Exam Questions Flashcards
What are two mechanisms that increase the transcription of a gene?
- Reassembling histones by modifying enzymes to change the local structure of chromatin
- Enhance bind to transcription factors to enhance transcription
Examples of coenzymes
- NAD+
- FAD
Examples of post-translational modifications
- Phosphorylation of serine
- Acetylation of lysine
- Ubiquitylation of lysine
Mechanisms of regulating cellular localization
- Dephosphorylation by phosphatase
- Binding a lipophilic signaling molecule to cross the plasma membrane
- Degradation of a regulatory subunit to release it from the transcription factor
Features of enzyme-coupled receptors
- Binds a hydrophilic signaling molecule ligand
- Activation involves cross-phosphorylation of tyrosine kinase domains
- Contains at least 2 separate transmembrane polypeptide subunits
Advantage of transcriptional regulation
Uses allosteric regulation to activate/inhibit protein activity
Advantage of activity regulation
- Conserves energy
- Once a protein is synthesized, activity regulation ensures that it is only active when needed
Dimerization
- Provides increased stability of a protein
- Increases the efficiency of transcription through allosteric regulation
Ways to regulate gene expression
- Ubiquitylation (protein)
- Alternative splicing (RNA)
- Allosteric regulation (protein)
- Promoters and enhancers (RNA)
Ways to regulate the function of a protein
- Post-transalational modifications
- Allosteric regulation
- Feedback control: a downstream enzyme or molecule can send a signal upstream to increase or degrade the production of a molecule
- GEF and GAP
Example of epigenetic regulation
A transcription factor regulating its own expression in a positive feedback loop
Transcytosis
- Transport of proteins from one side of a polarized cell to the other cell (apical to basolateral)
Mechanisms for regulating ion channels opening and closing
- Distortion of cell membrane (open)
- Changes in voltage (close)
- Binding neurotransmitters to sites that are away from channel pore (close)
Describe treadmilling
- When the rate of ATP-bound actin being added to the (+) end is equal to. the rate at which ADP-bound actin is leaving the (-) end
- Creates dynamic instability
How can directional movement be derived from a reversible process
- Can be derived with ATP
- When motor proteins bind to ATP, this is reversible
- However, when ATP is hydrolyzed, it is NOT reversible and allows motor proteins and molecular pumps to move along the cytoskeleton
Constitutive secretory pathway vs. Regulated
- Constitutive: does not require a signal for the vesicle to travel and fuse with the plasma membrane to transport cargo
- Regulated: requires an outside stimulus that binds to the plasma membrane and creates signal transduction that tells the vesicle that it can fuse with the membrane and release cargo
Mechanism to degrade mRNA
- miRNA binds to complementary target mRNA
- This binding will facilitate the degradation by RISC
Mechanism to degrade protein
- Ubiquitylation via ATP hydrolysis
- Protein gets tagged by ubiquitin and is marked for degradation
- A proteasome comes in and cuts it into smaller pieces
What do vesicles do
Use cargo receptors to capture proteins being transported
Simple diffusion
- Transport kinetics show a linear relationship with concentration
- Down the gradient
Transport-mediated diffusion
- Transport can be saturated
- Transport can occur against the gradient
What is true of nuclear localization sequence
Contain at least 5 basic amino acids in a row
SRP purpose
Co-translational transport of proteins
Rabs
Regulate vesicle trafficking
SNARES
Regulate membrane fusion
Retrograde transport
Allows cargo receptors to be recovered from the Golgi and return to the ER
Kinesins
Motor proteins that move from the (-) end of microtubules to the (+) end
TOM complex
- Transporter of the outer mitochondrial membrane
- Uses ATP hydrolysis to unfold proteins and bring them into the intermembrane space
Describe a process that involves GTP hydrolysis
- RAN cycle is involved with nuclear import and export
- During import, RAN-GAP phosphorylates RAN-GTP into RAN-GDP, which allows cargo to be picked up in the cytosol and brought to the nucleus
- During export, RAN-GEF phosphorylated RAN-GDP into RAN-GTP, which releases the cargo in the nucleus
- RAN-GTP leaves the nucleus and the cycle repeats
- The Rho family of GTPase is vital in regulating the formation of actin filaments in specific structures
- Rho-GTP stimulates actin bundling which results in stress fibers forming
- Cdc42-GTP stimulates actin bundling and polymerization
- This family regulates actin cytoskeleton formation
Dynamic model
- When the vestibular tubular cluster that is formed from the vesicles in the ER becomes the new cis Golgi cisternae
- The new cisternae will shift down the stack as more vestibular tubular clusters form
- Vesicles will only form during retrograde transport when contents in the Golgi want to go back to the ER
Major components of the cytoskeleton and the structural component
- Microtubules: tubulin
- Microfilaments: actin
- Intermediate filaments: keratin
Facilitated diffusion
- Moves substances down an electrochemical gradient
- Does not require energy
- Occurs within ion channels and mediated transporters
- Ion channels open and close in the presence or absence of a stimulus
- Mediated transporters undergo conformational change to allow contents to flow through the membrane
Active transport
- Moves substance up the concentration gradient
- Requires energy
- Occurs within ATPases and coupled transporters
- ATPases such as the V pump use energy from ATP hydrolysis to push H+ up its concentration gradient
Name 3 mechanisms used by cells to move proteins across compartments
- Gated transport between the cytosol and nucleus through nuclear pores that requires a nuclear localization sequence
- Transmembrane transport occurs between organelles that are topologically different such as from the cytosol to the ER which requires an ER signal sequence
- Vesicular transport occurs between topologically similar organelles such as from the ER to the Golgi through vesicles coated with proteins
What are the 3 post-transcriptional processing events in eukaryotic mRNA
- 5’ cap addition
- Splicing
- 3’ poly-A tail addition
Describe 2 types of ion channels
- Ligand-gated: a ligand is required to bind to the channel to open it which will cause a conformation change, this allows the cell to control what molecules enter the channel
- Voltage-gated: requires a specific voltage for the cell to open and is based on electrical potential
Describe how the 3D structure of RNA is important for the regulation of protein translation
- The 3D structure of the ribozyme is made of RNA
- Ribozymes are enzymes that catalyze reactions such as RNA cleavage
- They can ensure that mRNA is not translated into proteins by cutting them which directly affects translation because it prevents mRNA from reaching the ribosome
One type of actin-based fiber that is formed after activation of a Rho family GTPase
Stress fibers
What are short RNAs encoded that form hairpin structures and can control the stability and translation of mRNA
miRNA
What does siRNA associate with to form the RISC complex
Argonaute
What is the coat protein involved in forming coated pits during endocytosis
Clathrin
What is the large proteolytic complex that degrades ubiquitylated proteins
Proteasome
In an aqueous environment, the outside of a soluble protein generally consists of side chains with WHAT chemical quality
Hydrophilic
What motif contains both DNA-binding and dimerization function
Leucine zipper
What is false about the nucleus
Does NOT only contain DNA and RNA
G-protein coupled receptors
They are coupled intracellularly to inactive heterotrimeric G proteins
Mechanisms of gene regulatory proteins
- A signal from a neighboring cell may lead to expression of the gene regulatory protein
- These proteins may positively regulate their own expression
- These proteins may be activated by phosphorylation or dephosphorylation
Which type of junction provides adhesive attachment between two cells
Desmosomes
Advantages of metabolic cycles
- Multiple entry points for alternative metabolic structures
- Productions of intermediate metabolites that can be used by the cells for other purposes
- Presence of multiple regulatory points
What lipid would be found mostly on the inner leaflet
Phosphatidyl-serine
What allows a nonspontaneous reaction to take place in a cell
Coupling the reaction to hydrolysis of ATP
Where does glycolysis take place
Cytosol
How do cells overcome the thermodynamic issue to allow polypeptide synthesis to occur
- Cells use the process of coupling tRNA by aminoacyl-tRNA synthetase
- Amino acids are bound to ATP
- ATP hydrolysis occurs which binds AA to AMP
- AA will attach to tRNA via aminoacyl-tRNA synthetase
- This enzyme will proofread the codon and anticodon pairings of the AA to tRNA
- tRNA brings the AA to the ribosome to be added to the growing polypeptide
Paracrine signaling
Sending a signal to nearby cells to induce a response
Endocrine signaling
Sending signals (hormones) far away from the source to distant cells usually through the blood
Contact-dependent signaling
Sending signals to cells that are in direct contact with the cell that sent the signal
Autocrine signaling
The cell releases signals that bind to its own receptors to induce a response
Explain how phosphoinositol lipids are used to distinguish different membranes
Inositol can be phosphorylated in different positions on the membrane and is recognized based on where it is phosphorylated
Describe two mechanisms that allow transport to go up its concentration gradient
- Coupled transport: a molecule can be transported up a gradient by being coupled to a molecule that is going down its gradient (ex. Na+/K+ ATPase pump acting as an antiporter)
- Using Non-ATP pumps that use physical forces such as light to generate their concentration gradient
