Bio1113 Exam 2

Prokaryote

organisms that do not contain a nucleus, and USUALLY do not contain any membrane bound organelles. Bacteria/archae

Eukaryotes

contain a nucleus and membrane bound organelles. Eukarya

How do eukaryotes overcome the lower SA/volume ratio caused by their larger size?

Compartmentalization (membrane bound organelles)

Nucleoid Region

the region of a prokaryotic cell where the singular circular chromosome is located

Plasmids

Small circular DNA molecules in prokaryotic cells. Contain “extra” info like resistance to certain poisons

How does DNA fit into a prokaryotic cell?

It is supercoiled

Prokaryotic Cell Wall

Protects cell from bursting. In bacteria, it is made of peptidoglycan.

Prokaryotic Flagella

Made of proteins. A molecular motor makes it rotate to propel the cell through water

Fimbria

Many, small, needle like. Helps cells stick to other cells or surfaces

Pili

Longer and fewer than Fimbria. Connect cells so plasmid DNA can transfer

Nucleus

Nuclear envelope, chromosomes, nucleolus, nuclear lamina. Function: info storage and transmission

Nuclear Membrane

double membrane with nuclear pores

Chromosomes

DNA and proteins. Loosely (light) and densely (dark) packed regions in the nucleus

Nucleolus

rRNA synthesis and ribosome subunit assembly (basically, makes ribosomes)

Nuclear Lamina

meshwork of lamin proteins (intermediate filaments) that supports the envelope.

Ribosomes

Non-membrane bound. Function: protein synthesis. Found in cytosol, attached to rER, or inside mitochondria/chloroplasts. In eukaryotes and prokaryotes.

Rough Endoplasmic Reticulum (rER)

Synthesizes proteins for export, membranes, or other organelles. Lumen is continuous with the nuclear envelope.

Smooth Endoplasmic Reticulum (sER)

No ribosomes. Synthesizes and modifies lipids, stores calcium ions, detoxifies compounds

Golgi apparatus

Stacks of flattened sacs (Cisternae). Has a cis (rER) and trans (external) face. Processes proteins, lipids, and carbohydrate groups. Sorts products for destinations.

Lysosomes

contain acid hydrolases (enzymes that break down molecules by hydrolysis). Proton pumps keep the lumen ~pH 5. Function: digestion and recycling. ANIMAL CELLS ONLY.

Receptor Mediated Endocytosis

Uses receptors to bring macromolecules into a cell in a vesicle that is pinched of from the plasma membrane. Brings them to lysosome

Phagocytosis

Brings smaller cell or food particles into cell by pinching off part of the plasma membrane into a phagosome. Delivered to lysosome

Autophagy

Encloses a damaged organelle within a membrane into an autophagosome, delivers to lysosome

Peroxisomes

detox/break down molecules. Break down fatty acids and other compounds using redox rxns, producing hydrogen peroxide that is then broken down by the enzyme catalase

Mitochondria

Double membrane. Inner membrane folds into cristae. The space inside is called the Mitochondrial Matrix. Contain their own circular DNA and ribosomes.

Vacuoles

Plants and fungi only! Functions: storage, turgor pressure, digestion(using hydrolases just like a lysosome).

Chloroplasts

Double membrane w/ internal membrane sacs (Thylakoids) stacked into grana. Function: photosynthesis. Have their own circular DNA and ribosomes.

Plasma Membrane

All cells! Phospholipid bilayer w/ proteins. Selectively permeable.

Cell Wall

Plants: cellulose, fungi: chitin, bacteria: peptidoglycan. Protein and structural support

Extracellular Matrix (ECM)

Animal cells have this instead of a cell wall. It’s like a gel with rebar running through.

Nuclear Pore Complex

Regulates nuclear transport. Small molecules move freely. Larger molecules need Nuclear Localization Signal (NLS) or Nuclear Export Signal (NES) to enter/exit.

Kinases

Add a phosphate group

How are proteins targeted to the rER?

ER signal sequence binds with a Signal Recognition Particle (SRP), which pauses synthesis, docs at a receptor, and lets the protein enter through a translocon.

What happens in the rough ER?

Chaperones assist with the start of protein folding. Glycosylation begins for some proteins (carb groups added). Then, folded proteins are sent to the golgi.

What happens in the golgi?

Vesicles bring proteins into the cis face. Carb groups are modified as proteins move through the cisternae. In the trans cisterna, proteins are sorted by binding to their specific receptors. Transport vesicles bud off and carry the proteins to their destinations.

Where can proteins go after the golgi body?

Plasma membrane/secretion (default), to lysosomes (Mannose-6-Phosphate Tag), or to other organelles (other sorting signals).

What is the secretory pathway?

Protein enters rER, vesicle, golgi, vesicle, plasma membrane, secreted.

Actin Filaments (microfilaments)

2 coiled strands made of actin with a + and - end. Cell shape, move cells, divide animal cells in two, move organelles in eukaryotes.

Intermediate Filaments

Fibers wound into thicker cables. Subunits are lamins, keratins, etc. cell shape, anchor some organelles

Microtubules

Hollow tubes with a + and - end. alpha and beta tubulin dimers. cell shape, move cells via flagella or cilia, move chromosomes during division, tracks for intracellular transport (w/ ATP and motor proteins).

Myosin

Motor protein involved in actin-myosin movement.

Actin Myosin movement

Myosin head binds actin, uses ATP, and pulls the filament. Muscle contraction, cell crawling, cell division, moving cytoplasm in plants.

Kinesins

Microtubule motor proteins. “walk” towards the plus end

Dynein

Microtubule motor protein. “walks” toward the minus end

Cell Junctions

Protein structure that joins two adjacent cells. Seal, hold together, or open a route.

Tight Junction

Stitch two plasma membranes together using claudins and occludins. Water tight! Good for linings or walls.

Desmosomes

Bind cells in the space between them, like a rivet. Cadherins cross the gap, Plaque Proteins anchor inside and bind to intermediate filaments to link the two cytoskeletons. Good for areas where tissue s pulled (like heart, skin, muscle).

Gap Junctions

(animals) Membrane proteins line up to form an open channel. 6 connexins form 1 connexon. 2 connexons from adjacent attach to make the channel. If the cytoplasms fuse outright, forming a mass of one cytoplasm with many nucleii called a syncytium.

Plasmodesmata

(plants): a pore through both cell walls, with a tubule of ER connecting the two cytoplasms. The connected cytoplasm is called a symplast

Autocrine Signaling

Cell releases a signal and receives it, self signaling

Paracrine Signaling

Signal diffuses a short distance away to nearby cells

Endocrine

Signal travels in the bloodstream to distant tissues

Ligand

signal molecule

Receptor

protein that the Ligand bonds to

What are the four steps of cell-cell signaling

Reception, signal transduction (message relayed and amplified in cell), Response, Deactivation

How do lipid-soluble signals get recieived?

Cross the plasma membrane on their own. Receptor is in the cytosol, and NO TRANSUCTION STEP IS NEEDED

How are lipid-insoluble signals get received?

Receptor is a transmembrane protein that changes shape to convert the signal to a signal inside the cell (signal transduction), the signal is then amplified.

G-Protein Coupled Receptor

The receptor causes the G-Protein to get activated (GDP→ GTP), and then split in two. Activated G Protein switches on an enzyme that makes a second messenger

Second Messenger

Small molecule that carries a signal through the cytosol. Examples Cyclic Adenosine Monophosphate (cAMP) and Calcium Ions.

Phosphorylation Cascade

activated Ras starts a chain where each kinase phosphorylates and activates the next. Each step costs ATP and amplifies

What are the two response options for a signal

Change in gene expression (binding to DNA and altering transcription) OR change in the activity of proteins the cell already has

Phosphatases

Remove phosphate groups

Crosstalk

signal pathways interact, so one pathway can block or boost a step in another

Enthalpy

total energy of a moleculre (dH).

Exothermic

-dH

Endothermic

+dH

Entropy (dS)

Measure of disorder

2nd law of thermodynamics

total entropy (rxn and system) always increases

Gibbs Free Energy

Total energy available to do work. dG = dS - T*dH

Endergonic

+dG

Exergonic

-dG

Redox Rxns

Transfer of electrons OIL RIG

ATP Hydrolysis

Transfer of a phosphate group

What are the 2 important electron carriers that facilitate redox rxns

FAD (gets reduced to FADH2), NAD+ (gets reduced to NADH)

How can you increase the speed of a reaction?

Increase temp, increase concentration of rxns

Catalyst

Speeds up a chemical rxn without getting used up in the process

Substrates

Enzymatic reactants

Where do substrates bind?

Active Site

What do enzymes change? What do they NOT change?

Enzymes lower Energy of Activation, but DO NOT change Gibbs Free Energy

What are the 3 steps of an enzyme-catalyzed rxn

initiation, Transition State Facilitation (lower Ea),Termination

Induced Fit

Enzyme changes shape when substrates bind (this shape change brings reactants close together)

Why does the rate of a catalyzed rxn plateau? How could you increase the max speed?

The plateau happens because all the enzymes are busy. To increase max speed, add more enzyme.

What determines the optimum temp and pH of an enzyme?

The conditions that the organism containing the enzyme lives in

Competitive Inhibition

Other molecules compete for the active site of the enzyme

Allosteric Activation/Inhibition

Something binds to a non-active site location on the enzymes, activating or inhibiting its function.

Feedback Inhibition

The product of a pathway inhibits an enzyme earlier in the pathway. typically allosteric

Catabolic Pathways

Break down molecules, usually release energy

Anabolic Pathways

Synthesize molecules, typically require the input of energy

Cellular Respiration

A set of catabolic pathways that oxidize organic molecules, such as glucose, to release their stores energy. Glycolysis, Pyruvate Processing, Citric Acid Cycle, ETC and OXPhos

Aerobic Respiration

Cellular Respiration that uses oxygen as the final electron acceptor

Anaerobic Respiration

Cellular Respiration that uses something other than oxygen as the final electron acceptor

Glycolysis

Glucose goes in. ATP, NADH, Pyruvate go out. Happens in the cytosol.

Pyruvate Processing

Pyruvate goes in, Acetyl CoA, NADH, and CO2 go out. Mitochondrial Matrix

Citric Acid Cycle

Acetyl CoA goes in, CO2, NADH, FADH2, and ATP go out. Happens in the mitochondrial matrix

ETC and OxPhos

Electrons (NADH, FADH2), O2 go in, ATP and H2O go out. Happens in inner mitochondrial membrane

Substrate Level Phosphorylation

Enzyme transfers a phosphate group from a phosphorylated substrate to ADP to make ATP. Happens in glycolysis and oncer per turn of the cytric acid cycle. Most ATP is NOT made this way (it’s made during OxPhos)

“energy investment” glycolysis

The first 5 steps. ATP is used

What regulates glycolysis?

Phosphofructokinase. Catalyzes rxn 3, which is the committed step. PFK has two ATP binding sites, an active site and a regulatory site. Feedback Inhibition by allosteric regulation.

How does Pyruvate Processing work?

Pyruvate dehydrogenase in the matrix! 1C goes to CO2, NAD+ gets reduced to NADH, remaining 2C acetyl group to coenzyme A to make acetyl CoA.

How many times does the citric acid cycle turn per glucose?

twice