Bio: Cell biology/Eukaryotic Cells Flashcards
RER (What gets made here?)
SER
**KNOW YOUR ORGANELLES
RER location of synthesis/modification of secretory, membrane-bound, and organelle proteins, post-translational modification of proteins
SER detoxification and glycogen breakdown in liver; steroid synthesis in gonads
Golgi apparatus
Vesicles from ER fuse with cis/trans stack, go to medial stack, and leave cis/trans stack
modification and sorting of protein, some synthesis
1) Modification of proteins made in the RER
2) Sorting and sending proteins to their correct destinations
3) The Golgi also synthesizes certain macromolecules, such as polysaccharides to be secreted
traffic to and from golgi mostly unidirectional
Vesicles from ER fuse with cis stack, go to medial stack, and leave trans stack
Lysosomes, what enzyme is present in lysosome and what does it do?
Peroxisomes, what does it do, produce, and what enzyme does it have?
lysosomes contain acid hydrolases that digest various substances (only when in acidic environments, so would not work if broke and went into cytoplasm)
Membrane bound organelle that is responsible for the degradation of biological macromolecules by hydrolysis
Organelles such as mito that have been damaged or are no longer functional may be degraded in lysosomes in a process termed autophagy (self eating), lysosomes also degrade large particle matter engulfed by cell by phagocytosis (ex. macrophages), crinophagy = lysosomal digestion of unnecessary (excess) secretory proteins
Peroxisomes metabolize lipids and toxins, contain enzymes that produce H2O2 as a by-product (dangerous chemical) but contains enzyme catalase which breaks H2O2 down to protect from peroxides and free radicals
The nucleolus function? What enzyme works in there?
The nucleolus is a region within the nucleus which function as a ribosome factory, it consists of loops of DNA, RNA polymerases, rRNA, and the protein components of the ribosome
The nucleolus is the start site of transcription of rRNA by RNA pol I
Protein components of ribosome are not produced in the nucleolus; they are transported into the nucleus from the cytoplasm (all translation takes place in cytoplasm for ribosome) and the protein components of ribosome are assembled in the nucleolus
After partial assembly, the ribosome is exported from the nucleus, remaining inactive until assembly is completed in the cytoplasm
The membrane of ER is at points contiguous with the outer nuclear membrane (The ER lumen is equivalent (contiguous with) the extracellular space)
The nuclear envelope is punctuated with large nuclear pores, what can go through? What is a nuclear localization sequence and how does it work?
Molecules smaller than 60 Kd, including small proteins can go through
Large proteins can go though if they have a nuclear localization sequence -> Proteins with nuclear localization sequence are translated on cytoplasmic ribosomes and then imported into the nucleus by specific transport mechanisms
Where is pyruvate dehydrogenase located?
Matrix
What does mito have that the whole cell also has? What does that thing do?
Mito possess their own genome which is far smaller than the cellular genome and consists of a single circular DNA molecule. It encodes rRNA, tRNA, and several proteins, including some components of the ETC and parts of ATP synthase although most mito proteins are encoded by nuclear genes
Maternal inheritance
Mito exhibit Maternal inheritance which means the mito is inherited only from the mother, since the cytoplasm of the egg becomes cytoplasm of the zygote, sperm only contributes genomic nuclear DNA
Maternal inheritance departs from the rules of Mendelian genetics
What are two sites of protein synthesis? What happens to proteins after each?
Describe pathway from RER
In Eukaryotes protein synthesis can either take place on ribosomes free in the cytoplasm or on ribosomes bound to the surface of the rough ER:
Proteins translated on free cytoplasmic ribosomes are head toward peroxisomes, mito, nucleus, or will remain in the cytoplasm
Proteins synthesized on the rough ER will end up either 1) secreted into the extracellular environment, 2) as integral plasma membrane proteins, or 3) in the membrane or interior of the ER, Golgi apparatus, or lysosomes (LEG acronym)
membrane bound vesicles pass b/w these three cellular compartments
Proteins synthesized on the RER are transported in vesicles that bud from the ER to the Golgi apparatus, then to the plasma membrane or lysosome
All proteins start translation…(location)
What determines if a protein is translated on the RER or not?
The mRNA for a secreted protein encodes for a longer protein than is actually observed in the cellular exterior. Why?
Determined by the sequence of the protein itself
All proteins start translation in cytoplasm however, some proteins have a aa sequence in N terminal called signal sequence which is recognized by the signal recognition particle (SRP), which binds to the ribosome
Answer: The signal sequence of the protein was removed in the RER
Integral membrane proteins
For a protein in the plasma membrane, does the portion of the protein in the ER lumen end up facing the cytoplasm or the cellular exterior?
Have sections of hydrophobic aa called transmembrane domains that pass through lipid bilayer membranes. The transmembrane domains are essentially signal sequences that are found in the interior of the protein (not N terminus) and they are not removed after translation
A single polypeptide can have several transmembrane domains passing back and forth through a membrane. During translation, the transmembrane domains are threaded through ER membrane, the protein is then transported in vesicles to the Golgi apparatus and plasma membrane in the same manner as a secreted protein
ends up facing the cellular exterior
What is the default path for proteins that go through the secretory path? What consists of the secretory path? What is needed if a protein going through this path needs to go elsewhere (e.g. Golgi, the ER, the lysosome)?
What do proteins that are made in the cytoplasm
Constitutive secretory pathway
regulated secretory pathway
Default is plasma membrane
Secretory proteins must proceed via a specific path: from the ER to the cis Golgi to the medial and trans Golgi and from there to the cell surface
If need to go elsewhere, targeting signals are needed
Constitutive secretory pathway -> continuous or unregulated proteins secreted
regulated secretory pathway -> Specialized secretory cells (B-cells, pancreatic cells, etc.) store secretory proteins in secretory vesicles and release them only at certain times, usually in response to extracellular environment
ALL transcription takes place in ______
ALL translation begins in _____
a. If you are a cytosolic protein, you finish translation in_______
b. However, if you are one of the following, you finish translation in _______
ALL transcription takes place in the nucleus
ALL translation begins in the cytosol
If you are a cytosolic protein, you finish translation in the cytosol
However, if you are one of the following, you finish translation in Rough ER
- Secreted protein
- Transmembrane protein
- Lysosomal protein
- ER/Golgi Resident Protein
(Super EG-celent Lion Tamer or LEG)
All of these proteins make signal sequence that triggers peptide complex to bring them to rough ER
What allows the proteins ….. to finish translation in Rough ER rather than in cytosol where it started?
proteins = secreted protein, ER/Golgi, lysosome, transmembrane
What happens when have mRNA of a secreted or lysosomal protein?
Co-translational translocation
What is it? What is signal sequence? What happens to the signal sequence? Why?
First come across mRNA and a ribosome comes across that mRNA and starts reading it at Kozak sequence
Signal sequence = signals to cytoplasmic ribosome to finish translation in Rough ER
- The signal sequence for a secreted protein is the first few aa and it is removed upon completion of protein
When use translocation pore in ER membrane and then the signal sequence embedded in the membrane (for secreted proteins) this shows how signal sequence aa are hydrophobic/nonpolar
Then protein keeps being made and while signal sequence still stuck in membrane, the protein becomes all folded up under it, inside the ER lumen
Then can package protein off and send to golgi for processing (glycosylated, sulfinated, phosphorylated) and then send it out of the cell
We have to cleave off that signal sequence bc it is stuck in ER membrane, need to cut it in order to detach the protein
What happens when you have mRNA of membrane bound protein (First come across mRNA and a ribosome comes across that mRNA and starts reading it at….)? Where is signal sequence? What happens to signal sequence at end?
How does membrane bound protein embed in plasma membrane (which OG side of ER is facing which side of plasma membrane? Intracellular or extracellular side)?
Why is ER equivalent to/contiguous with extracellular environment?
First come across mRNA and a ribosome comes across that mRNA and starts reading it at Kozak sequence
Signal sequence can be anywhere in aa sequenc e, may appear several times, and remains as part of the final protein
signal recognition particles (SRP) bring whole complex (ribo, aa, mRNA) to RER ribosome docking site
We use translocation pore and do co-translational translocation, signal sequence farther along in aa sequence and still has high preference for inter-membrane region of ER bc its hydrophobic so signal sequence portions (can have more than one) will be the ones embedded in the membrane
In order to let protein go to the membrane, keep signal sequence, create vesicle with sequence in it that can travel to plasma membrane
The part of the protein that was touching the cytosol (OG intracellular environment) when embedded in membrane is still touching the cytosol
*The ER contiguous with extracellular environment bc of this process
**Targeting signal
**Targeting signal:
Needed if a protein is going to stay in the secretory pathway
The default target for proteins that go through secretory path is the plasma membrane. Targeting signals are needed if a protein going through that path needs to end up elsewhere (e.g. Golgi, ER, lysosome)
Proteins that go through secretory pathway but need to stay there - ER resident proteins or some stop at golgi - and if you want your protein to stop in a certain segement of secretory pathway it’s not enough for it to have a signal sequence, it needs another sequence to tell it to stop there =
**Localization signals
- *COMMONLY REFERED TO ON MCAT
ex. nuclear localization signal, mitochondrial localization signal
Needed if protein will be sent to an organelle that is not part of the secretory pathway (nucleus, mitochondria, peroxisomes)
Targeting signal means stay in the cytosol, but there are so many places to be within the cytosol (nucleus, mito, etc.), so in order to specify where in the cytosol you want protein to stay, you need the localization signal
What is the secretory pathway?
Online: The secretory pathway carries proteins to the cell surface membrane where they can be released.
Would the following have a signal sequence, localization signal, transmembrane domain and/or targeting signal?
1) ab/Neurotransmitters/peptide hormones
2) acid hydrolases
3) enzymes for protein modificaton
4) enzymes required for lipid synthesis
5) glycolysis enzymes
6) histones, DNA/RNA, polymerase
7) PDC/Krebs cycle enzymes
8) Catalase
See pg. 182
Proteins for Smooth ER needs signal sequence and targeting signal
What does the plasma membrane consist of? What is it made of?
Can CO2, O2, and steroids pass through?
Phospholipid (hydrophilic and hydrophobic parts), glycolipid (fatty acid groups and carb side chains also have both hydrophilic and hydrophobic parts), cholesterol
2 long hydrophobic fatty acids esterified to glycerol, and (for one type of phospholipid) charged phosphoryl choline group (choline + phosphate)
yes they can all pass bc nonpolar
What are Integral membrane proteins?
embedded in membrane
Integral membrane proteins
embedded in membrane (but does not cross it like a transmembrane protein)
Transmembrane domain with hydrophobic residues
Peripheral membrane proteins
not embedded in the membrane at all, but stuck to integral membrane proteins, held there by hydrogen bonding and electrostatic interactions
Fluid mosaic model
Mosaic of lipids and proteins are free to move back and forth fluidly but only sideways/ in two dimensions
Molality equation (m) Why is this different than molarity?
Mole fraction?
# moles of solute/ # kg of solvent This is different than molarity bc molality does not change with temperature Since 1 liter of water = 1 kg water the molar and molal concentrations of dilute aqueous solutions are nearly the same
Mole fraction of S = Xs = # mole of substance S/ total # moles in solution
Useful way to express concentration when more than one solute is present