1. all organisms made of cells

2. cells are smallest unit of life

3. new cells only come from old cells dividing

magnification

resolution

contrast

1. light

2. electron

plant and animal cells (most)

nucleus

most bacteria

mitochondria

smallest bacteria

viruses 

ribosomes

proteins

lipids

transmission (TEM)

scanning (SEM)

you slice your sample into thin slices, then stain it with heavy metal, then shoot beam of electrons at it. 

some electrons are scattered (when hit metal), others are transmitted thru sample. 

--> forms an image, shows you cell ultrastructure

sample is coated with heavy metal

beam of electrons scans surface, creating 3d image

--> shows contour

1. prokaryotes

2. eukaryotes

lack membrane enclosed nucleus (genomic DNA of cell is in cytoplasm)

either bacteria (abundant, most not harmful) or archaea (in extreme environments) 

plasma membrane (barrier) 

cytoplasm inside plasma membrane (contains organelles and DNA which is circular in bacteria)

nucleoid (where genetic material is found)

ribosomes (found throughout) 

bacterial chromosomes- generally tethered to inside of cell

plasmids- free within the cytoplasm

cell wall (for support and protection)

glycocalcyx- (saccaride coat on outside) traps water preventing dehydration, provides protection, esp against immune system

appendages- pilli (attachment) and flagella (for locomotion) 

cytosol is central coordinating region for many metabolic activities of eukaryotic cells

takes place in ribosome

polypeptide synthesis- mRNA come here, the tRNA bring the amino acids. the rRNA (two subunits) facilitate

3 different types of protein filaments

1. microtubules

2. intermediate filaments

3. actin filaments

long hollow cylindrical structures that have dynamic instability

help with cell division, mobility (compose flagella), transport (can interact w/ proteins that help move things intracellularly) 

twisted filament (ropelike) with staggered alignment of filament proteins (multiple component proteins)

helps with cell shape, mechanical shape, anchorage of cell and nuclear membranes

ion electrochemical (both electrical and chemical gradient)

transmembrane (concentration of a solute on either side) 

diffusion across the plasma membrane: what is v. permiable? 

less so? 

not at all?

v. permiable: gases, v. small uncharged polar molecules

medium: water, urea, glucose

not at all: ions, macromolecules, ATP

properties of amino acids lining inside of channel

inside: hydrophylic (otherwise ions couldn't cross into it)

outside: non-polar (they are associating with phospholipid tails) 

Aquaporins are proteins embedded in the cell membrane that regulate the flow of water.

Aquaporins are integral membrane proteins

Vacuoles are sacs within the cell made out of the same material as the cell membrane. That's because vacuoles are usually formed by budding off of the membrane. Vacuoles may contain large food particles, enzymes, water, or many other substances. Autotrophic cells, which require a great deal of water, often have one large vacuole filled with water. On the other hand, animal cells do not usually have very large vacuoles.

Vesicles is a term given for very small vacuoles. Often vesicles are formed at an organelle known as a Golgi body in order to carry protein molecules either to other organelles or to the cell membrane.

1. uniporter- single molecule or ion

2. symporter/co-transporter- 2 or more ions of molecules transported in same direction

3. antiporter- 2 or more ions or molecules transported in opposite directions

1. primary- using a pump and energy directly to transport solute

2. secondary- using pre-existing gradient to drive transport of solute

amino acids

made up of an amino group (NH2), a carboxyl group (COOH), and a side chain R- all attached to a central carbon

2ndary: hydrogen bonding between amino and carboxyl groups

3rdary: attractions/repulsions between side groups of amino acids

Amino acids are joined together by a peptide bond. It is formed as a result of a condensation reaction between the amino group of one amino acid and the carboxyl group of another.

interactions between the side chains of the distinct amino acids

includes hydrophobic and ionic interactions, hydrogen bonds, covalent cross links, disulfide bridges.

phospholipid bilayer

peripheral, intergral, and transmembrane proteins

head is hydrophillic (so is water soluble)

head is hydrophobic (so is water insoluble)

active (against an existing gradient; requires energy)

passive (moves according to gradient of its concentration or according to molecular charge; requires no energy)

1. integral or intrinisic membrane proteins

2. peripheral or extrinsic proteins

1. transmembrane

2. lipid anchored

one or more regions are physically embedded in the hydrophobic region of the phospholipid bilayer

-the amino acids of the proteins in the middle are hydrophobic to be able to interact with the hydrophobic phospholipid tails they are stuck to

-the amino acids on the outer edges of this protein are hydrophillic (interact with the aqueous enviroment on either side of the membrane)

non-covalently bound either:

-to regions of integral membrane proteins coming out of the membrane

-to the polar head groups of phospholipids

cholesterol tends to stabalize membranes but depends on temperature

-in colder environments, cholesterol keeps membrane from geling

-in hot temperatures, cholesterol prevent membrane from being too fluid

1. pinocytosis

2. phagocytosis

surrounded by- nuclear envelope

inside- chromosomes and nucleolus

atom is mostly empty space

the nucleous is slightly positivly charged (deflects a positivly charged alpha particle)

orbitals are s,p,d,f,etc; orbitals only hold 2 electrons each

shells are made up of orbitals- shells can contain different numbers of orbitals

1st shell:

2nd shell:

what is in them and how many electrons can they hold?

1st shell: 1s orbital; holds 2 electrons total

2nd shell: 1s orbital, 3 p orbitals; holds 8 electrons total

protons + neutrons

(may not be a whole number because of prevalence of isotopes)

hydrogen and oxygen (in water)

nitrogen (in proteins)

carbon

covalent (either polar or nonpolar)

hydrogen

ionic

differences in electronegativity of the atoms in the molecule resulting in uneven distribution of electrons

ex. water

hydrophobic or hydrophylic?

molecules with ionic bonds

hydrophobic or hydrophylic?

molecules with polar covalent bonds

hydrophobic or hydrophylic?

nonpolar molecules

hydrophobic or hydrophylic?

amphipathic molecules

adding solute to water:

lowers freezing point

raises boiling point

shape & function of molecules

rates of chemical rxns

ability of two molecules to bind

ability of ions or molecules to dissolve in water

carbonic acid (CO2 & H20) to bicarbonate (H+ & HCO3-):

too much H+ in blood and lungs remove CO2, which raises the pH (by shifting rxn to produce carbonic acid)

to make blood more acidic- kidneys can remove bicarbonate, which will lower pH (break down more carbonic acid into bicarbonate and H+)

polar or nonpolar:

C-C

C-H

C-O

C-C: nonpolar

C-H: nonpolar (similar electronegativity)

C-O: polar (oxygen much more electronegative)

selected biologically important functional groups that bind to carbon:

amino

selected biologically important functional groups that bind to carbon:

ketones and aldehyde (a carbonyl group and something else)

steriods, waxes, proteins

keytones tend to be more in middle of molecules

aldehydes tend to be towards the end of molecules

selected biologically important functional groups that bind to carbon:

carboxyl

selected biologically important functional groups that bind to carbon:

hydroxyl

identical bonding relationships but in different spatial orientations

can either be cis/trans or enantiomers

lipids

carbs

proteins

nucleic acids

a carboxylic acid with a long unbranched aliphatic tail (chain), which is either saturated or unsaturated.

the hydrogens from each hydroxyl group in glycerol are removed

[image]

hydroxyl (OH) groups from each carboxyl group of the 3 fatty acids is removed

cis unsaturated forms naturally

trans unsaturated formed by synthetic process- disease link!

more efficient energy storage

cushion

insulation

size

polarity (or nonpolarity)

charge

R group and hydrogen

amine group and carboxyl group

begins with amino terminus

ends with carboxyl terminus

covalent (so harder to break)

Disulfide bonds in proteins are formed between the thiol groups of cysteine residues.

hydrogen bonds

ionic bonds (and other polar interactions)

hydrophobic effects

Van der Waal forces

hydrogen bonds

ionic bonds and other polar interactions

hydrophobic effects

van der waals forces

motor proteins move cargo from one place to another

motor protein is in place, causes filament to move

motor protein attempting to walk, but both it and filament are restricted in movement, so filament bends

mRNA, tRNA, rRNA, linc RNA

(mRNA is copied from the DNA, comes out of the nucleus, rRNA facilitates creation of proteins by tRNA which carry amino acids)

delta H: the total energy that is added or released

delta S: changes in entropy

the delta G prime

the temperature

the concentration of products and reactants

values only depend on the current state of the system and not how it achieved that state

(because of this, you can add delta G values --> coupling)

releases lots of energy when hydrolyzed

can phosphorolate (donate phosphorus) to other molecules

coupling changes the overall delta G by pairing with a negative delta G

enzymes ONLY lower the activation energy, making the reaction occur more quickly

enzymes DO NOT change the delta G (so a nonspontaneous rxn with a positive delta G won't occur even in the presence of an enzyme)

strain bonds in reactants to make it easier to achieve transition state

position reactants together to facilitate bonding

change local environment thru v. temporary binding, making rxn more favorable to occur

1. prosthetic groups

2. cofactors

3. coenzymes

--> ALL OF THESE ARE NON-PROTEINS

the concentration of substrate at which you reach 1/2 of Vmax

it is used as a measure of enzyme affinity for substrate

X intercept (-1/Km) moves

slope (Km/Vmax) increases

yintercept (1/Vmax) does not change

glucose

pyruvic acid

hydrogen is given up or water is formed at every step.

every time hydrogen is broken up, energy within molecule is more concentrated and this energy is eventually stored in the bond of ATP

substrate level phosphorolation

chemiosmosis

fermentation uses an endogenous electron accepter (usually an organic compound)

respiration is where electrons are donated to an exogenous electron acceptor via an electron transport chain

starts with the 2 pyruvates

forms 2 acetyl CoA, releases  2 NADH and 2 carbon dioxide

2 pyruvate

2 ATP

2NADH

long thin filaments

help with muscle contraction, intracellular movement of cargo, ameboid movement, cytokinesis in cells

begins with 2 acetyl coA

ends with 4 CO2

also ends with 2 ATP (via substrate level phosphorolation), 6 NADH, and 2 FADH

34 ATP

38 ATP

energy investment

cleavage

energy liberation

2 ATP hydrolyzed to make fructose 1,6 biphosphate

fructose 1,6 biphosphate is broken down into two 3-carbon molecules of glyceraldehyde 3-phosphate

NADH is used in anabolic pathways

H+ gradient is used for other purposes

when bacteriorhodopsin (a light driven H+ pump) is deprived of light, no H+ gradient is established and no ATP is produced by the ATP synthase

when bacteriorhodopsin is exposed to light, an H+ gradient is established and ATP synthase makes ATPs

1. use substance other than O2 as final electron acceptor in electron transport chain

2. produce ATP only via substrate level phosphorylation

when there is too much NADH

pyruvate is converted into either lactate (in muscle cells) or ethanol (in yeast)

produces far less ATP

secondary metabolite- an antioxidant with intense flavors and smells

examples- flavanoids in vanilla

anthocyanins in pelargonidin (responsible for colors in geraniums, strawberries, etc)

type of secondary metabolyte

bitter tasting molecule for defense

like atropine in the deadly nightshade

secondary metabolyte

intense smells and colors

like beta carotene

secondary metabolyte

chemical weapons

streptomycin

head, hinge, and tail

(ground is cytoskeletal filament, leg is the head of the motor protein, and the hip is the hinge) (the body is the tail I suppose)

flagella- usually longer than cillia and there are only one or two of them

cilia- shorter than flagella, tend to cover all or part of a surface of a cell

share the same internal structure (9+2 microtubal array)

in basal body- triplet microtubal

in outer dublet microtubal: a central microtubal pair and then 9 pairs around it

the nucleus, the endoplasmic reticulum, the golgi apparatus, lysosomes, and vacuoles; also includes plasma membrane

maybe directly connected or pass materials via vessicles

osmosis occurs more quickly in cells with transport proteins that allow the facilitated diffusion of water

(chip 28 codes for aquaporin, the integral membrane protein; frog cell with gene encoding for chip 28 had way more aquaporins and burst more quickly in hypotonic soln than a control cell)

mouse and human cell fused together to create a heterokaryon, and mouse cells have proteins which bond to flourescent antibody

-@ cold temperatures, antibody only bonds to 1/2 of the cell

-@ normal T, membrane is fluid, so mouse protein spreads out, antibodies that have bound are distributed over entire cell

1. could be bound to cytoskeletal (so no lateral movement)

2. could be attached to molecules outside of cell, such as extracellular matrix

how does FRAP allow for the measurement of the lateral movement of membrane proteins?

you color a cell by engineering a cell to produce GFP (green flourescent protein) and then photobleach it by shining a light on it, eliminating the flourescence there

-if the area recovers, then you know there is fluidity in the plasma membrane

1. recognition signals for other cellular proteins

2. plays a role in cell surface recongition

3. protective effects- cell coat (glycocalyx): carb rich coat on cell surface that shileds the cell.

1. if the protein is going to stay in the cytosol, then ribsomemakes the peptide, then it folds and dissociates

2. if a protein being made is destined to go to an organelle, then protein is made with a signal sequence or localization sequence that helps direct it to where it needs

1. bind to the enzyme so tightly as to permanantly block activity

2. be a reagent that chemically modifies residues

is an irreversible inhibitor- binds to the sering residue of an enzyme that catalyzes the crosslinkage in the bacterial cell wall

-penecillin looks like the R groups that would fit in the active site, so it binds covalently with active site, and thus impairs bacterial ability to grow cell wall (and thus its ability to grow)

competitive- substance directly competes with normal substrate for binding (does not affect catalytic activity of enzyme)

non-competitive- affects both substrate binding and catalytic activity

like the substrate

transition state analogs look like the transition state intermediate

like neither of these

both alcohol and methanol compete for enzyme alcohol dehydrogenase

(injesting methanol is bad because alcohol dehydrogenase converts it to formaldahyde and then to formic acid (bad!) but if consume ethanol or alcohol instead, will compete for alcohol dehydrogenase and prevent formation of formic acid)

anti-viral drugs can inhibit virus's enzyme HIV protease

HIV protease inhibitors have the ring structure of the transition state substrate, so can bind to the HIV protease

catalytic subunit (where the active site is located)

regulatory subunit (where inhibitors and activators bind)

aka end product inhibition

the final product acts as a noncompetitive inhibitor of the commitment step, thus shutting down the pathway.

feedback inhibition of ATCase (that makes N-carbamoyl aspartate from carbamoyl phosphate and aspartate in process to make CTP);

CTP is the high energy molecule (kinda like ATP) that helps synthesize RNA

proteases are most active at the enzyme of the organism in which they break down proteins

pepsin, in the stomach, is best around pH 2

arginase, which works in liver and kidney, is most operational in pH 9.5

chymotrypsin, trypsin, elastase

--> these all have serine as an amino acid in their active site

enzyme that catalyzes the same reaction, but have different properties, such as the optimal temperature

isozymes can be used to adjust to temperature changes

most most large molecules exist for a relatively short peroid of time

half-life: time it takes for 50% of molecules to be broken down and recycled

you remove faulty copies of mRNA

you conserve energy by degrading mRNA for proteins you don't need anymore

exonucleases

exosomes

its an enzyme that cleaves off nucleotide from the end

the 5' cap is removed and RNA is degraded from 5' end to 3' end

proteosomes break down proteins

the target proteins, which are misfolded and need to be broken down rapidly, have something come along and stick ubiquitin to them; then the protein goes to the proteasome cap and is unfolded and threaded thry the cap

they use hydrolases to digest substances taken up by endocytosis

break down proteins, carbs, nucleic acids, and lipids

autophagy

(done by autophagosomes)

freeze fracture electron microscopy

specialized kind of transimission electron microscopy

can be used to analyze the interiors of phospolipid bilayers

the P face: protoplasmic face (had been next to cytosol)

the E face: the extracellular face

within the protein, there is a signal sequence (aka localization sequence) that helps direct it to where its supposed to go

(so sorting occurs post-translation)

there exists a signal in the first few amino acids that tells the ribosome that it need to go to the ER; ribosome goes to the ER where completion occurs and it is shuttled to the golgi to be packaged to be sent out into the plasma membrane

(called cotranslational sorting to the ER)

signal recognition protein

it recognizes the sequence in the 1st few amino acids of a protein that signals cotranslational protein needs to occur; then SRP binds to the ribosome and brings it from the cytosol over to a channel protein in the ER membrane. the ribosome finishes making protein and it is "pooped out" into the ER lumen

there are t-snares (target snare) on the surface of the golgi membrane that grab certain v-snares (vessicular snare) that form coat proteins on the vessicle budding off from the ER membrane