Unit 1: Chemistry and Cells Flashcards
Alanine - Abbreviations and properties
Ala, A
Aliphatic, Nonpolar (hydrophobic)
Glycine - Abbreviations and properties
Gly, G
Aliphatic, Nonpolar (hydrophobic)
Valine - Abbreviations and properties
Val, V
Aliphatic, Nonpolar (hydrophobic), Essential
Leucine - Abbreviations and properties
Leu, L
Aliphatic, Nonpolar (hydrophobic), Essential
Isoleucine - Abbreviations and properties
Ile, I
Aliphatic, Nonpolar (hydrophobic), Essential
Methionine - Abbreviations and properties
Met, M
Nonpolar (hydrophobic), Sulfur-containing, Essential, Start codon (AUG)
Proline - Abbreviations and properties
Pro, P
Aliphatic, Nonpolar (hydrophobic)
Phenylalanine - Abbreviations and properties
Phe, F
Aromatic, Nonpolar (hydrophobic), Essential
Tryptophan - Abbreviations and properties
Trp, W
Aromatic, Nonpolar (hydrophobic), Essential
Tyrosine - Abbreviations and properties
Tyr, Y
Aromatic, Polar (hydrophilic)
Serine - Abbreviations and properties
Ser, S
Hydroxylic, Polar (hydrophilic)
Threonine - Abbreviations and properties
Thr, T
Hydroxylic, Polar (hydrophilic), Essential
Asparagine - Abbreviations and properties
Asn, N
Amidic (derived from ammonia), Polar (hydrophilic)
Glutamine - Abbreviations and properties
Gln, Q
Amidic (derived from ammonia), Polar (hydrophilic)
Cysteine - Abbreviations and properties
Cys, C
Sulfur-containing, Polar (hydrophilic) - though only weakly
Histidine - Abbreviations and properties
His, H
Basic (positively charged), Essential
Lysine - Abbreviations and properties
Lys, K
Basic (positively charged), Essential
Arginine - Abbreviations and properties
Arg, R
Basic (positively charged)
Aspartic Acid - Abbreviations and properties
Asp, D
Acid (negatively charged)
Glutamic Acid - Abbreviations and properties
Glu, E
Acid (negatively charged)
How does a light microscope work?.
Visible light is passed though the specimen and then through glass lenses. The lenses refract (bend) the light in such a way that the imagine of the specimen is magnified.
What is magnification? (In the context of microscopes)
Magnification is the ratio of an object’s imagine size to its real size.
What is resolution? (In the context of microscopes)
Resolution is a measure of the clarity of the image. It is the minimum distance two points can be separated and still identified as two separate points.
What is staining?
The specimen is enhanced with dyes. Most staining procedures require that the cells be fixed, thereby killing them.
What is phase-contrast? (microscopes)
Variations in density within the specimen are amplified to enhance contrast in unstained cells; useful for examining living, unpigmented cells.
What is differential interference (Nomarski)? (microscopes)
Optical modifications are used to exaggerate differences in density; image appears almost 3D.
How does a confocal image work? (microscopes)
Using a laser, this “optical sectioning” technique eliminates out-of-focus light from a thick sample. By capturing sharp images at many different planes, a 3D reconstruction can be recreated.
What does a scanning electron microscope (SEM) do?
The SEM is especially useful for detailed study of the topography of a specimen. The electron beam scans the surface of the sample (usually coated with a thin film of gold). The beam excites electrons on the surface, and these secondary electrons are detected by a device that translates the pattern of electrons into an electronic signal sent to a video screen.
What does the transmission electron microscope (TEM) do?
The TEM is used to study the internal structure of cells. The TEM aims an electron beam through a very thing section of the specimen. The specimen must be stained with atoms of heavy metals. This enhances the density of some parts of the specimen.
What is cell fractionation?
In cell fractionation, broken-up cells are placed in a tube that is spun in a centrifuge. The largest components settle on the bottom of the tube, forming a pellet. The liquid above the pellet is poured into a new tube and centrifuged again. This is repeated several times, creating a series of pellets that consist of different pieces of the specimen.
What are fimbriae (prokaryotes)?
The attachment structures on the surface of some prokaryotes (not visible on TEM).
What is the nucleoid (prokaryotes)?
The region where the cell’s DNA is located (no membrane).
What is the glycocalyx (prokaryotes)?
The outer coating of many prokaryotes consisting of a capsule or a slime layer.
What do microvilli do?
Microvilli increase the cell’s surface area without increasing its volume much.
Describe the nuclear membrane
The nuclear envelope is a double membrane which is each a lipid bilayer separated by a space of 20-40 mm. The envelope is perforated by pore structures (around 100 mm in diameter). At the lip of each pore, the inner and outer membranes of the envelope are joined. An intricate protein called a pore complex lines each pore and regulates the entry/exit.
What is the nuclear laminae?
A netlike array of protein filaments (intermediate filaments in animal cells) that maintains the shape of the nucleus by mechanically supporting the nuclear envelope.
What does the nucleolus do?
The nucleolus is where rRNA is synthesized. Proteins are assembled with the rRNA are assembled into ribosomes. The ribosomes exit the nucleus via the nuclear pores.
What are the functions of the smooth ER?
- The synthesis of lipids - including steroids (sex hormones)
- The metabolism of carbohydrates
- The detoxification of drugs/poisons (adding hydroxyl groups to drug molecules; more drugs = proliferation of smooth ER = higher tolerance to the drugs)
- The storage of calcium ions (in muscle cells, calcium ions are pumped from the cytosol into the lumen)
What are the functions of the rough ER?
- Creates secretory proteins (most of which are glycoproteins - proteins with carbohydrates covalently bonded to them)
- Membrane factory (grows in place by adding membrane proteins and phospholipids to its own membrane)
What are the flattened membranous sacks of the Golgi Apparatus called?
Cisternae
Cis-side vs trans-side of the Golgi Apparatus
The cis-side usually faces the ER and receives vesicles. The trans-side gives rise to vesicles that pinch off and travel to other sites.
What does the lysosome do?
The lysosome is a membranous sac of hydrolytic enzymes that many eukaryotic cells use to digest macromolecules (the enzymes of the lysosome work best in the acidic environments found in lysosomes). Lysosomes also play a role in phagocytosis. The food vacuole fuses with the lysosome and hydrolytic enzymes digest the food particles.
What are cristae?
Cristae are the infoldings found in the inner membrane of mitochondria. They give the inner membrane a higher surface area, enhancing the productivity of cellular respiration.
What is the intermembrane space and the mitochondrial matrix?
The intermembrane space is the space between the two membranes of mitochondria. The mitochondrial matrix is the area enclosed by the inner membrane.
What are thylakoids? Granum? Stroma?
Thylakoids are the flattened interconnected sacs found in chloroplasts. Granum are stacks of thylakoids. Stroma is the fluid outside the thylakoids.
What are plastids?
A family of closely related plant organelles.
What do amyloplasts store?
Amylose - starch
What do chromoplasts store?
Pigments
What does the peroxisome do?
It removes hydrogen atoms from certain molecules and transfer them to oxygen producing hydrogen peroxide. They have a granular or crystalline core that to be a dense collection of enzyme molecules.
What are microtubules made of?
Tubulin a dimer made of alpha-tubulin and beta-tubulin. They form a hollow tube.
What are the functions of microtubules?
Maintenance of cell shape; cell motility; chromosome movements in cell division; organelle movements
What are microfilaments made of?
Filaments of actin
What are the functions of microfilaments?
Maintenance of cell shape; changes in cell shape; muscle contraction; cytoplasmic streaming (movement of cytoplasm around in plant cells); cell motility; cell division (animal cells)
What are intermediate filaments made of?
One of several different proteins (such as keratin) coiled into cables
What are the functions of intermediate filaments?
Maintenance of cell shape; anchorage of nucleus and certain other organelles; formation of nuclear lamina.
What is a centrosome?
A region that is often located near the nucleus and organizes microtubules.
- Composed of a pair of centrioles which is each composed of 9 sets of triplet microtubules arranged in a ring
What are flagella and cilia made of?
Microtubules
What is the arrangement of microtubules in flagella and motile cilium? Nonmotile cilium?
Motile cilia and flagella: 9 doublets of microtubules arranged in a ring with 2 single microtubules in the center. “9+2” pattern
Nonmotile cilia: Same as motile cilia, but lacking the 2 microtubules in the center. “9+0” pattern
What is a basal body?
A structure that anchors the microtubule assembly of a cilium or flagellum. Structurally similar to a centriole (microtubule triplets in a 9 + 0 pattern)
What are dyneins?
Large motor proteins that attach along each outer microtubule doublet. A typical dynein protein has two “feet” that “walk” along the microtubule of the adjacent doublet, using ATP for energy.
Primary vs secondary cell wall
The primary cell wall is the first cell wall a young plant secretes which is relatively thin and flexible. When the cell matures and stops growing, it strengthens its wall. Some plants cells do this by simply secreting hardening substances into the primary wall. Others add a secondary cell wall. The secondary wall is often deposited in several laminated layers and has a strong and durable matrix that affords the cell protection and support.
What is middle lamella?
Middle lamella is a thin layer rich in sticky polysaccharides called pectin. It glues adjacent cells together and is between the primary and secondary cell walls.
What are proteoglycans?
A small core protein with many carbohydrate chains covalently atached
What are integrins?
Cell-surface receptor proteins that bind on their cytoplasmic side to associated proteins attached to microfilaments and transmits signals between the ECM (extracellular matrix) and the cell.
What are tight junctions?
A junction that occurs at the plasma membranes of neighboring cells that are tightly pressed against each other, bound by specific proteins. This prevents leakage of extracellular fluid.
Describe desmosomes
Junctions that function like rivets, fastening cells together. Intermediate filaments made of keratin proteins anchor desmosomes in the cytoplasm.
Describe gap junctions
Junctions that provide cytoplasmic channels from one cell to an adjacent cell (similar to plasmodesmata in plants).
Muscle cells are attached by…
Desmosomes
What is the nuclear matrix?
The nuclear matrix is an intricate meshwork of proteins spread throughout the nucleus. The matrix plays a role in essential nuclear functions, which include gene expression, RNA splicing, RNA export, and nuclear protein import and export.
In what cells is the Golgi Apparatus wide-spread?
Secretory cells
What are glyoxysomes?
Fat-storing tissues in plant seeds. They convert fatty acids into sugar.
What bond angle to tetrahedrons have? (CH4)
109.5º
Name some examples of aldoses (carbohydrates)
Glucose, galactose
Name some examples of ketoses (carbohydrates)
Carbonyl in the middle of the chain
Fructose
What links two monosaccharides?
Glycosidic linkages
What is the most abundant organic molecule on Earth?
Cellulose
What type of structure does amylose have?
Helical
What type of structure does amylopectin have?
Branched
What type of structure does glycogen have?
Heavily branched
α-glucose vs ß-glucose
α-glucose has an H on top and an OH on the bottom of Carbon 1, while ß-glucose has an OH on top and an H on the bottom of Carbon 1.
ß glucose is more stable and harder to break down in humans’ digestive systems.
In cellulose, every ß glucose is upside down.
What type of bond is between glycerol and a fatty acid?
An ester linkage
What type of bond is between amino acids (to form a protein)?
Peptide bonds.
In a peptide bond, the O double-bonded to the C of the carboxyl group and the N from the amine group are on opposite sides.
Describe the structure of an amino acid
An alpha carbon has an amine group (NH2) and a carboxyl on the other. An H is attached above the alpha carbon, and an R group is attached below the alpha carbon.
What are the functions of a protein?
Storage, enzymes, defensive, transport, hormones, receptors, motor, structure
Between which amino acids do alpha-helices form?
The xth amino acid and the (x+4)th amino acid.
Ex. Between the 1st amino acid and 5th amino acid.
What are the characteristics of a purine?
2 rings, Guanine and Adenine
What are the characteristics of a pyrimidine?
1 ring, Cytosine, Uracil, Thymine
What direction is DNA built in?
5’ to 3’
What are catabolic pathways?
A pathway in which a substance is broken down into smaller parts
What are anabolic pathways?
A pathway in which a substance is formed from smaller parts
What are the 2 laws of thermodynamics?
- Energy is not created or destroyed
- Entropy continuously increases
What is enthalpy?
The total energy of a system
What is a spontaneous process?
Something that is thermodynamically favorable. Either enthalpy decreases or entropy increases.
What is an exergonic reaction?
When there is a net release of free energy, -ΔG
What is an endergonic reaction?
When there is a net consumption of free energy, +ΔG
What is phosphorylation?
The transfer of a phosphate group
How does a phosphorylated intermediate help an endergonic reaction become exergonic?
Phosphorylation makes a molecule less stable, so there is more free energy.
This also converts ATP to ADP.
What do enzymes do?
They lower the activation energy of a reaction
What happens in an enzyme-substrate complex?
The shape of the enzymes changes, and the enzyme helps facilitate the reaction (can be holding the reactants in place, creating a microenvironment, etc.)
What are the two types of enzyme inhibition?
Competitive and non-competitive.
The competitive inhibitor binds to the active site and prevents the substrate from binding there. The noncompetitive inhibitor binds to a different site on the enzyme; it doesn’t block substrate binding, but it causes other changes in the enzyme so that it can no longer catalyze the reaction efficiently.
What is allosteric regulation?
When the activity of an enzyme is regulated by another molecule
What is cooperativity?
When a substrate binding to a multi-subunit enzyme triggers shape change in all subunits.
Amplifies response of enzyme to substrates
What is feedback inhibition?
The activity of the enzyme is suppressed by its product
How does saturated fat/tails affect a cell membrane?
They allow it to be more rigid (Seen in warmer environments)
How does unsaturated fat/tails affect a cell membrane?
They allow it to be more fluid (Seen in colder environments)
How does cholesterol affect a cell membrane?
It restrains phospholipid movement at high temperatures, but also lowers the temperature required for solidification.
What are integral proteins? (Cell membrane)
Proteins that penetrate the hydrophobic interior of the lipid bilayer
What is a transmembrane protein? (Cell membrane)
A protein that spans the whole membrane
What are peripheral proteins? (Cell membrane)
Proteins that aren’t embedded in the cell membrane
What is a hypotonic solution?
A solution that is less concentrated in something (ex. salt).
What is a hypertonic solution?
A solution that is more concentrated in something (ex. salt).
Which type of solution do plants do best in?
Hypotonic. It allows them to remain turgid (water pressure pressing their cell walls)
What happens if a plant is left in isotonic solution?
The plant becomes flaccid.
What happens when a plant cell becomes plasmolyzed?
The plant cell shrivels.
This occurs in a hypertonic solution.
What happens when an animal cell is left in a hypotonic solution?
It lyses (bursts open)
What happens when an animal cell is left in a hypertonic solution?
It shrivels up
What are the 2 types of proteins which assist in passive transport?
Channel proteins: Molecule or ion channels (are often gated by ligand or voltage)
Carrier proteins: Bind to specific solutes and transfer them across the membrane
What is active transport?
Transport that moves solute against its concentration gradient. It requires ATP. It can maintain membrane potential
What is cotransport? The role of proton pumps in it?
Proton pumps use ATP to pump a molecule/ion (say Na+) against its concentration gradient outside the cell. When the molecule/ion naturally diffuses back in, it brings another molecule with it (say glucose).
What is exocytosis?
The secretion of vesicles through the cell membrane
What are the 3 types of endocytosis?
Phagocytosis - The cell takes in a large particle via a vesicle
Pinocytosis - The cell takes in many “gulps” of vesicles
Receptor-mediated endocytosis - Receptors to specific substrates cluster in coated pits (takes in cholesterol)
What are the 3 steps to signaling?
Receptor, transduction, response
What is endocrine signaling?
Long-distance signaling (with hormones)
What roles do local signaling play?
- Embryonic development
- Immune response
What is a ligand?
A binding molecule that leads to a change in the shape of the receptor
What does epinephrine do? (On a molecular level)
It attaches to a GPCR which causes the activation of adenylate cyclase (by the alpha subunit). Adenylate cyclase then takes ATP and produces cAMP (cyclic adenosine monophosphate). cAMP (the secondary messenger) then activates Protein Kinase A, which then stimulates the breakdown of glycogen.
What is the Michaelis-Menten equation?
V0 (or d[P]/dt) = (Vmax[s])/(Km + [s])
Where V0 is current rate of reaction, Vmax is maximum rate of reaction and Km is a constant
What in the Michaelis-Menten equation changes when there is a competitive inhibitor?
Lower Km, Same Vmax
The concentration of the substrate at which half of the active sites of the enzyme are occupied by the substrate changes (is lower)
The maximum velocity achieved stays the same
On a graph, the curve/slope of the line is different, but the peak is the same.
What in the Michaelis-Menten equation changes when there is a noncompetitive inhibitor?
Same Km, Lower Vmax
The concentration of the substrate at which half of the active sites of the enzyme are occupied by the substrate is the same
The maximum velocity is lower
On a graph, the curve/slope would look very similar, while the peak would be lower.
How does a G-protein coupled receptor (GPCR) work?
When a ligand binds to a GPCR, it undergoes a conformational change (its shape changes), and it binds to the G-protein, activating it and causing the GTP to bump out the GDP. This causes the alpha subunit to dissociate from the beta and gamma subunits. The alpha subunit (and the beta/gamma dimer both) can regulate protein functions. The target protein can relay signals via 2nd messengers. The GTP is then hydrolyzed back to GDP (the RGS (regulation of G-protein signaling) protein can accelerate this).
Describe the structure of a G-protein coupled receptor (GPCR) in a cell membrane
They have 7 transmembrane alpha helices (that is why they are also called “7 transmembrane receptors”
What is a G-protein?
G-proteins that associate with GPCRs are heterotrimeric meaning that they have 3 different subunits. The first subunit is called alpha, the second beta, and the third gamma. The alpha and gamma subunits are attached to the cell membrane, (by lipid anchors) while the beta subunit is attached to the gamma subunit. A G-protein can either be on or off depending on whether GTP (guanosine triphosphate) or GDP (guanosine diphosphate) is bound to the alpha subunit, respectively.
What is a kinase?
An enzyme that catalyzes the transfer of a phosphate group to another molecule/protein (ex. insulin)
What is the structure of a receptor tyrosine kinase? (RTK)
It is a protein complex with a signal-binding site and tyrosine attached to it.
How do RTKs work (receptor tyrosine kinases)?
When a signaling molecule attaches to the signal binding sites, 2 separate polypeptides (of RTK) will come together and become an unphosphorylated dimer (with activated tyrosine regions). Each tyrosine attaches a phosphate onto a tyrosine on the opposite side (as it is a dimer). When all the tyrosines have a phosphate attached to them, this dimer becomes phosphorylated. A relay protein will then bind to phosphate on a tyrosine region, undergo a conformational change, and lead to a cellular response. There can be multiple cell responses all from one signaling molecule.
What is a scaffolding protein?
Proteins that bring 2 or more proteins together in a relatively stable configuration.
What are the characteristics of an ion channel?
- Only allows ions in when a ligand binds to it
- Closes when the ligand unbinds
How do steroids work?
Because steroids are fat-soluble, they can pass directly through the membrane. When inside the cell, they bind to receptors in the cytoplasm. This hormone-receptor complex enters the nucleus and binds to genes, acting as a transcription complex stimulating the creating of mRNA.
What do protein kinases do?
Protein kinases phosphorylate proteins with Pi (phosphate) from ATP
What is a phosphorylation cascade?
A chain of events in which one protein/enzyme phosphorylates another, producing ADP.
What is a protein phosphatase?
An enzyme that removes a phosphate from a phosphorylated molecule. This helps “reset” a phosphorylation cascade.
What are the two most common secondary messengers?
cAMP and Ca2+
What is a somatic cell?
Any cell in an organism that is not a reproductive cell
What is a gamete?
An organism’s reproductive cell(s)
What is a sister chromatid?
A duplicated chromosome (in the shape of an X). NOT mother and father chromosomes. Sister chromatids are identical and attached by cohesin protein complexes.
What is a centromere?
The part of a chromosome which attaches to the spindle fiber. It is made of repetitive sequences and the attachment to the microtubules are facilitated by proteins which recognize this repetitive sequence.
What is the shortest phase of the cell cycle?
The mitotic (M) phase
What happens in the G1 phase of the cell cycle?
The cell rapidly grows and protein/organelle production occurs
What happens in the synthesis (S) phase of the cell cycle?
The cell grows and copies its chromosomes. This accounts for around half the cycle in the average cell.
What happens in the G2 phase of the cell cycle?
The cell grows and gets ready for cell division
What happens in prophase?
The chromatin condenses (visible under an LM), the nucleoli disappear, and the mitotic spindle of microtubules begins to form.
What is cytokinesis?
The step that follows mitosis, where the cytoplasm is divided and 1 cell becomes 2 cells.
What are the radial arrays of shorter microtubules that extend from the centrosomes called?
Asters (“stars”)
What happens in prometaphase?
The nuclear envelope fragments and the microtubules extending from each centrosome can now invade the nuclear area. The chromosomes become even more condensed. A kinetochore forms at the centromere of each chromatid (2 per chromosome) and some of the microtubules attach to the kinetochores, becoming “kinetochore microtubules”, which move the chromosomes. Nonkinetochore microtubules lengthen the cell.
What is a kinetochore?
A specialized protein structure that forms at the centromere of each chromatid during prometaphase.
What happens in metaphase?
The centrosomes are now at opposite poles of the cell, and the chromosomes have all arrived at the metaphase plate (a plate along the middle of the cell).
What is the shortest stage of mitosis?
Anaphase
What happens in anaphase?
The cohesin proteins connecting the two sister chromatids of each pair are cleaved. Each chromatid becomes an independent chromosome. The kinetochore microtubules shorten, moving the daughter chromosomes toward opposite ends of the cell (at a rate of 1 µm/min). Nonkinetochore microtubules lengthen, elongating the cell.
What happens in telophase?
Two daughter nuclei start forming in the cell (nuclear envelopes arise from the fragments from the parent cell’s nuclear envelope). Nucleoli reappear and the chromosomes become less condensed. Any remaining spindle microtubules are depolymerized.
What is the centrosome?
A subcellular region containing a pair of centrioles. It organizes microtubules, but is not essential for cell division.,
How do kinetochore microtubules shorten during anaphase?
A motor protein walks the chromosome backward, as the microtubule depolymerizes at its kinetochore end, releasing tubulin subunits.
What is a cleavage furrow?
A shallow groove in the cell surface near the old metaphase plate
How does cytokinesis work in animal cells?
On the cytoplasmic side of the cell is a ring of actin filaments working with molecules of myosin. Actin and myosin work together, causing the ring to contract (like a drawstring), and splitting the cell in 2.
How does cytokinesis work in plant cells?
In telophase, vesicles from the Golgi Apparatus move via microtubules to the middle of the cell where they gather to form a cell plate. The cell plate enlarges until it fuses with the surrounding membrane. This creates two cells. A cell wall is then created between the two cells.
How do prokaryotic cells replicate?
Binary fission
What is the origin of replication (in bacteria)?
A specific place on a bacterial chromosome where replication begins. When replication begins, it produces two origins (like opening a ziplock bag) and as the chromosome continues to replicate, one origin moves rapidly toward the opposite end of the cell.
How does the DNA of bacteria move (when replicating)?
An actin-like protein.
How are 2 daughter cells made when bacteria replicate?
A tubulin-like protein pinches the cell membrane inward.
How does mitosis work in dinoflagellates?
Chromosomes are attached to the nuclear envelope and microtubules pass through cytoplasmic tunnels in the nuclear envelope to facilitate division.
How does mitosis work in diatoms and some yeasts?
The nuclear envelope remains intact and the microtubules form a spindle within the nucleus. Microtubules separate the chromosomes, and the nucleus splits into two daughter nuclei.
What is a checkpoint (in terms of the cell cycle and mitosis)?
A control point where stop and go-ahead signals can regulate the cycle. It prevents errors in the end products of mitosis
What are the 3 most important checkpoints in the cell cycle?
G1, G2, and M phases
What type of protein helps regulate the cell cycle?
Cyclin-dependent kinases
When a cyclin is present, it activates the CDK giving the “go-ahead” signal for the cell cycle
What does the maturation promoting factor (MPF) do?
MPF is the cyclin-CDK complex that promotes the entrance into mitosis from the G2 phase by phosphorylating multiple proteins needed during mitosis (condensins for chromatin condensation, lamins for the degradation of the nuclear envelope, etc.). It is activated at the end of G2 by a phosphatase which removes an inhibitory phosphate group added earlier.
How does MPF (maturation promoting factor) prevent cytokinesis?
It phosphorylates inhibitory sites on myosin, which prevents cytokinesis. When MPF activity falls at anaphase, the inhibitory sites are dephosphorylated, and cytokinesis proceeds.
How is MPF (maturation promoting factor) deactivated?
When anaphase-promoting complex (APC) marks cyclin B (the cyclin of MPF) for degradation in a negative feedback loop. This begins shortly after the onset of anaphase.
What happens in the G1 checkpoint?
The G1 checkpoint (also called “restriction point” in mammalian cells) determines whether a cell will complete the cell cycle and divide, or else it will exit the cycle, switching into a non-dividing state called the G0 phase.
What has to happen in the G2 checkpoint?
Enough MPF (maturation promoting factor) must be produced
What happens in the M checkpoint?
Anaphase must wait for assembled sister chromatids
What does an important checkpoint in S phase do?
It stops cells with DNA damage from proceeding in the cell cycle
What is a growth factor?
A protein released by certain cells that stimulates other cells to divide.
What is density-dependent inhibition?
An external physical factor on cell division in which crowded cells stop dividing.
What is anchorage dependence?
A property most animal cells exhibit: to divide the cell must be attached to something (ex. like the inside of a flask or the extracellular matrix of a tissue)
What is transformation (in cells)?
When cells acquire the ability to divide indefinitely, causing them to behave in cell division like cancer cells.
What is aerobic respiration?
A catabolic pathway in which oxygen is consumed as a reactant along with organic fuel.
What is the overall process for aerobic respiration?
Organic compounds + oxygen -> carbon dioxide + water + energy
What does it mean if a substance is oxidized?
It loses electrons
What does it mean if a substance is reduced?
It gains electrons (its charge is being reduced)
What is an oxidizing agent?
The reactant that ends up accepting the electron. It oxidizes the reducing agent.
What is a reducing agent?
The react that ends up losing the electron. It reduces the oxidizing agent.
What is NAD+’s role in cellular respiration?
(nicotinamide adenine dinucleotide) It is an electron accepter and functions as an oxidizing agent (it becomes NADH). “Electron shuttle”
Where does glycolysis happen?
The cytoplasm. It can happen with or without oxygen.
Where does the citric acid cycle (Krebs cycle) happen?
The mitochondria
Where does oxidative phosphorylation happen?
The mitochondria
What is substrate-level phosphorylation?
ATP formed directly in a few reactions of glycolysis and the citric acid cycle (NOT oxidative phosphorylation)
What are the 2 phases of glycolysis? What are the products of glycolysis?
Energy investment and energy payoff. The cell uses 2 ATP in the investment phase but ends up generating 2 NADH, 2 Pyruvate, and 4 ATP in the payoff phase (net 2 ATP).
What happens in glycolysis?
Glucose first gets a phosphate attached to it (from one of the investment ATPs; makes it more chemically reactive). It then is converted to fructose (6-phosphate). Another phosphate gets attached to it (from the 2nd ATP), making fructose 1,6-biphosphate. The 6-carbon sugar molecule is then cleaved into two 3-carbon sugars: G3P and DHAP. G3P is used as soon as it forms and DHAP is converted into G3P (this equation never reaches equilibrium). G3P is then oxidized by the transfer of electrons to NAD+ forming NADH (two molecules). Using the energy from this exergonic redox reaction, a phosphate group is attached to the oxidized substrate making a high-energy product. One phosphate from this product (1,3-bisphosphate-glycerate) is transferred to ADP (substrate-level phosphorylation; this yields 2 ATP in total). At some point, a molecule called phosphoenol-pyruvate is formed. A phosphate group is transferred from PEP to ADP (forming in a total of 2 ATP molecules). This results in pyruvate being created (twice).
How is pyruvate converted into acetyl CoA?
CO2 is removed, and the remaining two-carbon fragment is oxidized, forming NADH from NAD+.
What is another name for the citric acid cycle?
The Krebs cycle
What are the inputs/outputs of the Krebs cycle?
CoA is the input, and 2 CO2, 3 NADH, 1 FADH2, and 1 ATP are produced.
How does the Krebs starts and end?
Acetyl CoA reacts with oxaloacetate to become citrate. After a series of reactions, products are released and oxaloacetate is the end result (ready to react with the next acetyl CoA).
Where is the electron transport chain located?
In the inner membrane of the mitochondrion in eukaryotic cells and the cell membrane in prokaryotic cells.
How many multiprotein complexes are involved in the electron transport chain in cellular respiration?
4
What happens in the electron transport chain (in cellular respiration)?
Electron carriers alternate between reduced and oxidized states as they accept and then donate electrons, releasing free energy at each step. The last electron carrier is oxygen (very electronegative).
What is the role of ubiquinone (Q) in the electron transport chain?
This small hydrophobic molecule is the only member of the electron transport chain that isn’t a protein/doesn’t belong to a protein complex. It acts as an electron transporter.
What are cytochromes (oxidative phosphorylation)?
An electron carrier with a heme prosthetic group (has an iron atom that accepts and donates electrons).
What is ATP synthase?
An enzyme that makes ATP from ADP and inorganic phosphate. It works like an ion pump running in reverse. ATP synthase uses the energy of an existing ion gradient to power ATP synthesis.
How does ATP synthase work to synthesis ATP?
The intermembrane space of the mitochondria has a high concentration of H+ ions. The H+ ions flowing down their gradient enter a channel in a stator (part of ATP synthase), which is anchored in the membrane. H+ ions enter binding sites within a rotor (another part of ATP synthase), changing the shape of each subunit so that the rotor spins within the membrane. Each H+ ion makes one complete turn before leaving the rotor and passing through a second channel in the stator into the mitochondrial matrix. The spinning of the rotor also causes an internal rod to spin, which activates catalytic sites on a knob below it that produces ATP from ADP and inorganic phosphate.
What is chemiosmosis?
The process in which energy is stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work.
How does the inner mitochondrial membrane/prokaryotic plasma membrane generate and maintain the H+ gradient that drives ATP synthesis?
The electron transport. The chain uses the exergonic flow of electrons from NADH and FADH2 to pump H+ across the membrane.
Per glucose molecule, how many ATP molecules are produced via oxidative phosphorylation and substrate-level phosphorylation? How many NADH and FADH2 molecules are produced by the end of the Krebs cycle?
4 ATPs by substrate-level phosphorylation (2 from glycolysis and 2 from the Krebs cycle), 26-28 ATP from oxidative phosphorylation. At the end of the citric acid cycle, either 8 NADH and 2 FADH2 are produced or 6 NADH and 4 FADH2 (6 NADH from the Krebs cycle, 2 FADH2 from the Krebs cycle, and 2 NADH from glycolysis which can be converted into FADH2).
What is the difference between fermentation and anaerobic respiration?
Anaerobic respiration uses the electron transport chain, while fermentation does not.
What is fermentation?
A way of harnessing chemical energy without cellular respiration.
How does fermentation generate ATP (generally)?
Substrate-level phosphorylation
What happens in alcohol fermentation?
Pyruvate (from glycolysis) is converted to ethanol (an alcohol) in two steps. CO2 is first released from pyruvate, and then the resulting product is reduced by NADH to ethanol. This generates the supply of NAD+ needed for the continuation of glycolysis. Many bacteria carry our alcohol fermentation under anaerobic conditions.
What happens in lactic acid fermentation?
Pyruvate is reduced directly by NADH to form lactate as an end product (no release of CO2). Human muscle cells utilize lactic acid fermentation when oxygen is scarce.
What are obligate anaerobes?
Organisms that carry out only fermentation or anaerobic respiration.
What are facultative anaerobes?
Organisms (including yeasts and many bacteria) can make enough ATP to survive using either fermentation or respiration.
What is deamination?
A process by which the amino groups of amino acids are removed.
What does beta oxidation do?
Breaks the fatty acids of fats down to two-carbon fragments, which enter the Krebs cycle as acetyl CoA.
