BSCI 330 - Exam II Study Guide: Major Organelles and Associated Terms

cyt c

- activates apoptosis without releasing contents of mitochondria

matrix

- cytoplasm of the mitochondria
- site of oxidative metabolism

- contains:
> mtDNA
> ribosomes
> other components for expression of mt genome

- all of this more closely resembles prokaryotes than eukaryotes

mitochondrial genome

- multiple copies of small circular DNA (~16 kb; 37 genes)
- much less genes from prokaryote
- probably moved to the nucleus instead

- only inherited from mother (unlike nuclear genome)
- all sperm gets destroyed; only inherit mom mtDNA

mitochondrial eve

- mtDNA is only inherited from mother
- researchers built an evolutionary tree based on human maternal lineage
- found convergence on a single woman in africa 140-200k years ago
- common ancestor of all living humans

4

RNA molecules in eukaryotes

55

proteins in prokaryotes

3

RNA molecules in prokaryotes

more RNA than protein

the riposome contains more RNA than protein in their complexes

rna
- functional part
- structural and catalytic core

protein
- stabilizes and refines

large and small subunits

- exist as these subunits when inactive; ribosomes dont exist as one organelle

- they are separately exported to cytosol

- assembles into the ribosome when protein synthesis initiates (translation)

prokaryotic ribosome

- 70s --> 50s + 30s

- 30s -> 16s; used for phylogenetic comparison

- large su: 34 proteins
- small su: 21 proteins

- solved at the atomic level through xray crystalization; know exactly how many proteins there are

prokaryotic ribosome

70s

prokaryotic large subunit

34 proteins

prokaryotic small subunit

21 proteins

80s

eukaryotic ribosome

eukaryotic large subunit

~49 proteins

sedimentation coefficient

- rough approximation of the size of a macromolecular complex
- not true MW
- not linear/additive (ex. 30s + 60s = 80s)

- more denser/heavier = sediments faster under centrifugation = higher s number

- s# dependent on density and shape
- more odd shapes = sediments slower undercentrifugation

antibiotics

- bacterial dells are different enough that we can target the differences between prokaryotic ribosomes and eukaryotic ribosomes

- however, we cannot target fungi with antibiotics because their euk cells are similar to our own; it would hurt us

- mitochondrial ribosome size = bacterial/prokaryotic ribosome size
- mitochondrial ribosome structure = bacterial/prokaryotic ribosome structure

rough ER

- associated with many ribosomes, giving it a rough appearance
- site of synthesis of transmembrane and secreted proteins
- proteins found in limens of organelles along secretory pathway (golgi, lysosome, cell surface protein0

smooth ER

- lacks attached ribosomes
- storage site for calcium ions (cell signaling)
- site for lipid synthesis (sterols) + detoxify lipid soluble compounds

Ca++

- calcium ion

ER
- uses it for cell signaling
- level of ca++ is detected by cells; more or less ca++ impacts cell function
- ca++ is stored in ER and can be released into cytoplasm for cell signaling events

Mt
- also stores ca++
- not involved in cell signaling
- requires ca+ for metabolic and enzymatic activities

lipid synthesis

- builds exclusively in cytoplasmic leaflet of the ER; not lumenal leaflet

delayed gratification

- net reaction: dehydration linkage

- FA + glycerol --> glyceride + H2O

- cell takes out water when FA attaches to CoA

- transfers CoA to glycerol

- water drops in the middle of the reaction and not the end of the final linkage

- er creates symmetric membrane

- plasma membrane reintroduces assymmetry

activation step

- need to attach substrate to some intermediate for the energetics to work

- need high AE = spontaneous reactions
- need reaction coupling = not spontaneous reactions

non-spontaneous reaction

usually needs reaction coupling

no steps are wasteful

- doing a seemingly "wasteful" step makes it more favorable
- two steps forward one step back

scramblase

- makes a uniform distribution of membrane
- asymmetric membrane -> symmetric membrane

- makes symmetric membrane in ER (gets rid of gaps that disrupts hydrophobic tails)

flippase

- regenerates asymmetry in lipids

- flips pserine inner to outer
- flips lipid from extracellular leaflet to cytoplasmic leaflet
- need to add new lipids to compensate

floppase

- outer to inner
- flips pserine lipid from cytoplasmic leaflet to extracellular leadlet

oligosaccharide

- rough ER proteins are covalently modified by adding a common oligosaccharide
- 12-20 sugar molecule
- all proteins get the same one to start
- pre-synthesized structure

- n-linked glycosylation

n-linked glycosylation

- added to NH2 group of asparagine

- amine attached to alcohol linkage of nitrogen

protein folding in ER:

- acts as a handle for chaperonin the goes through cycles of folding

- sugar molecule gets chopped off

- then is tested to check its properly folded

modified:

- later in golgi apparatus to provide additional functions

- starts with common carb

properly folded

if other proteins detect: a properly folded protein has all hydrophobic residues buried in the center and should only have a hydrophillic outside

then protein exits ER and continues to modification in golgi

golgi apparatus

- central sorting station for proteins and membranes along secretory pathway

- synthesis site for most cellular carbohydrates: n-linked oligosaccarides + o-linked glycosylation

- unusual organelle in the sense that it is always discontinuous disks (cisternae)

cisternae

- flattened disks
- golgi contains series of them arranged in stacks
- two faces: cis and trans

cis face

- closest to ER
- receives vesicles containing ER syn proteins

trans face

- furthest from the ER
- close to plasma membrane
- represents the exit from Gapp

gapp struct

1. cis face (w/ golgi vesicle)
2. cis golgi network
3. cis cisterna
4. medial cisterna
5. trans cisterna
6. trans golgi network
7. trans face

cis golgi network

- sorting
- phosphorylation of oligosaccarides on lysosomal proteins

cis cisterna

removal of Man

medial cisterna

- addition of Gal
- additional of GlcNAc

trans cisterna

- addition of Gal
- addition of NANA

o-linked glycosylation

- some proteins gets carbohydrates added to the hydroxyl groups of serine or threonine

- each protein gets a unique sugar added

- doesnt start with common carb

why do you think n-linked glycosylation uses a pre-formed common carbohydrate that is later modified for each protein?

- process simplifies self regulation
> most assembly steps and seq of attachment site are the same for all proteins; need one common build and can make small tweaks based on function

- common carbohydrate haws 1 function in the ER and then now new functions can be added by modifying carb on the individual proteins later
> carb has 1 func in folding proteins
> can upcycle and use it for something else; so that it isnt completely lose
> more E fav and and isnt thrown awat

endosymbiont theory

- one protoeukaryotic cell engulfed another free living cell
- instead of it digesting it, the prokaryote survived engulfing and evolved a symbiotic relationship
- now they cant exist independently

evidence for endosymbiont theory

- mitochondria/chloroplast contains ribosomes

mitochondria

- site of major oxygen dependent metabolism of carbs, amino acids, and lipids
- more energy when using oxygen as the final electron acceptor
- generates most of the cell's ATP
- powerhouses of the cell

- double membrane struct
> outermembrane
> innermembrane
> intermembrane space
- matrix
- cristae

mitochondrial double membrane

- two completely separate membrane
- protein content/ lipid content are completely different in teach membrane (endosymbiont theory)

mitochondrial outer membrane

- contains porins
- resembles plasma membrane
- most likely a remnant of endosymbiosis

mitochondrial innermembrane

- rich in cardiolipin
- folded into cristae
- site of ETC
- more surface area than outer membrane
- more SA = more ATP synthesizsed

cardiolipin

- lots of my found in bacteria
- remnant of endosymbiosis

cristae

- folds in the inner membrane of mitochondria
- allows membrane to make sharp bends to increase SA (tight u-turns)

mitochondrial intermembrane space

- contains cyt c
- contains several factors that regulate apoptosis
- outer membrane ruptures before inner membrane

ribosomes

- protein synthesizing organelles in all cells

- fundamentally different from other organelles

- found in mitochondria and chloroplasts
- not enclosed by membrane

- not necessarily an organelle---macromolecular assemblies by definition
- large complexes of proteins and RNA

- large and small subunits

- associated with ER

80

proteins in eukaryotes

eukaryotic ribosome

- 50% larger

- 80s --> 60s + 40s

- 40s -> 18s; used for phylogenetic comparison

- large su: ~49 proteins
- small su: ~33 proteins

- has not been fully characterized due to eukaryotic variation; protein numbers are just an estimate

eukaryotic ribosome

80s

eukaryotic small subunit

~33 proteins

endoplasmic reticulum

- complex membranous organelle that extends throughout the cytoplasm
- "meshwork inside cytoplasm"

- accounts for 50% of membrane in eukaryotic cell
- the other membranes combined are the remaining 50%

- continuous with nuclear membranes
- ER lumen continuous with perinuclear intermembrane space

- RER and SER
- can't change between rough and smooth
- structurally different parts of the ER

plasma membrane

- the membrane at the boundary of every cell that acts as a selective barrier
- accounts for < 50% of the cell membranes
- this is because ER SA > plasma membrane SA

fatty acid binding protein

proteins that bind to fatty acids to mask their hydrophobic region to allow them to freely float in the cell

spontaneous reaction

usually needs high activation energy

improperly folded

if other proteins detect: a improperly folded protein has some hydrophobic residues available on the outer surface

then sugar gets added back and reinteract with chaperone for further folding

trans golgi network

- sulfation of tyrosines and carbohydrates
- proceeds to sorting into final destinations
(lysosomes, plasma membrane, secretory vesicle)

n-linked oligosaccharides

- trimmed and further processed by addition of other sugars
- generates a wide range of:
> complex oligosaccharides (many types of sugars are added)
> high mannose oligosaccharides (only have N-acetylglucosamine kink + mannose as the other sugar)

porins

- channel proteins
- allow for exchange of information