Principles of Bio Test 2 Review

What sort of range of object sizes is a light microscope good for?

Light Microscopes are good to visualize structures down to micron (10-6m) range. Can see eukaryotic cells, many organelles, especially with fluorescence. Prokaryotic cells generally appear as dots.

What are the limits to visualization?

Limits imposed by wavelengths of visible light: can only resolve structures down to λ2 size.

What tools are used to visualize smaller objects, and what size range of objects do they visualize?

Smaller bacteria, viruses, & macromolecules require electron microscope: beam of electrons focused by magnets. Structures on atomic scale visualized & manipulated using an atomic force microscope.

What is the difference between SEM and TEM?

Scanning electron microscopy (SEM)

Transmission electron microscopy (TEM)

Why would you want to use stains for light microscope use?

To enhance visualization of the cell or certain cellular components under a microscope

What does cell fractionation do?

Allows study of macromolecules & organelles: may still be biologically active. Biochemical analysis possible via fractionation

What structures are present in bacteria?

Bacterial cells lack internal membrane bound organelles: surrounded by a plasma membrane, usually a cell wall, and often a capsule.

The single bacterial chromosome is usually a closed circle collected in a bundle called a nucleoid found in the cytoplasm. Ribosomes also in the cytoplasm. Locomotion may involve flagella, structures extending out of the cell completely unlike eukaryotic flagella.

What imposes limits to cell growth?

SA/V ratios impose a limit to growth: intake of nutrients and excretion of waste all have to take place across the plasma membrane. This is why cells are generally microscopic. More efficient eukaryotic cells are generally larger than prokaryotes. If a cell is to grow past these limits it must reproduce in order to do so.

What are the organelles found in both plant and animal cells, and which are unique to each?

Both: Nucleus, cell membrane, ER, mitochondria, and cytoplasm

Plant: chloroplast, cell wall, and vacuole

Animal: centrioles

Where are ribosomes found?

Found in prokaryotes & eukaryotes: not membrane bound

Simpler in prokaryotes

Found in cytoplasm; also embedded on the surface of the rough endoplasmic reticulum of eukaryotes

Also found in chloroplasts & mitochondria: prokaryote-like

What do ribosomes do?

Main function is making proteins

What is the nuclear envelope, nuclear matrix, nucleoplasm, nuclear lamina, what are nuclear pores?

Nucleus: defining organelle of eukaryotes: cell 'command center'

Genetic information (DNA) mostly resides here in the form of chromosomes

Surrounded by 2 membranes, the nuclear envelope, pierced by nuclear pores that regulate transport

Nucleoplasm organized by nuclear matrix, a webwork of filamentous proteins that attach to nuclear lamina on the inner nuclear membrane

What is the function of smooth ER? Rough ER?

Rough ER: extends from outer nuclear membrane: studded with ribosomes performing protein synthesis. Also manufactures phospholipids, which along with membrane proteins are used to expand cellular membranes

Smooth ER: Smooth ER synthesizes lipids & steroids. Also involved in detoxifying alcohols, drugs & other poisons Smooth ER also can function as a storage compartment for calcium, which is then released into the cytoplasm in response to various signals to trigger further events.

What does the Golgi Apparatus do?

Receives vesicles from the ER: finishes modifications on proteins (processing glycoproteins bound for the plasma membrane or secretion, e.g.) & ships vesicles off to various endomembrane system destinations via micro tubular transport.

What are lysosomes?

Contain hydrolytic enzymes: used for

- Digesting phagocytosed food

- Autophagy (cellular 'recycling' of damaged organelles)

- Apoptosis (programmed cell death)

What is phagocytosis?

Process by which certain living cells called phagocytes ingest or engulf other cells or particles

What is the tonoplast?

A single membrane that bounds the vacuoles and separates it from the cytoplasm- plant cells

The central vacuole?

Holds internal cell sap under pressure, keeping plant cells rigid: turbot pressure. Often majority of interior of cell. Surrounded by a membrane called the tonoplast.

Serves as storage for organic compounds (proteins, etc) inorganic ions, also can be a dump for toxic metabolic byproducts, contain pigments for non-green colored plant parts, contain antifeedants to discourage predators as well

Provides force (turgor pressure again) that helps cell expand during growth

Turgor pressure?

The force within the cell that pushes the plasma membrane against the cell wall

Food vacuoles?

Essentially the lysosome; membrane-bound organelle associated with a digestive function. They process the digestive enzymes that help with the breaking down of nutrients

What is in the endomembrane system of the cell?

A group of membranes and organelles in eukaryotic cells that works together to modify, package, and transport lipids and proteins

What is the plasma membrane made of?

lipids and proteins

What are mitochondria?

Main ATP production site in cell: cells with higher energy needs to have more & larger mitochondria.

Contains its own ribosomes & DNA in the matrix for some of its proteins: similar to prokaryotic ribosomes & DNA, as is the inner membrane. Believed to be once free-living alpha-proteobacteria, engulfed by early eukaryote: symbiotic relationship where nutrients & protection were exchanged for the much more efficient ATP production of aerobic metabolism. No longer free living: an endosymbiont.

Chloroplasts?

Like mitochondria, also an endosymbiont, descended from cyanobacteria. Has own DNA & ribosomes in the stroma, also prokaryotic-like.

Uses light energy to make ATP in plants & algae through complexes embedded in the thylakoid membranes, which are assembled into stacks called grana.

Also fixes & reduces CO2 to useful sugars via enzymes in the stroma.

Non-photosynthetic chloroplasts called plastids.

What is the endosymbiont theory and what sorts of evidence do we see to support it?

Theory: The mitochondria and chloroplasts in eukaryotic cells were once aerobic bacteria (prokaryotic) that were ingested by a large anaerobic bacteria (prokaryotic)

Evidence: membranes (double membrane bound) Antibiotics & Division (mode of replication)

What is the matrix?

Ground substance that occupies spaces, especially between the cell or the inside of cell organelles

What are cristae?

Folds in the inner mitochondrial membrane. Major function is to increase the surface area of the mitochondrial membrane.

What are grana and thylakoid membranes?

Internally bound membranes are known as thylakoids, which are arranged in stacks called grana

Where are grana and thylakoid found?

Plant cells

What is the stroma?

The fluid filling up the inner space of the chloroplasts which contain the grana and thylakoids

What are peroxisomes and what do they do?

Like mitochondria & chloroplasts not part of the endomembrane system: grow & divide in cytosol.

Manufacture & degrade H2O2 (peroxide): needed for certain chemical reactions but destructive, compartmentalized to peroxisome.

Also break down long chain fatty acids & help with detoxification

What is the cytoskeleton, what are the 3 components of it, and what monomers are they each made of?

Cytoskeleton: Network of proteins that form the internal framework of the cell

3 components include: Microtubules (tubulin), Microfilaments (actin), and intermediate filaments (keratin)

What do microtubules do?

Maintain cell shape

Cell mobility

Chromosome movement in cell division

Organelle movements

What are motor proteins (kinesin and dynein)?

Motor proteins can also move entire organelles. Two major motor proteins: kinesin & dynein, which more along microtubules in opposite directions, powered by ATP

What is the structural organization of cilia and flagella?

Flagella (few or one) & cilia (usually many) are static arrays.

What are microfilaments involved in and what is myosin?

Subunits made up of actin monomers that polymerize into filaments involved in cell shape & movement

Some arrays are static (muscle), others more dynamic with Microfilaments assembling where needed: amoeboid movement, cytoplasmic streaming, cleavage furrow formation in cytokinesis dynamic.

Act in concert with another filament forming protein, myosin, which converts ATP into motion when it attaches to actin filaments & slides filaments past each other

What is a primary plant cell wall? Secondary? Middle lamella? Plasmodesmata?

mixture of cellulose, other polysaccharides, & proteins: cellulose synthase (an enzyme) lays down cellulose directed by microtubules.

Primary wall laid down first

Middle lamella rich in pectins, sticky polysaccharides that hold cells together.

Rigid secondary walls may be laid down between plasma membrane & primary membrane & primary wall after the cell stops growing, or the primary wall may be reinforced. Plasmodesmata connect plant cells

What kinds of junctions attach animal cells

Tight Junctions

Desmosomes

Gap Junctions

What does each kind of junction do?

Tight: form watertight seals

Desmosomes: attach cells to each other strongly

Gap junctions: pass electrical currents from cell to cell

What sorts of molecules comprise the animal extracellular matrix?

proteoglycans, proteins such as collagen and elastin, extracellular vesicles, hyaluronic acid, fibronectins and glycoproteins.

What are cell membranes made of?

Lipids

Proteins

Also a role for carbohydrates attached to both

What are cell membranes made of?

phospholipids and proteins

What is a phospholipid?

a lipid containing a phosphate group in its molecule membrane lipids are dominated by these. main component of cell membrane

Sphingolipids

Lipids with sphingosine or sphenoid backbone. Many are phospholipids but others can for glycolipids by making glycosidic bonds with sugars. - maintains the structural integrity of our cell membrane

amphipathic

having both a hydrophilic region and a hydrophobic region

Cholesterol

- helps keep membrane at a low temperature/ more stable at high temperature - plugs gaps in membrane, making a tighter barrier

Saturation

more stable/ less fluid

fluid mosaic model

model that describes the arrangement and movement of the molecules that make up a cell membrane

what regulates cell membranes fluidity temperature

cholesterol, fatty acids in the phospholipids that form cell membranes

integral membrane proteins

proteins that are at least partially embedded in the plasma membrane- may be anchored or span the membrane

peripheral membrane

temporarily attached to the membrane through non covalent bonds with membrane components ALSO dont enter bilayer

membrane -associated proteins

may act as recognition molecules or enzymes - proteins being associated or attached to the membrane of a cell or organelle inside the cell

where is membrane synthesized

the ER

passive transport

the movement of substances across a cell membrane WITHOUT the use of energy by the cell

active transport

the movement of substance across the cell membrane that requires the cell to use energy

Diffusion

Movement of molecules from an area of higher concentration to an area of lower concentration.

osmosis

diffusion of water - movement of solvent particles across a semipermeable membrane from a dilute solution into a concentrated solution

simple diffusion

across a membrane movement of a solute from an area of high concentration to an area of low concentration

facilitated diffusion

- Movement of specific molecules across cell membranes through protein channels- transporter aids the substance to cross the membrane

transport proteins

allows for selective passage of specific molecules from the external membrane

Hypertonic

lower concentration of fluid, sugars, salt than blood

hypotonic

higher concentration of fluid, sugars, salt than blood

Isotonic

similar concentration of fluid, sugars, salt than blood

membrane potential

The voltage across a cell's plasma membrane.

electrochemical gradient

combination of chemical and electrical difference across the membrane

sodium-potassium pump

active transport in animal cells burns 1 ATP to pump 3 NA+ out of the cell and +2K+ in both against concentration gradient generates bulk of voltage

electrogenic pumps

main voltage generating pumps for plants, fungi, bacteria,

pumps H+ out of cells

Contransport

a single ATP-powered pump that transports a specific solute can indirectly drive the active transport of several other solutes in a mechanism

(basically 2 things being moved at once)

3 types of endocytosis

phagocytosis, pinocytosis, receptor-mediated endocytosis

Phagocytosis

large items engulfed (example: bacteria)

Pinocytosis

-process by which a cell takes in liquid from the surrounding environment

-smaller items (such as molecules)

receptor-mediated endocytosis

specific molecules are taken in after they bind to a receptor and then internalized

What are catabolic pathways?

Catabolic pathways break down complex molecules to simpler compounds, releasing energy

What are anabolic pathways?

Anabolic pathways build complex molecules from simpler ones, using energy (often in catabolism)

What is bioenergetics?

Bioenergetics: the study of how organisms manage energy resources & transform or transfer energy, the power to do work

What is the 1st of Thermodynamics?

1st Law: energy can neither be created nor destroyed

What is the 2nd Law of Thermodynamics?

2nd Law: Everytime energy is converted there is an increase in the randomness entropy of the universe

What is entropy?

The measure of a system's thermal energy per unit temperature that is unavailable for doing useful work

What do exergonic/spontaneous and endergonic/nonspontaneous mean?

If free energy is released by a chemical reason (products have less energy than reactants) that reaction is said to be exergonic & spontaneous.

In a spontaneous reaction free energy remaining in the system decreases.

If free energy required to make reaction occur (products have more energy than reactants) reaction is endergonic & non spontaneous)

What is total energy?

Total energy: enthalpy; energy free to do work

What is free energy?

Energy free to do useful work: power life functions

How are total and free energy related?

Total energy is all of the energy you personally have available, free energy is the amount of energy able to do work.

What is the free energy at equilibrium?

At equilibrium ΔG = 0.

What is the main energy coupling molecule of the cell?

ATP, adenosine, Tri phosphate, is the molecule that does the most cellular reactions

What do enzymes do?

Enzymes allow reactions to occur at life-useful rate

What is activation energy?

The amount of energy needed to initiate a reaction

What is the active site of an enzyme?

The part of the enzyme where the substrate binds

How does the active site work?

The active site binds the substrate it is given and orients it for catalysis

What is the induced fit model?

Enzyme changes shape so that its active site enfolds the substrates

how to remember redox

LEO says GER- Loss of Electrons is Oxidation

Gain of Electrons is Reduction

Reducing agent: electron donor

Oxidizing agent: electron acceptor

What is kinetics?

The study of the chemical reactions that are catalyzed by enzymes

What effect do pH and temperature have on enzyme activity?

Temperature: higher temperature, faster molecular motion, more collisions, faster reaction... to a point where the enzyme denatures & rate -> 0. Fever.

PH: narrow optimum range- remember active site uses polar/charged amino acids

What is a competitive inhibitor?

Competitive inhibitors resemble substrates, competing for active sites. Can overcome with more substrate, easily reversible.

A noncompetitive inhibitor?

A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its conformation so that it no longer binds to the substrate.

What is allosteric regulation?

Regulation where the regulatory molecule (an activator or inhibitor) binds to an enzyme someplace other than the active site

An allosteric site?

The site that allows molecules to either activate or inhibit (or turn off) enzyme activity

Can allosteric regulation also turn an enzyme's activity on?

Yes- it can enhance or reduce enzyme activity

What is cooperativity?

Another type of allosteric activation

Feedback inhibition?

End-product inhibition.

Noncompetitive allosteric regulation where end product of pathway allosterically regulates enzyme in pathway for which it isn't substrate or product, usually enzyme near start of pathway

What cellular process produces partial catabolism?

partial catabolism can occur in the absence of oxygen via fermentative pathways: glycolysis is a fermentative pathway.