubes. Lumen is on inside.
2. Rough ER has ribosomes. Proteins made and translocated into the lumen.
3. Smooth ER has no ribosomes. Used for lipid and carbohydrate
metabolism and detoxification.
4. Buds vesicles to Golgi.
ii. Golgi Complex – “post office” (Fig 4.11)
1. Sorts incoming proteins and lipids
2. Receives at cis and ships at trans end.
3. “Tags” or modifies some for destination
4. Packages them for final destination in vesicles.
iii. Lysosomes – “digestive system” (Fig 4.13)
1. Contains hydrolytic enzymes at low pH.
2. Digests all classes of macromolecules. White blood cells phagocytose
other cells.
3. Tay-Sach’s disease is genetic and is caused by missing digestive enzyme.
The enzyme digests lipids. Lipids build up and kill cell. Death occurs in
children
iv. Peroxisomes – “detox center”. Metabolize small organic compounds. E.g.
Hydrogen peroxide and ethanol. (Fig 4.14)
v. Vacuole – “storage and recycling plant” (Fig 4.15)
1. Store water, food, salts, pigments, and wastes.
2. Like a large vesicle.
3. Some protists have contractile vacuole
4. Huge in plants=central vacuole
e. Mitochondria – “powerhouse”
i. Produce ATP from glucose
ii. Structure: double membrane, intermembrane space, cristae (folds), matrix that
has enzymes. (Fig 4.16)
f. Chloroplasts – “solar power plant” (Fig 4.17)
i. Family of plastids that produce and store food.
ii. Makes glucose using chlorophyll and carotenoids
iii. Has three membranes. Inner most makes up thylakoid. Grana are stacks of
thylakoids. Stroma is inside space. Thylakoid lumen is inside thylakoid. Enzymes
in both stroma and thylakoid lumen.
C. Cytoskeleton
a. Involved in support, movements, and cell division
b. Fibers (Fig 4.19)
i. Microfilaments – made from actin monomers. Small and helixed. Involved in
structure and movements. E.g. muscle contraction, cytoplasmic movements
ii. Intermediate filaments – medium sized. Structural role.
iii. Microtubules – alpha and beta tubulin subunits wrapped in large helix.
1. Vesicle movement using motor proteins (Fig 4.21)
2. Centrosomes – organizing center for cell division. Animal cells contain a
centriole (Fig 4.20)
3. Cilia and Flagella – movement and water movement. (Fig 4.23)
a. Cilia are small and numerous, “eyelash”
b. Flagella are large and few, “whip”
c. Uses microtubules connected by dynein arms. Mechanism of
movement is similar to motor protein movement
D. Extracellular Components
a. Extracellular matrix is outside of membrane (Fig 4.26)
b. Junctions in animal cells (Fig 4.28)
i. Tight junctions – “cement” – leak proof.
ii. Desmosome – “staple” – attaches adjacent cells
iii. Gap (communicating) junctions – hole that allows messages through.
c. Plant cells have a cell wall. (Fig 4.25)
i. Made from tough cellulose.
ii. Have plasmodesmata to allow communication (Fig 4.29
Chapter 5 – Membrane Structure and Function
A. Membrane Structure
a. Fluid-Mosaic Model – Singer and Nicolson 1972 (Fig 5.3)
i. Phospholipid bilayer is fluid
1. Fluidity
a. Amphipathic phospholipids – polar head and nonpolar tails (Fig
5.1)
b. Phospholipids move freely within its layer
2. Semipermeable to small nonpolar molecules only (water is exception)
3. Cholesterol helps stiffen membranes
ii. Proteins and carbohydrates give mosaic
1. Integral are embedded into hydrophobic part (Fig 5.8) while peripheral
are only attached to a surface.
2. Variety of functions (Fig 5.7). Transport, cell recognition, signaling, and
structure
b. Evidence of structure
i. Frye and Edidin 1970: different cells were labeled with different color tags.
Fusion of cells prove fluidity because colors blended (Fig 5.5)
B. Transport Across Membranes
a. Passive transport – diffusion (Fig 5.9)
i. Down a concentration gradient (high  low)
ii. Osmosis – diffusion of water across a membrane (Fig 5.11)
iii. Tonicity – relation of solute concentrations across a membrane (Fig 5.12)
1. Isotonic: =
2. Hypotonic < (in relation to cell)
3. Hypertonic > (in relation to cell)
4. These lead to certain conditions in plant and animal cells
a. Plant cells become turgid when in hypotonic solution and
plasmolysed when hypertonic solution.
b. Animal cells will lyse when in a hypotonic solution and crenate
when in a hypertonic solution.
iv. Proteins (e.g. carrier, channel protein) can allow solutes across that are too big to
cross lipid bilayer (Fig 5.10).
1. Channel proteins are pores that are non-specific.
2. Carrier proteins bind specific substances.
b. Active transport
i. Against concentration gradient
ii. Requires energy
iii. Examples
1. Na-K pump – a bi-directional pump (Fig 5.13)
a. Binding of Na allows ATP hydrolysis  conformation shift 
Na out.
b. K binding releases phosphate  shift  K in.
2. Coupled transporters use one active transporter to create a gradient to
drive a cotransporter. (Fig 5.14)
C. Exocytosis and Endocytosis
a. Transport of large particles (bulk transport) uses vesicles
b. Exocytosis – particles are excreted. (Fig 5.16)
c. Endocytosis – particles are taken in. (Fig 5.15)
i. Phagocytosis – large particles are taken in – “cell eating”. Vacuole is formed
which may fuse with a lysosome.
ii. Pinocytosis – small particles are ingested – “cell drinking”.Vesicle then allows
contents to bleed into cytosol.
iii. Receptor-mediated endocytosis – uses a receptor for specific particle uptake. E.g.
LDL uptake
1. Receptors wait on surface. LDL binds.
2. Coat proteins bind and organize receptors. This causes endocytosis.
3. Vesicle forms and coat is removed.
4. Vesicle sent to lysosome. LDL released and receptors recycled.
iv. Disease, hypercholesterolemia, due to defective LDL receptors.
Chapter 6 – Enzymes
A. Enzymes Characteristics
a. Enzymes are catalysts that lower energy of activation (Fig 6.5)
b. Enzyme
i. Specific for certain substrates
ii. Reaction must already be exergonic
iii. Reusable
c. Substrate (reactant)  Product
B. Catalytic cycle: E + S  ES  EP  E + P (Fig 6.10)
a. Substrate binding: binds to active site of enzyme. Uses “induced fit” model instead of
“lock-and-key”. (Fig 6.8)
b. Reaction: active site provides correct environment to create product.
c. Release: enzyme releases product and can be reused.
C. Regulation
a. Environmental factors
i. Optimal pH, temperature, salt produce bell curves (Fig 6.12)
ii. Substrate concentration produces logarithmic curves
b. Activators
i. Cofactors (non-organic)
ii. Coenzymes (organic)
c. Inhibitors (Fig 6.13)
i. Competitive – binds active site
ii. Noncompetitive – binds allosteric site
d. Complex Regulation
i. Feedback inhibition (Fig 6.15)
ii. Enzyme complexes
1. Allosteric activation and inhibition as a complex
2. Cooperativity – when substrate binding assists further substrate binding
of other enzymes in complex
iii. Localization – enzymes are held in separate compartments
D. Metabolism – the sum of all reactions in a cell
a. Catabolism – breakdown molecules
b. Anabolism – build
c. Reactions tend to be organized in pathways (Fig 6.14)
Chapter 7 – Cellular Respiration
A. Overview of Aerobic Respiration
a. C6H12O6 + 6 O2 + 38 ADP  6 CO2 + 6 H2O + 38 ATP
i. Glucose oxidized carbon dioxide
ii. Oxygen reduced to water
b. Relationship with photosynthesis
c. Energy harvest – slow breakdown of glucose can allow ATP synthesis (Fig 7.2)
d. ATP made in 2 ways
i. Substrate-level phosphorylation – direct transfer by an enzyme (Fig 7.4)
ii. Oxidative phosphorylation – uses an electron transport chain.
1. Two important coenzymes: NAD and FAD. These pick up electrons
from glucose and transfer them to electron transport chain to make ATP.
(Fig 7.3)
2. NAD makes 3 ATP, FAD makes 2 ATP.
iii. Occurs in 4 sets of reactions: Glycolysis  Acetyl-CoA Formation  Citric
Acid Cycle  Oxidative Phosphorylation. Glycolysis occurs in cytosol, other
three in mitochondria (Fig 7.5)
B. Stages of Aerobic Respiration
a. Glycolysis (Fig 7.6, 7.7)
i. Glucose  Pyruvate
ii. Yields 2 ATP and 2 NADH
iii. Energy investment steps
1. 2 ATPs used in 3 steps.
2. C6  2C3 (G3P) in 1½ steps.
iv. Energy harvesting steps
1. 4 ATPs and 2 NADHs produced in 5 steps. Remember, these totals
reflect doubling of reactions because of 2C3 molecules.
2. These ATPs are made by substrate level phosphorylation
v. Pyruvate moves to mitochondria.
b. Acetyl-CoA formation (Fig 7.9)
i. Yields 2 NADH (1 per pyruvate)
ii. Occurs in matrix of mitochondria.
iii. Pyruvate + CoA  CO2 + Acetyl-CoA
c. Citric Acid Cycle (Fig 7.10, 7.11)
i. Yields 2 ATP, 6 NADH, and 2 FADH2 (2 turns for 2 acetyl-CoA)
ii. Occurs in matrix of mitochondria.
iii. C4 (oxaloacetate) + Acetyl-CoA  citrate (C6) + CoA
iv. C6  C5  C4 yielding 2 CO2 + energy.
d. Oxidative Phosphorylation (Fig 7.12)
i. Occurs on the inner mitochondrial membrane.
ii. Converts energy from NADH and FADH2 to ATP
iii. Electron transport chain made from cytochromes.
a. 3 carriers pump protons out
b. NADH donates electron at 1st pump, FADH2 donates after 2nd pump.
c. Oxygen is needed to pick up electrons from last cytochrome.
iv. Chemiosmosis – production of ATP by a proton (H+) gradient. Protons have been
pumped into intermembrane space. High concentration drives movement of
protons back into matrix. ATP synthase: force of proton movement turns matrix
portion which powers ATP synthesis. (Fig 7.14)
e. Balance sheet: 38 ATP (34 from 10 NAD and 2 FAD)
f. Efficiency: glucose gives 2870 kJ/mol. ATP hydrolysis gives 32 kJ/mol. 38 X 32 gives
1216 kJ/mol. Therefore, aerobic respiration has about 42% efficiency.
C. Metabolic pools – nutrients other than glucose can fuel respiration. They can also be made from
respiration intermediates (Fig 7.17).
a. Catabolism – breakdown of molecules can feed into respiration pathway
b. Anabolism – excess can be built into storage molecules
c. Proteins require deamination (Fig 7.21), fats require beta-oxidation (Fig 7.22)
d. Regulation – feedback on phosphofructokinase. AMP can stimulate. ATP and citrate can
inhibit.
D. Fermentation – a “shortcut” respiration process.
a. Regenerates NAD+ to run glycolysis. This produces ATP by substrate level
phosphorylation only. Inefficient but very fast. (Fig 7.8)
b. Alcohol fermentation – done by yeast. Ethanol and CO2 produced.
c. Lactic acid fermentation – humans do. Lactic acid produced which may cause muscle
fatigue.
Chapter 9 – Cell Signaling
A. Overview
a. Mating types of yeast (a and ) lead to early cell communication studies. Mating factors
are specific for mating receptors of opposite mating types. Binding causes shmoos
(mating projections)
b. Types of signaling depends on range/speed (Fig 9.2)
i. Direct contact – cells must touch. Direct
ii. Paracrine – short distance with neighboring cells using chemical signals.
iii. Endocrine – long distance, uses hormones
iv. Synaptic – long/short distances using electrical/chemical signals.
c. Stages of cell signaling (Fig 9.1)
i. Reception – signal is received. Binding of signal to receptor and information
transmitted to inside of cell.
ii. Transduction – relays and amplifies signal
iii. Response – a cellular response. Can be enzyme activity, gene activation, etc.
d. Phosphorylation
i. Important mechanism in signaling.
ii. A kinase is the enzyme that phosphorylates, phosphatase dephosphorylates
iii. Reaction involves transfer of phosphate. Often uses ATP as source (Fig 9.3)
iv. Usually causes a significant change of shape of a protein
B. Reception – receives stimulus from a ligand binding a receptor.
a. Intracellular receptors (Fig 9.5)
i. Loose in cytosol, e.g. steroid hormone receptors
ii. When bound, the complex travels to nucleus and initiates gene activity.
b. Ion channel receptors
i. Membrane bound. A signal opens a channel and ion flux initiates response (Fig
9.4a)
c. Tyrosine kinase receptors (Fig 9.6)
i. Used by growth factors.
ii. Steps
1. Signal binds receptor monomers.
2. Receptors dimerize.
3. Autophosphorylation of tyrosines.
4. Relay proteins bind P-tyrosines and get activated.
5. Relay proteins signal downstream.
iii. Insulin receptor is an example (Fig 9.7)
d. G-protein coupled receptors (Fig 9.4c)
i. Oldest and largest family. A “7 span” intermembrane protein
ii. G protein has three subunits:
. Complex is membrane bound.
iii. When inactive, all three are bound, with GDP.
iv. Steps (Fig 9.11)
1. Signal binds receptor
2. Full G protein binds receptor via .
3. GDP is released from
and GTP replaces it.
4.
releases
. Both are active. Each active parts bind relay proteins.
5. Hydrolysis of GTP inactivates alpha and it binds back
.
C. Signal Transduction Pathways
a. Goals
i. Links reception and response
ii. Amplification – signal increases in strength (Fig 9.8b)
iii. Divergence – signal can split off
iv. Convergence – signals can merge
b. Phosphorylation cascades (Fig 9.8a)
i. A cascade is a series of phosphorylations
ii. A scaffolding protein can organize the cascade (Fig 9.9)
c. Second messengers
i. cAMP
1. Adenylyl cyclase converts ATP to cAMP (Fig 9.12)
2. cAMP activates PKA which begins a phosphorylation cascade (Fig 9.13)
ii. IP3 and Ca-calmodulin (Fig 9.15)
1. IP3 is formed by phospholipase C
2. IP3 signals calcium release from organelles by a channel.
3. Ca can directly activate pathways or bind calmodulin in other pathways.
Ca is loaded into certain organelles
D. Response
a. Two main cellular responses
i. Enzymatic response – E.g. formin activation in shmooing. Formin builds actin at
growing end of shmoo.
ii. Gene activation – E.g. growth hormones activate specific cell division genes.
1. Regulation - specificity is combinatorial. Pathways can converge or
diverge to give unique responses. These may form signaling “networks”