Bio 314 - Exam 1

Prokaryotic cells

small, bacteria + archaea, no membrane bound organelles, circular chromosomes in cytoplasm (nucloid)

Eukaryotic cells

large, animals, protists, fungi, plants, membrane bound organelles, chromosomes in nucleus

What do prokaryotic and eukaryotic cells have in common?

Both bound by a plasma membrane, both with DNA and ribosomes for gene exp.

plasma membrane

Controls what enters or leaves a cell, functions in cell-cell signaling and cell adhesion

mitochondria

Surrounded by a double membrane, generates ATP by oxidation of glucose and fatty acids

Lysosomes

Have acid lumen, degrade material internalized by the cell, worn-out cellular membranes, and organelles

nuclear envelope

A double membrane that encloses contents of the nucleus, outer nuclear membrane is continuous with rough ER

nucleolus

A nuclear subcompartment where most of cells rRNA is synthesized

nucleus

Contains DNA and proteins in eukaryotic cells, site of mRNA and tRNA synthesis

smooth ER

Synthesizes lipids and detoxifies certain hydrophobic compounds

rough ER

Synthesizes, processes, and sorts secreted proteins, lysosomal proteins, and certain membrane proteins

golgi complex

Processes and sorts secreted proteins, lysosomal proteins, and membrane proteins synthesized on the rough ER

secretory vesicles

Store secreted proteins and fuse with the PM to release their contents

peroxisome

Detoxifies molecules and breaks down fatty acids to produce acetyl groups for biosynthesis

cytoskeletal fibers

Form networks and bundles to support cellular membranes, organize organelles, and for cell movement

microvilli

Increase surface area for absorption of nutrients from surrounding medium

cell wall

Composed of cellulose, maintains plant cells shape and provides protection against mechanical stress

vacuole

Stores water, ions, nutrients, degrades macromolecules, and functions in cell elongation during growth

chloroplasts

Carry out photosynthesis, surrounded by a double membrane and contain a network of internal membrane-bounded sacs

plasma membrane

mitochondria

lysosomes

nucleolus

smooth ER

rough ER

golgi complex

secretory vesicles

peroxisomes

microvilli

chloroplasts

phosphatidylethanolamine

phosphatidylserine

phosphatidylcholine

sphingomyelin

visible light

radiation source and most limiting factor in a light microscope

limit of resolution

the separation that occurs at which the specimen becomes blurry, depends on wavelength and numerical apperature

bright field microscopy

light passes through a cell and forms the image directly

dark field microscopy

Oblique light is angled to not pass through the objective. Low density areas (cytosol) don’t scatter light, high density areas do and appear bright

Phase contrast and differential-inference contrast

Low density areas remain in phase to appear brighter, high density areas deviate waves to appear darker

fluorescent molecules

absorb light at a specific wavelength and emit it at a lower frequency. Used to detect specific proteins and target molecules

Indirect immunohistochemistry

Primary antibodies bind to a specific antigen, and secondary antibodies tagged with fluorescence amplify the signal by binding to primary antibodies

confocal microscopy

Focuses a laser onto a specific point at a specific depth to photograph a given plane, software compiles images to produce a clear “optical section”

Transmission electron microscope

Electrons pass through specimen to view intracellular structures, samples exposed to vacuum, samples dehydrated, permeated with monomeric resin, sliced with ultramicrotome, and covered with heavy metal salts or immunogold

scanning electron microscope

Electrons reflect off specimen to produce 3D structure of specimen surface, specimens are dried and prepped with thin layer of heavy metals. Smaller, simpler, and cheaper than TEM

glycero-phospholipids

p-ethanolomine, p-serine, p-choline

sphingolipids

sphingomyelin

glycolipid

a sugar containing lipid found facing the ECF, involved in cell recognition like blood type

cholesterol

Found 1:1 with phospholipids in PM, amphiphilic and rigid rings decrease fluidity

Why is it important for the plasma membrane to be asymmetrical?

The intracellular layer has more negatively charged lipids, and during apoptosis the bilayer flips to move (-) charges outside the cell

lipid raft

concentrated areas of specific lipids and proteins used for signaling

lipid droplet

stored excess neutral lipids formed from the smooth ER that sit in the cytoplasm until needed

What makes an amino acid?

R-group, amino group (H3N), carboxyl group (COO-), hydrogen around an alpha carbon

peptide bond

dehydration rxn that bonds AAs

What bonds do AA side chains form?

Noncovalent bonds- H bonds, electrostatic attraction, or Van der Walls forces

Main protein folding patterns

a helix and b-sheet, bonds are between AA backbone

transmembrane proteins

amphiphilic and extend through bilayer, single pass, multi-pass, beta barrel

integral membrane proteins

Don’t pass through the bilayer, anchor in membrane via a-helix, GPI, or lipid anchor (covalent bond w/lipid)

peripheral membrane proteins

Don’t enter membrane, non-covalent interactions

hydropathy phot

Use protein sequences to predict hydrophobic membrane spanning regions, only works for a-helices

hydropathy index

How much it takes something hydrophobic to go into water, plotted against AA #

glycosylation

Sugar residues get attached to proteins to protect from chemical/mechanical damage or prevent cell-cell interaction

detergents

Disrupt hydrophobic interactions to degrade the PM and allow proteins to be solubilized and purified

Membrane transporters

• Exposed to one side of the membrane at a time

• strong interaction with substrate

• energetically active/passive transport

Channel proteins

• Exposed to both sides of membrane

• weak interaction with substrate

• only passive transport (faster)

What drives passive transport?

The solutes electrochemical gradient

What cells have the highest permeability in the membrane?

hydrophobic molecules and small uncharged polar molecules

What cells have the lowest permeability in the membrane?

large uncharged polar molecules and ions

What factor influences solute transport?

Membranes have electrical potentials that favor influx of (+) ions and oppose (-) ions

transporter saturation (Vmax)

max rate of transport, speed transporter can flip b/t conformation states

transporter affinity (Km)

affinity of transporter to a solute

transporter abundance

alterations in the amount of transporters in the membrane

coupled transporter

Use energy from electrochemical gradient to transport a solute actively, only change conformation when both binding sites are full

ATP-driven transporters

Pump solutes across membranes through hydrolysis of ATP, p-type pumps and ABC transporters

Pathway of p-type pumps

1. Substrate binds to open transporter

2. ATP transfers P, forms ADP

3. 2nd conformation change

4. Substrate leaves transporter

5. Removal of P resets pump to original conformation

P-type: Ca2+ pump

Actively holds Ca concentrations low in the cytoplasm to allow for rapid influx of Ca from ECF

P-type: Na+/K+ pump

Maintain steep concentration gradients of Na and K, is electrogenic (allows uneven mov’t of charges)

ABC transporter

Transport a huge variety of substrates, have 2 ATP binding cassettes on the cytosolic side of membrane

ion channels

Only passive transport, control ion specificity with selectivity filter (accounts for ion size and charge)

membrane potential

Difference in electrical charge on two sides of a membrane (mV), created by Na/K pumps

Measuring membrane potential w/whole cell

Record electrical currents through multiple ion channels

Measure membrane potential w/patch clamp

Record electrical current from ion flow through one singular ion channel

Mechanically gated channels

Respond to physical touch. Ex. in animals a sensation or change in blood pressure, in plants respond to mechanical stretching for turgor pressure regulation

Ligand and voltage gated channels

A ligand gated channel is amplified by a voltage gated channel until the ligand is released

voltage gated channel

generates action potentials, a traveling wave of electrical excitement triggered by depolarization

Mechanism of voltage-gated channel

1. channel is closed, membrane depolarization is detected via voltage sensors

2. a local change occurs and gate opens

3. Na+ flows in causing changes in other channels until inactivation gate closes

4. membranes repolarize through voltage-gated K+ channels

5. return to resting membrane potential

Charge of ions in ECF

Na+=145mM, Mg2+=1-2mM, Ca2+=1-2mM, Cl=110

Charge of ions in ICF

K+=140mM

cytosol

The site of protein synthesis and degradation

Proteins: Gated transport

cargo moves through gates b/t two spaces w/the same composition

Protein translocation

Proteins move from cytosol into something w/a distinct composition (crossing a membrane)

vesicular protein transport

Proteins start in ER and go to other parks of the endomembrane system

How do proteins get sorted?

Receptors recognize a sorting signal (AA sequence) and guides proteins to their target

nuclear pore complexes (NPCs)

Gates in the nuclear envelope made of nucleoporins, lined with FG motifs that regulate what goes through

Ran GTPase

Molecular switch localized in the nucleus that changes form when bound to GTP or GDP nucleotides

Function of Ran GTPase

1. Nuclear protein in cytosol binds to importin receptor and moves through nuclear pore

2. Ran GTP binds to importin receptor to cause unloading of protein

3. Protein falls off and is discharged in the nucleus

4. Importin-Ran GTP complex goes back out to the cytoplasm

5. Cytosolic GAP hydrolyzes Ran GTP to Ran GDP

6. Ran GDP and importin dissociate

GTPase activating protein (GAP)

Transforms GTP→GDP

Guanine exchange factor (GEF)

Transforms GDP→GTP