Final Exam Flashcards
Main steps of RNA synthesis?
- Initiation
- Elongation
- Termination
RNA polymerase travels along DNA until the promotor site is found. The promotor region is the starting point of transcription. RNA polymerase recognizes the promotor because of transcription factors on it. The process of adding nucleotides to form a new RNA stops when RNA polymerase reaches a termination signal.
What are transcription factors?
These proteins are involved in transcription in all eukaryotes. They bind to specific spots on DNA and control the rate of transcription. Transcription factors are the most common form of gene expression regulation.
What are the ways in which RNA can be transcriptionally regulated?
- Transcriptional regulation is mediated by regulatory signals binding directly to intracellular receptors. This process is when a ligand binds to an intracellular receptor which activates the receptor. This complex together is called a dimer. The dimer can bind directly to DNA to act as a transcription factor. Can increase or decrease gene expression.
- Transcriptional regulation is mediated indirectly by cell-surface receptors. This process is when a ligand binds to a cell surface receptor which causes a cell signalling cascade all the way to the nucleus.
What is a Single Nucleotide Polymorphism (SNP)?
This is the most common type of polymorphism. This is when only one nucleotide letter is changed. Accounts for 90% of human genetic variation.
What is RNA splicing?
RNA splicing is a form of gene regulation that occurs post-transcriptionally in RNA but before the protein is created. Splicing cuts out the introns that code for nothing and leaves the exons to form a mature mRNA molecule. Splicing creates isoforms of a single gene.
What is the role of tRNA?
Transfer RNA is the RNA that transfers amino acids to the ribosome to attach to a growing peptide chain to form a protein. tRNA does not become a protein.
What is the role of rRNA?
Ribosomal RNA is the RNA that serves as the location for protein synthesis. rRNA does not become a protein.
What is mRNA?
Messenger RNA is the RNA that is actually translated into sequences of amino acids. The final product of mRNA will be a new protein.
When does post-translational modification occur?
Polypeptide chain covalently modified after it is released from ribosome.
When does co-translational modification occur?
Polypeptide chain covalently modified while still attached the the ribosome.
What are the 2 products of gene expression?
RNA or Protein
What is the function of DNA polymerases?
DNA polymerases synthesize the new DNA strands in the 5’ to 3’ direction.
What is nutrigenomics?
The study of the effect of specific nutrients on the expression of genes. An example includes SFA increasing inflammation while PUFAs block that activity.
What is nutrigenetics?
The study of how variations in our genes may increase of decrease the body’s needs for a specific nutrient.
What is epigenetics?
Refers to the influence of the environment, lifestyle, age, and disease conditions to change gene expression without changing the actual DNA sequences.
What are the proteins called that bind to distinct sites on DNA that controls DNA transcription to RNA?
Transcription factors
Types of bonds associated with the primary structure of a protein?
Peptide bond
Types of bonds associated with the secondary structure of a protein?
Hydrogen bond
Types of bonds associated with the tertiary structure of a protein?
Hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bonds
Types of bonds associated with the quaternary structure of a protein?
Hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bonds
Which protein folding level do side chains/ R interact?
Tertiary structure is when R groups begin to interact.
What are some different functions of protein in the body?
Proteins can be enzymes, they are in muscle fiber, used in transport, make hormones, antibodies protect body, and overall regulation.
A dehydrogenase enzyme indicates what type of reaction is going to take place?
Reduction reaction
What is non-competitive enzyme inhibition? How is Vmax and Km affected in this situation?
Non-competitive inhibition occurs when the inhibitor and substrate bind at different sites on the enzyme. Inhibitors can bind just the enzyme or the enzyme-substrate complex. Non-competitive inhibitors decrease the Vmax and cause no change in the Km.
What is competitive inhibition? How is the Vmax and Km affected in this situation?
Competitive inhibition occurs when the inhibitors bind reversibly to the same site the substrate would normally bind to. Competitive inhibitors do not affect Vmax but increase the Km.
What is Vmax?
The maximal velocity of an enzyme-catalyzed reaction at saturating substrate concentration.
What is Km?
This is the Michaelis constant. It measures the affinity an enzyme has for its substrate. Basically, this is the substrate concentration when the reaction velocity is half Vmax.
What does having a high or low Km mean for an enzyme?
High Km values correspond to low enzyme affinity for a substrate. This means more substrate concentration is needed to reach 50% of Vmax.
Low Km values correspond to high enzyme affinity for a substrate. This means less substrate concentration is needed to reach 50% of Vmax.
What is the purpose of the two sites on an allosteric enzyme?
There is a catalytic site that fits the substrate and an allosteric site that fits the effector/ allosteric modulator.
What is the difference between a homotropic and a heterotropic enzyme?
An allosteric enzyme is homotropic if the substrate itself is also the modulator. It is heterotrophic when the modulator and substrate are two different molecules.
What type of curve do allosteric regulators generate?
Sigmoidal curve
What is cooperativity?
Cooperativity refers to the observation that the binding of a substance to one binding site increases or decreases the binding to another site.
Where is most NADH/FADH2 generated that goes to the electron transport chain?
The Krebs cycle/ citric acid cycle
Which pathways/ reactions generate CO2?
PDH complex and Krebs Cycle
What are the end products of oxidative phosphorylation? (Includes redox rxns and complex V)
NADH is broken down to release NAD+, 2 Hydrogens, and 2 electrons. FADH2 is broken down into FAD, 2 electrons, and 2 hydrogen atoms. We also form water and ATP.
Where does the electron transport chain take place?
The inner layer of the mitochondrial membrane. Both ETC and oxidative phosphorylation continue consistently in all tissues that contain mitochondria.
Where does the kreb’s cycle take place?
TCA/ Kreb’s/ Citric acid cycle occurs in the mitochondrial matrix, so it can be close to the ETC.
Where does gluconeogenesis take place?
90% in the liver and 10% in the kidneys
Where does glycolysis take place?
Carried out by all tissues and occurs in the cytosol.
What is the end product of gluconeogenesis, and what is the energy investment?
The end product is glucose. The energy investment for making 1 glucose molecule is 6 high-energy phosphate bonds (ATP/GTP), 2 NADH, and 6 carbons (coming from pyruvate, lactate, glycerol, or glucogenic amino acids).
What is the end product of glycogen breakdown?
90% of the product is glucose-1-phosphate and 10% of product is free glucose
Which macronutrient is used to generate glycogen?
Carbohydrates broken down into glucose.
In which tissues is glycogen stored and released?
100 grams stored in liver and 300-400 grams stored in skeletal muscle
Liver glycogen is broken down to provide energy for which tissues?
Tissues that can use glucose as an energy source to make ATP. The whole body basically
Muscle glycogen is broken down to provide energy for which tissues?
Muscle is selfish, the glycogen broken down here is used by the muscle to make energy.
Are glucagon and epinephrine receptors located on the liver and muscle tissue? What is the significance of the location of these receptors?
The liver has both glucagon and epinephrine receptors, while the muscle just has epinephrine receptors.
What are the end products of aerobic glycolysis?
2 Pyruvate, 2 ATP (made 4 but invested 2), and 2 NADH
What are the end products of anaerobic glycolysis?
2 lactate, 2 ATP, 0 NADH
Which enzymes are irreversible steps in glycolysis?
- Glucose to Glucose-6-phosphate by enzyme hexokinase/glucokinase.
- Fructose-6-phosphate to fructose-1,6-bisphosphate via phosphofructo kinase-1 (PFK1).
- Phosphoenol pyruvate to pyruvate via enzyme pyruvate kinase
Which enzymes are irreversible steps in gluconeogenesis?
- Pyruvate to oxaloacetate via enzyme pyruvate carboxylase
- Oxaloacetate to phosphoenol pyruvate via enzyme phosphoenol pyruvate carboxylase (PEPCK)
- Fructose-1,6-bisphosphate to fructose-6-phosphate via enzyme fructose-1,6-bisphosphatases (F16BP)
- Glucose-6-phosphate to glucose via the enzyme glucose-6-phosphatase