1. Water solvates proteins

2. water is polar

3. forms hydrogen bonds

4. interacts with hydrophobic and hydrophilic molecules

5. interacts via noncovalent attractions

***makes up 70% of cell weight***

Changes the way that water interacts with itself and other molecules. Depends on both the kinds of ions and the number involved.

***1% of cell weight and 20 kinds***

1. intermediate metabolism, energy source

2. signaling/cell recognition

3. polysaccharides that bind other molecules

4. isomers of C6H12O6 have different functions

5. combinations of the isomer into disaccharides also have different functions

 ***1% of cell weight and 250 kinds***

1. monomer of protein

2. signaling and homrones

3. key metabolites

4. energy source (atkins)

5. buffer pH change (histidine)

5. osmolites

***0.4% of cell weight and 100 kinds***

1. Energy currency (ATP)

2. Nucleic acids (RNA/DNA)

3. signaling (GTP, cAMP, cGTP,etc)

4. coenzymes (NADH)

5. carrier molecule for electrons (NADH)

6. redox reactions

***0.4% of cell weight, 100 kinds*** 

1. membrane constituents

2. energy source

3. cholesterol used in hormones and signaling

4. post translational modifications

alpha helix

beta pleated sheets

the globular protein

sum of primary, secondary structures, etc.

True biological catalyst:

True because it is not consumed in the reaction

Biological catalyst: speeds up processes that happen on their own, it does not make the impossible, possible.

Can be made of protein or an RNA (ribozyme)

so proficient that their turnover is only limited by diffusion within the system

Example: Acetylcholinesterase

determines if glycolisis is going to be aerobic or not.

pyruvate + NADH <--> lactate + NAD+

4 subunits: either m-or h-type

-m= muscle (lactate)

-h= heart (pyruvate)

-M4, M3H, M2H2, MH3, H4

binding of one molecule facilitates the binding of the next molecule, so it increases the reaction speed

- Hemoglobin is an example of this

-Organization of enzymatic activitics during fatty acid synthesis, prevents backward reaction, lowers the concentration needed for the next step to occur

- 7 distinct enzymatic functions are involved

- mitochondria may be a metabalon attached to a cytoskeletal element

1. control synthesis of enzyme = control product

2. control degradation rate of product

3. control substrate, michaelis mentin kinetics

4. allostery (positive or negative binding to change the shape of the protein)

5. positive cooperativity (binding of one increases the likely bonding of the second)

6. post translational modifications

7. metabalon

8. compartmentalization

9. abiotic stresses (pH, salts, temperature)

10. diffusion (especially affects perfect enzymes)

model of a membrane

fluid- because allows movement

mosaic- very heterogeneous structure

phosphatidyl-ethanolamine (PE)

phosphatidyl-serine (PS): negative charge

phosphatidyl-choline (PC)

sphingomyelin

phosphatidyls=glycerol head, sphingomyelin has serine head

PE/PS on inner monolayer

PC/sphingo on outer monolayer

PS signals for cell deathj

- rigid steroid ring structure with a nonpolar,hydrophobic, hydrocarbon tail

- helps balance a membrane between sol and gel state by keeping a specific space between phospholipids

- lateral diffusion

- rotation: can kick other molecules near them with kinked tails

- flexion: stretch tails apart

- flip-flop: from inner to outer membrane (rare)

unsaturated lipids = thicker/longer, and more space between because of kinks in the tails

Saturated = thinner/short, stocky, and close together

glycolipid

- lipid + sugar

- glycosylation occurs to 5% of lipids in the outer bilayer

Functions:

1. electrical conduction

2. cell-cell interactions

3. receptor use

4. protection against low pH

a pore protein formed by multiple beta pleated sheets in a barrel shape

Different kinds:

1. 8 stranded: ompA receptor protein

2. 12 stranded: OMPLA is a lipase

3. 16 stranded: porin, example is aquaporin

4. 22 stranded: fepA, iron transport molecule

how hydrophobic or hydrophilic certain molecules are

- hydrophobic are more likely to participate in intermembrane reactions

- hydrophilic are more likely to be extracellular

localization within a single cell, caused by a physical feature of the cell

- example: tight junctions can form a physical barrier that prevents lateral diffusion of proteins

- with or without a physical barrier

- aggragation of proteins (collection/group)

- assemblage via extracellular interactions

- intracellular interactions

- cell-cell interactions

Intracellular: 5-15 mmol

Extracellular: 145 mmol

intracellular: 140 mmol

extracellular: 5 mmol

intracellular: 0.5 mmol

extracellular: 1-2 mmol

intracellular: 10^-4 mmol

extracellular: 1-2 mmol

intracellular: 7x10^-5 mmol

extracellular: 4x10^-5 mmol

intracellular: 5-15 mmol

extracellular: 110 mmol

P-type ATPase pump: utilizes phosphorylations for a conformational change

F-type (V-type) ATPase proton pump: uses a hydrogen ion, pump rotates, pops a sater which creates energy, transforming ADP + Pi into ATP

ABC transporter: ATP binding cassette, involves an ATPase, a binding protein, and a channel protein

1. voltage: potential difference

2. temperature: hot=fast ion and positive force

3. Z (valence): charge on an ion, greater charge= need to exert a greater effect

4. faraday value: capacitance = magnitude of separation of charge divided by distance btn charges

5. concentration *** the differnce of concentration intra and extracellularly has more importance than the total number of ions

summation of all nernst potentials.

average btn -70 to -90 mV.

can vary as low as -9 mV and as high as -200 mV

what has more influence on cellular function when comparing nernst potentials of Na and K?

the cell is more leaky to K than to Na.

K has much more influence on cellular function

but Ca has the biggest role in nernst potential of any ion in the cell

transient regenerative electrical impulse

1. open voltage gated Na channels, Vm depolarizes

2. threshold needs to be reached to continue opening Na channels, peek depolarization

3. K channels open, K leaks out, cell repolarizes

4. usually undershoots, hyperpolarizing phase, then returns to normal

Volume does not hint at importance, the percentage of membrane dedicated to an area hints at a cell's function.

stores fat, oil, or starch

started from a proplastid

Gated

transmembrane

vesicular

"across a membrane"

taking a protein through a membrane in an unfolded state and then refolding it

FG repeats

phenylalanine/glycine

binds a cargo protein

there are multiple types that use different adaptor proteins

This is a gated transport where

- anything <5000 daltons enters freely.

- anything 200,000 daltons will be gated

- those ~30,000 may or may not be regulated

small, monomeric, GTPase's that cleave GTP

used in nuclear gated transport

- GTPase activating protein

- activates Ran-GTP which removes a phosphate from GTP to create GDP

located in the cytosol

guanine exchange factor

- exchanges GDP for GTP

- located in the nucleus

1. TOM: translocase of outer mitochondrial membrane

2. SAM: beta barrels, 5000 dalton mesh, builds outer membrane protein constituents

3. TIM-23: translocase of inner membrane that spans both membranes

4. TIM-22: translocase of inner membrane that spans only the inner membrane

5. OXA: builds inner membrane protein constituents

thermal ratchet

electrochemical gradient

a specific sequence in the forming protein that signals for transport through a membrane to stop

can be used to create a protein membrane constituent

False. A protein can go through without unfolding it.

 this is called post-translational transport

allows for crosstalk between ER and golgi

involved in detoxification (cytochrom p450)

steroid production

has ribosomes: protein synthetic machinery

stops the translation of a protein as soon as it starts, then the ribosome can take a protein to the ER

it binds to the signal sequence on the nascent polypeptide chain

released because of GTPase

- 6 peptides around an SRP RNA molecule

- translational pause domain

- signal sequence with binding pocket

- hinge

- sec61 translocator

glycosylated

N-linked glycosylation

binds to N-asparagine

occurs in the lumen

Dolichol

Asparagine

bound in membrane and Ca dependent

participates in glycosylation proofreading

chaperone free in the ER but Ca dependent

used in glycosylation proofreading in the ER

adds glucose

used during glycosylation proofreading in ER

removes glucose

used in glycosylation proofreading in the ER

protein in the ER membrane used to move proteins in or out of the ER

has an open section that can allow lateral diffusion of a protein during transport

response of a cell to an increased number of incorrectly folded proteins

intracellular signaling cascade that promotes transcription of additional chaperones

phosphorylates translation/initiation factors for an alternative form of translation of mRNA. This encodes for stress proteins and gene regulatory protein 2

used during unfolded protein response

regulates mRNA splicing, produces a mature mRNA that encodes for gene regulatory protein 1

used during unfolded protein response

regulated proteolytic event , releases gene regulatory protein 3

used during unfolded protein response

catalyzes flipping of a phospholipids to the cytoplasmic monolayer in the plasma membrane

is an ABC transporter, and is thus ATP dependent

1. clathrin: golgi and plasma membrane

2. COP I: golgi

3. COP II: ER

5. retromer: endosome to golgi return

three pronged light chains associated with heavy chains

incorporated into the structure of clathrin

cargo + cargo receptor --> adapter protein--> clathrin

all of these proteins together pull the membrane up and out and produce a budding of plasma membrane

retromer subunits

(a second type of coated vesicle)

SNX1: binds to the membrane via binding of phosphoinositle

VPS29

VPS35:interacts and holds onto cargo

VPS26

Monomeric GTPase protein that wraps itself around the stalk of a budding vesicle to help pinch the clathrin vesicle off from the lipid bilayer

Uses GAP's and GEF's, as well as hsp70, atp and others to pinch of the vesicle

promote the formation of the coat of a vesicle

- Arf 1: used with COP I and clathrin recruitment

- SAR 1: monomeric GTPase used with COP II

SAR1 process of recruiting COP II

(hint involves GEF)

- Sar1-gdp--> sar1 GEF exchanges GDP to GTP, the resulting conformation change exposes an amphipathic helix

- Sar1 GTP attaches to plasma membrane (ER) to hide the helix

- SEC23 attaches, then SEC24 (with cargo receptor),

- cargo is attracted to the receptor on the inside of the ER 

- sec13 and sec31 attach vesicle buds away

monomeric GTPases that guide coated vesicles to the right location, they change depending on the compartment

- use rab effector molecules to help with function

Soluble, NSF protein, Attachment protein, Receptor

pairs are used to help fuse a vesicle with another vesicle or membrane

n-ethylmaleamide sensitive fusion protein

it blocks ATPases and binds proteins that require ATP

LECTIN

a protein that binds a carbohydrate

glycosylation can change what protein attaches

BIP

binding protein

binds certain proteins, until it is time for them to be secreted from a vesicle

used in protein sorting

globular combination of homo/hetero-typic fusions that forms a large irregular shaped grouping different vesicles

Found somewhere between the golgi and the ER and has a mixture of proteins from both compartments

a retrievel sequence on ER resident proteins, which is recognized by receptors and sent back to the ER via COPI coated vesicles

affinity for binding to receptos increases with pH. The farther from the nucleus you get, then the greater the affinity because the pH changes.

Sit on asparagine (N in the amino acid alphabet)

- two types show if they are sensitive to Endoglycodase H enzyme

1. sensitive =high mannose

2. resistant= complex oligosaccharide

O = deals with OH group (sometimes on threonine, serine, or hydroxylated lysines)

can change the function of a protein during protein folding, proteases resistance, cell/cell adhesion, and regulatory roles in signaling

vesicles are moving, differentiation of the golgi occurs as they move

a model of golgi formation

the vesicles are maturing by constantly adding and subtracting things

a model of golgi formation

Acidic (pH~5.0) established  by a V-A ATPase and a tight membrane to keep them in

***The acidic environment doesn't prevent the protons from being functional, it just inactivates them***

40 different hydrolytic enzymes

engulfing one's self

something signals for the collection of membrane around an organelle and things are added to it to create an autophagosome (lysosome)

one cell engulfing another (bacterium) and addition of endosome/lysosomes forms a phagosome

pseudopods are used to grab and engulf once triggered. These are driven by phosphoinositol to structure the cytoskeleton

continuous process where a cell takes up a small sample of its plasma membrane to sample the environment around it

continuous, not triggered like phagocytosis

an aggregation of caveolin protein that creates a vesicle at the plasma membrane which is then brought into the cell

- a type of pinocytosis

- not a coated vesicle, it is coat independent

LDL

type of pinocytosis used to move fatty acids and cholesterol around your body in the blood stream

involves 1500 cholesterols and 800 phospholipids

moved into a cell via an LDL receptor protein

moving a receptor cell with a bound ligand by endocytosis across a cell to release it on the other side

once endocytosed the receptor may also be recycled, or degraded

endocytosis

when insulin is bound to a receptor, the cell is stimulated to send glucose to the cell surface via endosomes

products are made due to a response from a signal

uses secretory vesicles

no signal is required, a product is released as soon as enough is made

often used to replace plasma membrane proteins

a precursor protein used by secretory vesicles within the pituitary gland to create multiple hormones via post translational processing

anterior pituitary: ACTH, a-MSH

posterior: y & B-liptropin, B-MSH, B-endorphin

stage 1: electron transport chain drives a pump, which pumps protons across a membrane

stage 2: the proton gradient is then used by ATP synthase to make ATP

used to create the transmembrane electrochemical proton gradient

provided by sunlight or food

driving active transport

bacterial flagellar rotation

production of ATP in mitos or chloroplasts

Mito: fat/carb+O2 -->H+gradient+CO2 +H20

chloroplast: CO2+H20--> H+gradient+O2+carbs

shape of mitochondria change as they fuse and seperate, used to control O2 levels

log phase: 2-3 large fused mitos and lots of oxygen

stationary phase ~200 mitos and very little oxygen

the matrix and the inner membrane

Matrix= TCA cycle (oxydation of pyruvate and fatty acids)

Inner membrane= electron transport, ATP synthase, transport proteins

allow the diffusion of molecules less than 5000 daltons in size

reside in the outer membrane of the mito

nicotine adenine di-nucleotide

used in electron transport chain for electron delivery

1. take high energy electrons to create H gradient (the e trans chain does not make ATP)

2. H gradient is used to create ATP

allows the slow drop of energy from a high energy electron and uses it for work so that combustion does not occur

work created is used in proton motive force

how motivated the protons are to get back in, membrane potential created from pumping out protons

Two parts

- electrochemical gradient of protons

-membrane potential

1. ph buffering (changes H concentration)

2. capacitance of membrane by chaging thickness

3. ion composition of extra-mito region

4. carriers and ionophores that release or dissipate the H gradient

rotor/sator complex changes conformation as one H comes through, part of the synthase pops out and this change produces ATP

3-4 H = 1 ATP

a dimer totaling 22 proteins

each monomer has 11 proteins, 3 hemes, and an iron sulfur protein

dimer of 26 proteins

eache monomer has 13 proteins, 2 cytochromes, and 2 coppers

a porfrin ring with iron in the middle

the iroon holds electrons

other functions of the mitochondria

-mobilize amino acids to fuel ATP production during starvation

- supply the cytosol with excess citrate to make fatty acids and esterols

- also supplies citrate or NADPH to the cytosol when the cell is short on oxygen and must revert to glycolisis. These help regulate the pathways

chloroplast envelope with inner and outer membrane and thus an inner membrane space

grana, the photosynthetic area, made of thylakoid membrane

**unlike cristae in the mito, the grana do no connect to the inner membrane

filled with stroma instead of matrix

granum, not the cytosol like with mitos

this means the f0-f1 atpase is located on the grana

a very inefficient system that uses 9 atps and 6 NADPHs to create one molecule of glyceraldyhide 3 phosphate

3 co2+ ribulose1,5 bisphosphate --> 6 molecules 3 phosphoglycerate (3 carbon), add 6 atp --> 3 bisphosphoglycerate add NADH --> glyceradehyde 3 phosphate

glyceraldyhide is the transported to the cytosol

ribulose bisphosphate carboxylase

enzyme, only works with 3 molecules/second

half of the proteins in the chloroplast are rubisco because it needs so many to keep up with the cell

- use oxygen instead to produce phosphoglycolate, which then goes and liberates CO2

- C3 vs. C4 plants

separate the tasks of respiration, and open and close the stoma for respiration

- mesophilia around stoma: take co2 and pyruvate, use co2 to produce malate

- bundle sheath cells: take malate to release CO2 and produce pyruvate

uses the chlorophyll

-photo reaction center contains photo system I and II

- photo system II gives photon to molecule A--> Q pool --> cytochrome B6F --> plastocyanine +photo sytem I--> pherodoxine NADP reductatse

receives electrons from molecule B, the electrons are bounced around so the energy lowers and the proton equivalents are pumped into the granum

the electron is passed to plastocyanine

uses photo system I to excite the e again then hands off to pherodoxine NADP reductase

- richly vascularized

- unmyelinated nerves for sympathetic stimulation

- lipid reserves depleted from cold exposure makes the color darken

- polygonal shape with lots of cytoplasm and multiple lipid droplets, round central nuclei

redox slip

proton leak

inhibition of F0-f1- atpase

protons enter independent of f0-f1 atpase into the mito. electron releases energy and heat but no work done

*** most efficient method of uncoupling

found in brown adipose tissue, uses primarily proton leak

GDP inhibits UCP1 hormonal and neurohormonal control via norepinephrine

lysosomal: nonselective, goo for big pieces like membrane patches, or mitos

ubiquitin dependent proteolysis:

a 76 amino acid peptide, incredibly conserved

responsible for 80-90% of degredation of short-lived regulatory proteins

selecting a protein for degredation by marking it with ubiquitin

this makes it appealing to the 26S proteasome

polyubiquitin makes it even more appealing

ubquitin acitivating enzyme, through ATP

only 1 type, ubuiquitin is then transferred to E2

ubiquitin carrier protein

~30 different ones

with or without E3, ubiquitin is then transferred to the protein that needs to be degraded

ubiquitin ligase, activated by phosphorylation

facilitates E2's transfer of ubiquitin to a protein

hundreds of different kinds

not always used

26S total

- 20S core protease, degradation site

19S regulatory cap

chaperoning with ATP sites

small ubiquitine like modifier

involved in nuclear localization

proteins

peptides: hormones

amino acids or derivatives: T4

nucleotides: ATP

steroids

retinoids

 fatty acid derivatives

 gasses: NO, H2S, CO

react with nuclear receptors to drive transcription

steroids

retinoids

tyrosine derivatives