- plasma membrane

- nucleus

- SER

- RER

- golgi

- lysosomes

- endosomes

- peroxisomes

- mitochondria

- ribosomes

- proteasome

- microtubules

- actin filaments

- intermediate filaments

- centrioles / basal bodies

- cilia / flagella

- inclusions

1) Channel

2) Pumps/Carriers

3) Receptors

4) Linkers/Structural

- voltage, ligand, or mechanically gated

- allow passage of particular ion

- physically bind to substrate and transport it across membrane

- Na+/K+, Ca++, glucose

- involved in receptor-mediated endocytosis

- signaling molecules

- kinases or kinase-associated (phosphorylate proteins)

- coupled w/ g-proteins (transduce signals)

- cytokine receptors

- steroid receptors

- smooth: lipid synthesis

- rough: protein synthesis

- continuous w/ outer nuclear membrane

- contains enzymes that metabolize drugs

- bidirectional traffic b/w golgi and ER

- has pumps and channel proteins that keep Ca++ levels high

create proteins for...

- plasma membrane

- secretory vesicles

- lysosomes

create proteins for...

- nucleus

- mitochondria

- peroxisomes

- terminally glycosylates proteins

- directs proteins to different sites w/ target signals

- contains degradative enzymes (that arrive at lysosome via phosphorylated mannose signal)

- destroys microorganisms delivered by phagosomes/endosomes

- surrounded by impermeable membrane

- contain enzymes that oxidize nutrients like fatty acids (though energy created not used for ATP)

- proteins for peroxisome created in cytoplasm

- ATP production

- double membrane

- have own DNA

- make some of own proteins

- reproduce by pinching in two

- lg (49 proteins + 3 RNA's) and small (33 proteins + 1 RNA) subunits that associate during transcription

- reusable

- 11-15 on one mRNA strand = polyribosome

- some bind to ER b/c of signal on polypeptide they are making

- no difference functionally b/w bound and free ribosomes

- contains proteases that degrade old, defective proteins

- proteins arrive via ubiquitin signal

- large cylinder (w/ core and cap) composed of protein subunits and RNA

- microtubules

- intermediate filaments

- actin filaments

1) structural support

2) track for motor proteins (dynein and kinesin)

3) form spindle fibers, pull chromosomes, and push apart cell halves during mitosis

4) components of cilia and flagella

- tubulin dimers (w/ alpha and beta subunits)

- dimers associate to form large cylinder

- dimers bound non-covalently (w/ H-bonds), but very strong

-polymerized in centrioles

- associated w/ cell motility via actin remodeling

- reinforces cell membrane

- composed of actin subunits

- genetic defect involving actin = muscular dystrophy

- composed of keratin subunits

- strong "rope" that reinforces cell structure and nuclear membrane

- unlike microtubules, can bend under great pressure

- inner and outer membrane

- outer: continuous w/ ER

- inner: associated w/ nuclear lamina

- traffic directed - w/ great energy cost - thru nuclear pores

- DNA that is not actively transcribed (e.g., DNA coding for antibodies in a neuron)

- associates near periphery of nucleus

- DNA that is actively transcribed

- 100+ proteins that provide only route of travel in and out of nucleus

- macromolecules require ATP to pass through NPC

- RNA passes through as ribonucleoproteins

- histones

- fibrous proteins

- nuclear matrix proteins

- ribosomal proteins

- transcription factors

- ribosomes assembled

- RNA synthesized

- functional unit of euchromatin

- histone proteins: 8 core, 1 peripheral

- 166 DNA base pairs

INTERPHASE

- G1 - normal cell activity

- S - replication of DNA

- G2 - bulking up cell contents for division; DNA proofreading

MITOSIS

apoptosis - programmed disassebling of obsolete cell

necrosis - cell death due to injury, disease

- epithelial

- connective

- muscle

- nerve

- polar and non-polar regions

- occur when water re-organizes H-bonds to surround hydrophobic solute

- results in decrease of entropy

1) protein folding

2) formation of quaternary structure

3) assembly of membranes

4) binding phenomena

Cooling - removes energy from system, breaks bonds

Warming (to physiologically appropriate temp) - adds energy to system, promotes bonding

pH = -log [H+]

10^(-pH) = [H+]

pK_a= - log (K_a)

*lower pK_a= stronger acid

pH = pK_a + -log([A-]/[HA])

* at isoelectric point, where [A-] = [HA], pH = pK_a (because -log(1) = 0)

-consists of weak acid and its conjugate base: [HA] + [A-]

- at point where these to constituents are equivalent, pH varies only slightly w/ increased base or acid

- in other words, buffers help maintain a constant pH

pH = pKa + log ([HCO3-]/[CO2])

- CO₂ becomes "conjugate acid" (see slides for derivation of formula)

- pH kept at around 7.4

- the a-COOH (carboxyl) and the a-NH₃⁺ (amino) groups of an amino acid covalently bond to form amide linkage, losing water molecule

- usually in trans formation

- has partial double bond character, so 6 atoms of peptide bond group are planar

1. Non-polar (hydrophobic)
2. Polar, uncharged
3. Acidic (negatively charged after deprotonation)
4. Basic (positively charged)

Non-polar

- establish (globular) folding pattern

- promote hydrophobic interactions

Polar

- establish (fibrous) folding pattern

- promote specific interactions (His, Ser, Lys, Asn, Cys)

S - used exclusively for robosomal synthesis of proteins in animal kingdom

- repeated sequence of N-C_a-C_o

- N = amide nitrogen

  C_a = alpha carbon 

  C_o = carbonyl carbon

- short polymers of amino acids

- >12 = oligopeptide

- several dozen = polypeptide

- patterns of polypeptide chain along 1 dimension

- caused by hydrogen bonds b/w amino acids

- helices or pleated sheets

- leucine

- proline

- alanine

- valine

- methionine

- tryptophan

- phenylalanine

- isoleucine

- aspartic acid

- glutamic acid

- histidine

- lysine

- arginine

- High Performance Liquid Chromatography

- reproducible, cheap

- long runtimes, needs protein precipitation

- robust, reproducible

- doesn't work well with thermolabile AA's

- HPLC for non-polar amino acids (those that are polar must first be derivatized)

- used in synthesis of drugs, which must have large non-polar component in order to get thru cell membrane

C_o - N

(a-C is the one with the R-group attached)

- separates proteins based on size

- larger molecules aren't trapped by gel beads, so they emerge from column faster than smaller ones

- proteins separated by size

- larger molecules move more slowly through gel than smaller ones

- proteins separated based on their affinities for binding to certain ligands (e.g., antibodies)

- ligands immobilized in column, and protein solution pushed thru

- specific proteins that bind with antibodies will not pass through column; everything else in solution will

What do each of the numbers mean in the following helix designation?

3.6₁₃ p = 5.4

3.6 = number of residues in each complete turn

13 = number of atoms in each residue

5.4 = measure of axial length of each complete turn (in angstroms)

- allows peptide chain in B-pleated sheets to reverse direction

- made possible by h-bond b/w carbonyl O of 1 residue to H on amino group of residue facing it

- consists of a-helical rods

- hair, fingernails, claws, horns, beaks

- stacked B-sheets

- silk fibers

- all a-helices

- all B-pleated sheets

- a-helices and B-sheets intermingled

- both a-helices and B-sheets present, but occupy different domains

- cancer

- emphysema

- cystic fibrosis

- alzheimer's

- creutzfeldt-jacob disease

- familial amyloidotic neuropathy

- stability (decreased surface to volume ratio)

- exclusion of mutated proteins

- small subunits more accurately made than huge proteins

- facilitation of catalytic site assembly

- cooperativity possible

- an increase in entropy

- Internal hydrophobic bonds are formed, which creates a decrease in enthalpy (-H), but bonds are also broken b/w protein and solvent, which creates an increase in enthalpy (+H)

- so, the folding must be entropy driven

- to keep them from binding to nearby proteins during synthesis

- to ensure correct folding

- to accelerate slow steps

- the iron atom to which the oxygen bonds is somewhat obscured below the plane of the porphyrin ring (it's pulled below by the 5 constituents it's bonded to)

- when oxygen initially binds to the Fe, it initiates conformational changes in other subunits that push the Fe out of its hole, facilitating subsequent bonding

- describes competition b/w H⁺ and O₂ for binding w/ Fe in hemoglobin

- in acidic environments, O₂ will be delivered more readily b/c it is displaced by protons

- in hemoglobin, the replacing of a glutamic acid with a valine creates a hydrophobic pocket which appears in the deoxy form

- certain hemoglobin molecules (hemoglobin S) will bind to this hydrophobic pocket, creating fibrous aggregates which elongate the shape of the RBC

- valine

- its side chain is totally hydrophobic, which facilitates the sliding of molecules back and forth on top of one another

- desmosine and isodesmosine

- composed of a pyridinium ring w/ 4 lysyl residues attached

- troponin

- tropomyosin

- 4 light chains

- 2 heavy chains

- repetitive primary structure

- hydrophobic residues on each chain interact, causing them to wrap around each other

- ATP hydrolysis detaches myosin head from actin, promotes resting state

- nerve impulse causes Ca to leave lumen of sarcoplasmic reticulum and go to muscle fibers

- Ca stimulates release of ADP and phosphates, and dissociates troponin and tropomyosin from actin

- latent energy from ATP hydrolysis released, and myosin head attaches to actin and undergoes power stroke

- ATP causes myosin head to release its clutch on actin and return to resting state

- calcium returns to SR lumen via ATP pump

epinephrine - affects lungs and heart; used for asthma

albuterol - affects mostly lungs; used to prevent premature labor

oxytocin - stimulates uterine contraction, inducing labor

- collagen

- two globular domains: 1 large @ C terminus, 1 small @ N terminus

- uninterrupted fibrous (Gly-X-Y) domain between

- small ahelical domain near  N terminus

-skin

- basement membranes (b/w dermis and epidermis)

- blood vessels (elastin)

- cartilage

- bones and teeth

- eye (sclera, cornea, vitreous humor, lens capsule)

- foods

- coatings

- capsules

- surgical dressing

- tissue engineering

- implants

- non-enzymatic browning

- rxn b/w amino acid and reducing sugar

- hemiacetals

- since sugars are both alcohols and aldehydes, they react with themselves to form rings

- honorary sugar found in chicken and pig (non-ruminant) manure

- binds to nutrients (Ca, Mg, etc.) and makes them unavailable ("anti-nutrient")

- sugar acetals

- C1 bonded to -O-R

- stable, do not mutarotate

- lactose synthase

- dimer of B-D-galactosyl transferase and a-lactalbumin

- long, unbranched polysaccharide consisting of repeating disaccharide units:

1. hexose or hexuronic acid

2. hexosamine

- consist of a protein core w/ one or more attached glycosaminoglycans

- usually heavily glycosylated

- occur in connective tissue

- very large proteoglycan in cartilage

- contains chondrotin sulfate, keratan sulfate, and oligosaccharide chains

- large heparan sulfate-containing proteoglycan found in basement membranes

- promotes attachment of cells and participates in assembly of basement membranes

- proteoglycan containing heparan sulfate chains

- modulates cell attachment and shape

- helps assemble extracellular matrix

- integral membrane proteoglycan (contains heparan sulfate and chondroitin sulfate)

- regulates shape and organization of epithelial cells

- SLRP that helps assemble collagen fibrils

- mice w/o decorin had easily damaged skin

- proteins w/ oligosaccharide side chains

- side chains typically smaller than those of proteoglycans

- usually integral membrane proteins, but found in blood serum and secretions

- linked to protein thru O of serine or threonine

- sugar attached to protein is GalNAc (N-acetylgalactosamine)

- a-linked

- linked to protein thru N of asparagine

- sugar linked to protein is GlcNAc (N-acetylglucosamine)

- B-linked

- membrane-associated and secretory glycoproteins

- cover mucosal epithelia

- provide barriers, modulate bacteria, lubricate, protect tissue surfaces

- sugars added in blocks, cotranslationally:

1) 2 GlcNAcs and 5 mannoses added (one at a time) to Dolichol on cytoplasmic side of ER

2) structure flipped to luminal side of ER

3) subsequent mannoses (4) and glucoses (3) attach to Dolichol on cytoplasmic side, then are flipped to lumen and added to growing chain

4) oligosaccharide chain transferred from dolichol to Asn on nacent polypeptide

5) 3 glucose and 1 mannose removed, which signals transport to golgi (if glycoprotein defective, 1 glucose added back, and structure returns to ER)

- processing in the golgi

- ER synthesis is highly conserved; same basic glycoprotein made in all animals and plants

- proteins that bind to specific sugar residues

- used in separation and analysis of glycoproteins

- some bacteria produce B-lactamase, which cleaves the B-lactam ring in penicillin, making it ineffective

(it no longer mimics D-ala-D-ala, so it does not complex w/ transpeptidase)

- large molecule containing lipid covalently bound to polysaccharide

- present on outer membrane of gram (-) bacteria

- endotoxin

- defines selectivity of enzymes for their substrates

- controlled by structure (unique fit of enzyme with substrate)

- dictates product yield

- ensures that the rate of metabolic reactions is appropriate for cellular requirements

- depends on availability of substrates and co-factors

- amount of enzyme present depends on genetic regulation of synthesis and decay

- kinetic activator constant

- derived from rate constants

- estimate of dissociation of E from S

- high K_m = weak binding (much dissociation)

- low K_m = tight binding (little dissociation)

- constant

- theoretical maximum rate of reaction

- never achieved

- measure of catalytic activity

- number of substrate molecules converted to product per enzyme molecule per unit of time

- measure of catalytic efficiency

- 2nd order rate constant

- measures how enzyme performs when [S] is low

- inhibitors compete with substrate for same site on enzyme

- alters K_m but not v_max

- can be overcome with increased [S]

- inhibitor binds to allosteric site (site other than active site) on enzyme

- alters enzyme, lowering affinity for susbstrate

- does not alter K_m , but lowers v_max

- cannot be overcome w/ increased [S]

- I binds only to ES complex, rendering it ineffective

- alters both K_m and v_max

- resembles the non-competitive, except that the EIS-complex has residual enzymatic activity

- alters both K_m and v_max

- leading substrate A binds to E

  - substrate B binds to AE

- A and B converted to P and Q

- Q released

- P released

- leading substrate A binds to E

- E converted to E' and A converted to P

- P released

- E' binds with substrate B

- B converted to Q and released