TA Study Guide Flashcards
Why is it helpful for a bacteria to have a cell wall?
It helps determine cell shape and protects against osmotic pressure
Describe the structure of peptidoglycan.
Linear polysaccharide chains that are cross-linked by peptides
How does penicillin affect peptidoglycan?
Penicillin inhibits the enzymes that cross-link the peptides
Why do we need to be concerned about the overuse of antibiotics like penicillin?
Penicillin destroys the integrity of cell walls, and mutations (antibiotic resistance) can develop from overuse
How is the structure of plant cell walls different from that of bacterial cell walls?
Plant cell walls are made of cellulose (beta glucose monomers) that interact with pectin and hemicellulose to make the cell wall
What do loose connective tissue, bone, tendons, and ligaments have in common?
They are all composed of ECM with different cells
What is the general structure of the extracellular matrix?
It’s composed of proteins in a gel-like polysaccharide ground substance
What are collagen fibers?
Main proteins in ECM; made of amino acids in a triple helix form.
What are GAGs?
Glycosaminoglycans are polysaccharides in the ECM
What are proteoglycans?
Combination of GAGs and proteins
What are adhesion proteins?
Proteins that help cells stick to each other and to the ECM
What do cells use to attach themselves to the ECM?
Integral (transmembrane) proteins
What is the relationship between integrins, focal adhesions, and hemidesmosomes?
Integrins are an example of integral proteins. Focal adhesions and hemidesmosomes are composed of integral proteins
What are adhesion junctions? What are the different types?
They are selective interactions between 2 calls (movement, recognition, and labeling).
Selectins bind to carbohydrates.
Integrins bind to the ECM
Ig superfamily binds to integrins
Cadherins bind to desmosomes
Do all cells have the same genomic DNA?
Yes
Why do cells have multiple types of adhesion junctions?
To provide different functions, and allowing for flexibility
How are plasmodesmata similar to gap junctions?
Plasmodesmata are gap junctions but for plants. One difference is that they are formed during cell division in plants (so the daughter cells never fully divide); while gap junctions form between established animal cells.
In which direction are mRNA molecules made?
During transcription, mRNA is read in 3’ to 5’ and made in 5’ to 3’
If all cells have the same genomic DNA, how are there so many different types of cells?
Because of RNA processing in transcription
Describe the bacterial RNA polymerase
A multi-subunit enzyme that catalyzes the formation of new RNA from DNA
What is the significance of the sigma subunit?
It facilitates DNA recognition and positions RNA polymerase at the transcription initiation site
Why are the -10 and -35 elements important?
The elements are approximately 10 and 35 nucleotides (respectively) upstream from the transcription start site. The sigma factor binds to them and makes transcription efficient, and with these 2 sequences being 60 base pairs long, it gives RNA polymerase a larger region to bind to.
How does initiation of transcription happen in bacterial cells?
Sigma factors guide RNA pol to the closed promoter. RNA pol unwinds 12 bp, making an open promoter. RNA pol joins two free nucleotides, and then after ~10 nucleotides are joined, the sigma factors leave the RNA pol.
How does elongation of transcription happen in bacterial cells?
RNA pol continues to unwind DNA in the 3’ to 5’ direction while winding in the 5’ to 3’ direction
How does termination of transcription happen in bacterial cells?
Elongation continues until RNA pol hits a termination signal. The RNA formed from the transcription of the termination site will form a stable stem-loop structure through base pairing.
How many polymerases do prokaryotes have?
One core one
How many polymerases do eukaryotes have?
three
What is the TATA box?
A sequence of DNA found around the -10 region in the core promoter complex of eukaryotes. It acts as a signal for where transcription should begin.
What is a transcription factor and what is the difference between a general transcription factor and a gene-specific transcription factor?
Transcription factors are proteins that work in tandem with RNA pol to initiate eukaryotic transcription. GTFs transcribe all genes, but gene-specific TFs transcribe specific genes.
How is initiation of transcription different in eukaryotes?
Instead of a promoter complex region of -10 and -35 (like in prokaryotes), there is the TATA box that needs RNA pol II and at least 5 TFs to find promoters and initiate transcription.
What is the pre-initiation complex and why is it important?
After RNA pol II binds to the third TF, TFs 4 and 5 form the pre-initiation complex, which interacts with the mediator, causing CTD to release active RNA pol II.
What are the three modifications done to pre-mRNA and why are they important?
Addition of a 5’ cap (exportation and prevents degradation), addition of a poly-A tail (prevents degradation), and RNA splicing (removes introns and makes a functional protein).
What would be the consequence of not having spliceosomes?
We would not be able to make functional proteins or have continual coding sequences
What is the difference between DNA and a gene?
A gene is a segment of DNA that encodes for a functioning molecule
What are the three types of RNA discussed in class? Name their functions.
mRNA: messenger and template for transcription
tRNA: transfer RNA that has a CCA sequence which allows an amino acid that corresponds to the anticodon to attach
rRNA: ribosomal RNA that is the organelle where translation and protein synthesis occur
Describe the process that adds amino acids to tRNAs.
Aminoacyl-tRNA synthetase attaches the correct amino acid to the 3’ end of the tRNA molecule
What is the immediate end product of transcription in eukaryotes?
pre-mRNA
How many base pairs encode one single amino acid? What is this sequence called?
Three; a codon
What is involved with pre-mRNA processing and why are each of these steps critical for proper protein synthesis?
5’ cap and poly-A tail helps exportation from the nucleus and prevent degrading; splicing removes introns and joins exons
How is RNA processing different in prokaryotes and eukaryotes?
There is only one RNA pol in prokaryotes, and three RNA pols in eukaryotes. Also, eukaryotes have mRNA processing.
Describe the role of introns and exons, and how these can create protein variability
Introns are non-coding sequences of DNA, and exons are coding sequences of DNA that create functional proteins. Introns always need to be removed. Alternative splicing at the end of transcription can allow for protein variability when combining different groups of exons.
What is the role of tRNA?
Adds amino acids to a polypeptide chain according to the mRNA sequence
How does tRNA work with mRNA and ribosomes during protein translation?
tRNA is the anticodon that is the complement of mRNA, which is the codon
What is the difference between polycistronic and monocistronic mRNAs, and how does translation start in each?
Monocistronic mRNA can only be transcribed by one polymerase and generates a specific protein. Polycistronic mRNA can be transcribed by many polymerases, and generates multiple relevant and functional proteins.
What are the three different sites on a ribosome and what happens at each of these sites? Does any of this require energy?
A site: accepts incoming aminoacyl tRNA (requires energy in the form of GTP).
P site: holds tRNA with amino acid attached; this is where peptide bond forms between existing chain and new amino acid (uses ATP).
E site: deacylated tRNA dissociates from ribosome
What are the three stages of translation? Describe them.
Translation occurs on mRNA in the 5’ to 3’ direction when a tRNA binds to a small rRNA and the small rRNA moves and finds the start codon (AUG, methionine). Then, initiation factors bring in the large rRNA to make the translation initiation complex. Elongation occurs at the sites A, P, E, in order (arrival, polypeptide, exit, including translocation which is the movement of tRNA from P to E). Termination is when a stop codon enters the A spot, and release factors bind to that codon, which triggers the release of the polypeptide from the ribosome.
What are elongation factors?
GTP-binding proteins that bring aminoacyl tRNAs to the A site of the large rRNA
Describe what a polyribosome is and why it might be beneficial for a cell to use this.
A single mRNA that can be translated simultaneously by several ribosomes in both eukaryotes and prokaryotes, which can increase efficiency
Describe ribosomal initiation
In eukaryotes, ribosomes are cap-dependent (recognize and bind to the 5’ cap before initiating translation). In prokaryotes, rRNA binds to the Shine-Dalgarno (SD) sequence, which is generally located around 8 bases upstream of the start codon.
What are key differences between rough ER and smooth ER?
Rough is studded with ribosomes, more flattened and sheet-like. Smooth has no ribosomes and is more tube-like.
What is made in the smooth ER vs. in the rough ER?
Smooth ER is the major site of phospholipid and cholesterol synthesis. Rough ER functions in protein synthesis for membrane-bound lumenal proteins or proteins that need to leave the cell.
Are the smooth ER and rough ER separate structures within the cell?
No
What is the role of flippases and why are they needed?
Flippases are enzymes that help phospholipids flip from the cytosolic layer to the lumenal layer (outside to inside) in the smooth ER.
What types of proteins are translated on the ER? Why?
Membrane-bound and secretory proteins destined for structures like the Golgi, plasma membrane, lysosomes, vesicles, endosomes, etc. because translating on the ER is a good way to get the proteins into the plasma membrane right away.
What types of protein modifications can be performed inside the ER?
Folding and quality control, adding sugars to proteins to make glycoproteins (glycosylation), and adding lipid anchors
What determines if a protein will be translated in the ER or in the cytosol?
It depends on if they have a signal sequence in their mRNA
Go through the steps of cotranslational translocation. What proteins are involved? What do each of these proteins do?
A signal recognition particle (SRP) binds to the signal sequence in the mRNA. The SRP then also binds to the SRP receptor (which is attached to the translocon). The ribosome opens up the translocon, and the SRP unbinds from the receptor. Translation resumes until the signal sequence is cleaved off. The finished product goes directly into the lumen of the ER.
What is BiP? Why does it need to be in the lumen?
A type of chaperone protein that helps correct unfolded proteins. It needs to be in the lumen because it needs to be where the newly synthesized proteins are.
What happens to proteins that are misfolded in the ER? What other proteins are involved in this process?
This process is called ERAD (ER-Associated Degradation). The misfolded proteins are marked with ubiquitin by the ubiquitin-ligand complex, then degraded by proteasomes.
What happens when there is an abundance of misfolded or unfolded proteins inside the ER?
There will be ER stress because there is an imbalance between synthesizing new proteins and correcting/processing the new proteins. This causes increased production of chaperones and proteasomes.
What indicates that a protein should be integrated into the membrane?
When the translocon reads the transmembrane sequence of 20-25 hydrophobic amino acids.
How can SRP help proteins become transmembrane proteins?
Signal recognition particles bind to the sequence to initiate and resume translation They bring transmembrane proteins to the ER through cotranslation translocation and post translation relocation
If a protein is supposed to have multiple transmembrane domains, how does this system integrate all of these domains?
With every new transmembrane sequence identified by the ribosome, the polypeptide chain is inserted into the membrane repeatedly, resulting in loops on either side of the membrane (cotranslational insertion)
How is cotranslational translocation different from post-translational translocation.
Cotranslational translocation is when ribosomes bind to the ER while simultaneously translating the proteins, so that the proteins can be dumped right into the lumen. Post-translational translocation is when free ribosomes translate proteins, which are then afterwards transported to the ER lumen.
Once glycoproteins and sphingomyelin are made, how will they be transported from the ER to the Golgi?
Glycoproteins will be on the lumenal side and sphingomyelin will be on the cytosolic side. Both are transported via transport vesicles to the Golgi.
What is the order of passing from the ER out to the rest of the cell?
ER to ERGIC (ER-Golgi intermediate compartment) to Golgi
Describe the structure of the Golgi apparatus
Cisternae are not continuous and are swollen at the margins. The cir face is the receiving side which faces the ER, and the trans face is the exiting side, which faces the rest of the cell.
What aspect of the Golgi do newly translated proteins enter? What aspect do they exit?
Enter the cis face and exit the trans face.
What are two important lipids created in the Golgi? What determines their final destination?
Ceramides are turned into glycolipids or sphingomyelin in the Golgi, and the coat proteins in the Golgi determine their final destination.
What is the difference between the cisternal maturational model and the stable cisternae model?
Cisternal maturational models are where the stacks move from cis to trans while maturing the proteins. The stable cisternae model is where the stack stays put but sends proteins from one stack to the next while maturing the proteins.
How do proteins, either lumenal or transmembrane, travel from one organelle to the next? What about these traveling structures allow them to integrate with a variety of different organelles?
Vesicles, which are formed by pinching the membranes of cells, so they can integrate with a variety of different membrane-bound organelles after being transported around the cell by dynein and kinesin.
What is a coat protein?
It determines where vesicles go. COP II goes from ER to ERGIC to Golgi, and COP I goes from Golgi to ERGIC to ER. Clathrin transports in both directions.
What about clathrin’s shape allows it to perform its function? How does dynamin help clathrin?
Clathrin is a triskeleton shape that becomes curved when it polymerizes. Dynamin helps by pinching off the stalk to release the vesicle into the cytosol.
Describe the roles of the following. proteins in the coating of clathrin: ARF, ARF-GEF, cargo protein, cargo receptor, and clathrin.
ARF-GEF activate ARF proteins (they’re activated once bound to GTP), which then recruit adaptor cargo proteins to the membrane. The cargo proteins interact with cargo receptors, which recruit clathrin. This creates a sphere, and dynamin pinches the stalk of the bud, and clathrin unbinds.
How does a vesicle fuse with the membrane of the target organelle or location?
Snares. The V snare of the donor organelle attaches to the T snare of the target organelle with the help of rab
What is KDEL?
A target peptide sequence that indicates the protein is an ER-lumenal protein and needs to go back to the ER via COP I.
What is the difference between endosomes, lysosomes, and proteasomes.
Endosomes are membrane vesicles that are formed by absorbing external material. Lysosomes are the cell’s stomach, and proteasomes (not membrane-bound) are the cell’s garbage can and shredder.
Describe the constitutive and regulated pathways.
Constitutive pathways happen continuously (default for most cells) and deliver proteins to the plasma membrane or ER if they have signal sequences. Regulated pathways wait for specific regulated signals (think neurotransmitters and calcium changes).
What is autophagy?
A mechanism done by lysosomes that breaks down and recycles the cell’s own components
How are Duchenne and Becker muscular dystrophies similar?
They are both a dystrophin gene mutation, but Duchenne has no dystrophin (due to a nonesense/frameshift mutation) and Becker has some misshapen dystrophin (due to a missense mutation). Becker is milder.
What is a sarcolemma?
Plasma membrane of a muscle cell.
What is a myofiber?
Muscle cell?
What is a myofibril?
Bundle of muscle cells
Where is the dystrophin protein found and why is it important?
It’s found in muscle cells. It links the cytoskeleton to the ECM.
What are premature termination codons and how do they relate to the diseases we looked at?
PTCs are the result of a nonsense mutation where translation finished early. They sometimes make a protein nonfunctional (like in cystic fibrosis and DMD).
Describe read-through therapy. How can it be used as a treatment for DMD and BMD?
When a random amino acid is added in response to PTCs. This can still result in a nonfunctional protein. It can treat DMD and BMD because it can allow the translation of mRNA to occur despite the PTC.
Describe nonsense-mediated mRNA decay. Is this helpful or detrimental to the cell?
It eliminates mRNA that contains PTCs. In a healthy cell, this is helpful, but in DMD/BMD, it’s detrimental.
Why would a combination of an NMD inhibitor and a read-through drug be better as a treatment than either of the drugs separately?
Using NMD after read-through therapy allows for a greater potential therapy for treating nonsense mutations.
What are fibroblasts in the context of the paper?
Places where NMD happens.
