C1 + C3: Week 3 Quiz

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What happens to terminally misfolded proteins in the ER? Explain.

(Dr. Robinson and Dr. Tatchell combined). Misfolded proteins can aggregate, causing serious problems for ER function as well as the loss of protein function. Proteins that fold inefficiently can sustain alterations that result in misfolding. These terminally misfolded proteins meet ERAD, or ER-Associated Protein Degradation. These misfolded proteins, despite many attempts by chaperones, are essentially exported from the ER and degraded by a cytosolic proteasome. First, recognition of improperly folded or slow-folding protein is done by BiP and other proteins in the ER lumen. Once targeted, the protein is translocated through the ER membrane to cytoplasmic face of the ER with the assistance of AAA+ ATPase Cdc48/p97/VCP. Multiple E3s ubiquitinate the partially translocated protein. The proteasome degrades the proteins. (CC)

The _____ consensus sequence is an AT-rich DNA sequence where the double-stranded DNA will be separated to initiate transcription.

-10

What are the two types of repressor proteins?

1. "Dedicated": These proteins always repress transcription. 2. "Situational": They function to repress transcription in some contexts, but activate transcription in others.

What are the two recognition sequences in the prokaryotic promoter?

1. -35 Consensus Sequence: 5'TTGACA3' 2. Pribnow Box (-10 Consensus Sequence): 5'TATAAT3'

What are the two parts of the proteasome? What are their functions?

1. 20S Core: contains a hollow chamber with active proteases 2. 19S Lids: regulates admission into the core protease

What are two examples of E3 specificity that occur in the cell cycle?

1. A cell protein, such as p27, is stable until it is phosphorylated. This phosphorylation targets the protein to E3. 2. A cell protein, such as cyclin, is stable until E3 is activated by phosphorylation. When E3 is activated, it targets the protein for degradation. (CC)

What are the three general steps of protein degradation through proteasomes?

1. A substrate containing a polyubiquitin chain of four or more ubiquitins and a specific linkage (mostly K48) is recognized by the proteasome. 2. The substrate is bound to the proteasome and destroyed. 3. Ubiquitin is recycled by DUBs to be used again.

What are two ways in which O-linked glycosylation is critical for recognition functions?

1. ABO Blood Groups: A, B, and O are alleles of a glycosyl transferase that can generate terminal GalNAc (type A) or terminal Gal (type B) on O-linked "H substance" carbohydrate chains on cell surface proteins and lipids. Type AB has both transferase activities, thus, both types of carbohydrate chains are present. Type O is a null allele of the transferase, thus neither modification occurs. 2. Selectin glycoproteins on endothelial cells bind mucin-like glycoprotein selectin ligands on white blood cells. This mediates white blood cell rolling in circulation that allows tight binding and extravasation. (CC)

What are the three receptors in the ER membrane that initiate the unfolded protein response?

1. ATF6 2. PERK 3. IRE1

What are the three primary mechanisms of chromatin remodeling?

1. ATP-Driven Chromatin Remodeling Machines 2. Covalent Modifications of Histone Tails 3. Histone Variants

What are the three functions of farnesyl transferase?

1. Adds farnesyl group to Cys residue. 2. Cleaves the last three amino acids of the the CAAX box. 3. Methylates the Cys residue on the C-terminus. (CC)

What are the two types of neurons? Differentiate between each.

1. Afferent Neurons: sensory division; from periphery to the central nervous system; "are affected" 2. Efferent Neurons: motor division; from the central nervous system to the periphery; "have an effect"

What are three ways to reconcile human complexity with genetic complexity? Explain each.

1. Alternative Splicing: Through alternative splicing, one pre-mRNA can give rise to several different isoforms of the mature mRNA molecule. 2. Combinatorial Control: For example, combinations of transcription factors can differ from cell to cell. Small numbers of gene products can be combined to generate diversity. 3. DNA with Undiscovered Functions: Maybe?

The tRNA synthetase has specificity for what two things?

1. Amino Acid 2. tRNA

What are the two steps of aminoacylation? Describe each.

1. Amino Acid Activation and Transfer to Adenylate: In step one, the aminoacyl-AMP is bound to the tRNA synthetase. The reaction is driven forward by PPi hydrolysis. This inorganic PPi is cleaved almost immediately by pyrophosphatase into inorganic phosphate. This removes products from the reaction. When products are removed, the reaction is driven in the forward reaction. Overall, this reaction requires the hydrolysis of two high energy bonds, providing the energy required to form the bond between the amino acid and the tRNA. 2. Transfer of Aminoacyl Group from Adenylate to tRNA: The hydrolysis of the high energy ester bond linkage will drive peptide bond formation. (CC)

Different aminoacyl-tRNA synthetases use different mechanisms to attain high fidelity of proper amino acid aminoacylation. What are those two mechanisms?

1. Amino Acid Affinity 2. Proofreading of Aminoacylation (CC)

What are the two aspects of infidelity?

1. Amino Acid Binding 2. tRNA Binding

What are the products of the proteasome?

1. Amino Acid Peptides (8-10) 2. Most peptides are degraded by aminopeptidases. 3. Some peptides are used for antigen presentation.

What are the three things regarding tRNA binding that contribute to aminoacyl-tRNA synthetase specificity? Explain each.

1. Anticodon Loop: This is most important, as this loop is what the mRNA sees during translation. As a result, aminoacyl-tRNA synthetase does interact with the anticodon loop. 2. Acceptor Stem: The acceptor stems of all tRNAs are not equal. A particular GU base pair in the stem can be changed to, for example, CG, and result in the misacylation of alanine. 3. Multiple Determinants: Both anticodon and acceptor stem elements and/or other sites, such as odd base pairs, on the tRNA can contribute to specificity.

What are the four steps of transcription? Which are the most commonly regulated?

1. Assembly 2. Initiation 3. Elongation 4. Termination

What are the two components of the motor (efferent) division of the peripheral nervous system? Differentiate between each.

1. Autonomic Nervous System: controls involuntary responses. The ANS involves the GVE fibers. 2. Somatic Nervous System: controls voluntary movement. The SNS involves the GSE fibers.

What are the three types of cross-sections used for CT images? Differentiate between each.

1. Axial: If a patient is lying supine and are sliced like a loaf of bread, axial images are produced. 2. Coronal: If a patient is lying supine, coronal images would be viewed from the top. 3. Sagittal: If a patient is lying supine, sagittal images are viewed from the side.

What are the two keys to fidelity in isoleucyl-tRNA synthetase?

1. Binding Step 2. Hydrolysis Step

What are the two components of the central nervous system?

1. Brain 2. Spinal Cord

Give some example of Ca2+ binding lectins.

1. Calnexin 2. Calreticulin

What are the steps of vesicular transport? Differentiate between each.

1. Cargo Recruitment: Cargo is protein that is carried in a vesicle. 2. Vesicle Budding: Specialized proteins act to pinch off the membrane and cause deformation of the membrane to form a vesicle with the cargo protein. 3. Targeting-Docking: Proteins within the vesicle target the vesicle to its final destination. 4. Fusion: The proteins on the outside of the vesicle will be recognized by proteins on the membrane face of the protein's final destination and allow them to fuse to the membrane. Docking is the process by which proteins bind together to allow fusion to occur.

What are the four postganglia of the aortic plexus? What are their respective preganglia?

1. Celiac Ganglion: Greater Thoracic Splanchnic Nerves 2. Superior Mesenteric Ganglion: Lesser Thoracic Splanchnic Nerves 3. Aorticorenal Ganglion: Least Thoracic Splanchnic Nerves 4. Inferior Mesenteric Ganglion: Lumbar Splanchnics

What preganglia and postganglia form the aortic plexus?

Codon assignment experiments used synthetic mRNAs that did not contain AUG codons. How was it possible to achieve protein synthesis from these synthetic mRNAs?

1. Cell-free translation systems are not as selective as translation in the cell due to the loss of regulatory proteins, and the cell-free translation systems do not have competing endogenous mRNA. 2. Translation of synthetic mRNA is very inefficient. The experiments utilized radiolabeled amino acids, which allowed the identification of low amounts of product.

What are the two main divisions of the nervous system?

1. Central Nervous System 2. Peripheral Nervous System

What are four ways in which chromatin structure is altered? Differentiate between each.

1. Chromatin Remodeling Machines: After the activator protein binds to DNA, they can recruit the chromatin remodeling machines. The machines can push the nucleosome to slide along the DNA so some parts are more or less condensed than others. 2. Histone Removal: After the activator protein binds to DNA, they can recruit the chromatin remodeling machines. The chromatin remodeling machines can bind to DNA and recruit histone chaperone proteins. These chaperone proteins can remove histone proteins, generating the DNase I hypersensitive site. This DNA region is very accessible to protein factors. 3. Histone Replacement: After the activator protein binds to DNA, they can recruit the chromatin remodeling machines. The chromatin remodeling machines can bind to DNA and recruit histone chaperone proteins. These histone proteins can replace conventional histones, remodeling the chromatin structure and making the DNA more accessible to protein factors. 4. Histone Modification: After the activator protein binds to DNA, they can recruit histone modification enzymes. For example, these enzymes can acetylate histone tails, making the chromatin more open and accessible to protein factors. (CC)

What four things do activator proteins recruit?

1. Chromatin-Remodeling Proteins 2. Co-Activators/Mediator 3. General Transcription Factors (TBP/TFII2, TFIIB, TFIIF, TFIIE, TFIIH) 4. RNA Polymerase

What are the six mechanisms by which eukaryotic gene regulatory proteins repress transcription? Differentiate between each.

1. Competitive DNA Binding: When the repressor protein binds to DNA, the activator protein cannot bind to the DNA. 2. Masking an Activating Surface: The activator protein can still bind to DNA; however, the activating surface is masked by the repressor protein. As a result, the activator protein cannot activate transcription. 3. Direction Interaction with General Transcription Factors: When the repressor protein interacts with general transcription factors, the activator cannot interact with the general transcription factor. The activator protein cannot activate transcription. 4. Recruitment of Chromatin Remodeling Complexes: The recruitment of chromatin remodeling machines can lead to the formation of the more compacted chromatin structure. 5. Recruitment of Histone Deacetylases: Repressor proteins can recruit HDAC to remove acetylation modifications and induce the formation of closed chromatin structure. 6. Recruitment of Histone Methyltransferases: The repressor protein can recruit histone methyltransferases to establish the H3K9me3 mark, forming heterochromatin and silencing transcription of those genes.

What were the two original models of translation? Describe each.

1. Conformation Model: RNA is full of small complementary pieces. The secondary structures formed by these complementary pieces would indicate what amino acid is incorporated into the protein. Further, mRNAs are very long, so they could encode for a long polypeptide sequence. This is obviously false. 2. Adaptor Model: tRNA uses its anticodon to determine what amino acid are incorporated into the protein.

What are the two types of E3 degradation?

1. Constitutive Degradation: E3 degrades proteins at all times. 2. Regulated Degradation: E3 is regulated to degrade proteins.

What are the two types of heterochromatin? Differentiate between each.

1. Constitutive: Constitutive heterochromatin is always condensed. It is concentrated at telomeres and centromeres and does not contain any functional genes. 2. Facultative: Facultative heterochromatin is a form of chromatin that is conditionally silenced. Facultative heterochromatin is expressed in some cells, but not other cells. For example, the globin gene is only expressed in red blood cells. As a result, in red blood cells, the globin gene locus is located in a euchromatin region because it is transcriptionally active. In all other cells, the globin gene locus is located in heterochromatin and will be transcriptionally inactive.

What are the two parts of the RNA polymerase holoenzyme?

1. Core Enzyme (α2ββ'ω) 2. Sigma Factor (σ)

What are the two types of meninges?

1. Cranial Meninges 2. Spinal Meninges

What are the two types of peripheral nerves?

1. Cranial Nerves 2. Spinal Nerves

What are the two classes of transposable elements? Differentiate between each.

1. DNA transposons use a cut-and-paste transposition mechanism that does not involved an RNA intermediate. These DNA transposons make up 3% of the human genome. 2. Retrotransposons are transcribed from DNA into RNA, and then, they are reverse transcribed into double-stranded DNA. They can serve as templates for multiple daughter elements, resulting in the expansion of transposable elements using a copy and paste mechanism. The three types of retrotransposons include LINEs, SINEs, and others.

What is the common structure of site-specific gene regulatory proteins?

1. DNA-Binding Domain: recognizes and binds a specific DNA sequence. 2. Effector Domain: involved in protein-protein interactions. The regulatory proteins can recruit additional protein factors to the local DNA sequence and regulate transcription of the local gene.

What are three differences between acetylation of the N-terminus and acetylation of lysine residues?

1. Different enzymes are used. 2. Different substrates are used. 3. Acetylation has different effects on proteins. (CC)

The grey matter of the spinal cord branches into:

1. Dorsal Horn 2. Lateral Horn 3. Ventral Horn

What are the three layers of meninges? Differentiate between each.

1. Dura Mater: outside layer 2. Arachnoid Mater: middle layer 3. Pia Mater: inner layer. It is attached to the surface of the brain and spinal cord.

What three enzymes are responsible for carrying out ubiquitylation?

1. E1 2. E2 3. E3

What are the three functions of E1 in ubiquitylation? Explain each.

1. E1 adenylates ubiquitin. Ubiquitin binds to a pocket in E1 and becomes adenylated by ATP hydrolysis, producing adenylated ubiquitin and pyrophosphate. This is a high energy bond, so there is a high amount of free energy is this ubiquitin bond. 2. E1 transfers ubiquitin to a Cys residue in the active site of E1, producing a thioester bond. 3. E1 contains a separate domain that recognizes E2. E1 binds to E2 and transfers ubiquitin to a Cys residue on E2. (CC)

What are the two functions of EF-Tu? Explain how it carries out both functions.

1. EF-Tu ensures correct codon-anticodon interaction. This is another contribution to translational fidelity. When the appropriate aminoacylated tRNA is bound, the appropriate conformation of the ribosome stimulates GTP hydrolysis and releases EF-Tu. 2. EF-Tu protects the ester linkage of the amino acid to the tRNA. Binding to the acceptor arm protects the linkage from hydrolysis before entry into A site, which minimizes energy waste. (CC)

What three factors are required for translation elongation in prokaryotes? What is the function of each?

1. EF-Tu is a GTPase that mediates the entry of aminoacylated tRNA into the A site. 2. EF-Ts is the corresponding GEF to EF-Ts. 3. EF-G is a GTPase translocase that mediates translocation, or the movement of deacylated tRNA from the P site to the E site as well as movement of acylated tRNA to the P site, coupled by the movement of the mRNA.

Give an example of personalized medicine.

1. EGFR is often elevated in NSCLC, pancreatic, breast, and colon cancer. The EGFR activates signaling cascades via tyrosine kinases. Patients who have elevated EGFR can be placed on tyrosine kinase inhibitors. However, if patients carry the mutation in exon 20 of the EGFR gene or the T790 mutation, these patients would not respond to a tyrosine kinase inhibitor. However, third generation tyrosine inhibitors specifically target these mutations. The tumor genome can be sequenced, and then it could be decided how to treat the patient. 2. Women who carry the BRCA mutation are predisposed to breast and ovarian cancer. BRCA mutations can be treated with PARP inhibitors.

What are the three layers of connective tissue that surround peripheral nerves? Differentiate between each.

1. Endoneurium: The endoneurium is the inner layer of connective tissue that surrounds individual axons. 2. Perineurium: The perineurium is the middle layer of connective tissue that surrounds fascicles. 3. Epineurium: The epineurium is the outer layer of connective tissue that surrounds the entire nerve.

What are two important consequences of the aminoacylation of tRNAs? Describe each.

1. Energetics: Peptide bond formation is not an energetically favorable reaction. An amino acid-tRNA ester linkage has favorable energy of hydrolysis, so transfer of an amino acid from the tRNA to another amino acid is energetically favorable. 2. Fidelity: tRNA synthetases are the genetic code decoders, so fidelity must be high because whichever amino acid is linked to the tRNA will be incorporated at the codon specified by that tRNA's anticodon.

How can we tell right and left on an x-ray?

1. Every x-ray must label by law right and left sides of the chest. 2. In most patients, the hemidiaphragm on the right side of the patient will be higher than the left side. 3. In most patients, the heart protrudes more toward the left side because the left ventricle is more muscular than the right atrium. 4. The aortic knob is located to the left side of the spine.

What are two long-lived proteins?

1. Extracellular Proteins (collagen, lens crystallin) 2. Selected Cellular Proteins (histones, nuclear pore proteins)

What are the three types of lipid modifications for proteins?

1. Farnesylation and geranylgeranylation (prenylation) at Cys residues 2. Myristoylation at the N-terminus 3. Palmitoylation at Cys residues

How are protein kinases and phosphatases important drug targets? Give an example.

1. Fk506 (Tacrolimus) is a phosphatase calcineurin inhibitor. This drug is used for immunosuppression. 2. Rapamycin (Sirolimus) is a protein kinase mTOR inhibitor. This drug is used for immunosuppression. 3. Imatinib (Gleevec) is a Bcr-Abl tyrosine kinase inhibitor. This drug is used to treat chronic myelogenous leukemia (CML). (CC)

Describe two single sugar O-linked modifications.

1. GalNAc can be added to many cytosolic and nuclear proteins in a reversible way, unlike other glycosylation. 2. Fucose is added onto circulatory and ECM proteins. (CC)

What are the four functional components of spinal nerves? Differentiate between each.

1. General Somatic Afferent (GSA): conduct sensory impulses from the skin, skeletal muscles, tendons, and joints to the spinal cord. They are the primary sensory fibers that convey touch, pain, and proprioception. 2. General Somatic Efferent (GSE): lower motor neurons that carry motor impulses from the spinal cord to the skeletal muscles 3. General Visceral Afferent (GVA): conduct sensory impulses (typically due to pain or reflex sensations) from the internal organs, glands, and blood vessels to the spinal cord 4. General Visceral Efferent (GVE): conduct motor impulses from the spinal cord to the internal organs, glands, and blood vessels

How does genomics impact medicine?

1. Genomics impacts medicine through personalized medicine. Personalized medicine refers to the knowledge of particular genomic variants that can help studying the effects of a particular drug, for example, and tailor therapy to a particular population. Patients can be grouped into several subgroups depending on the toxicity and benefit of the drug to the patient. But how would we know how to group these patients? Genomic variants could help group these patients and better treat their ailment. 2. Genomics can allow the identification of genetic susceptibility to disease. For example, the use of genomics can identify individuals with the lipoprotein LPA polymorphism and treat these individuals with baby aspirin to prevent coronary heart disease. 3. If the mutant gene can be identified that cause a disease, RNAi can be used to specifically silence the expression of the mutant protein. 4. CRISPR-Cas9 can be used to fix diseases at the DNA level.

What are the five major classes of histone proteins?

1. H1 2. H2A 3. H2B 4. H3 5. H4

What are the two mechanisms that aid in the formation of the 30 nm fiber?

1. H1 controls the direction of the DNA after the DNA emerges from the nucleosome core. It helps position the nucleosome in such an angle that the nucleosome can form the left-handed helix. This allows the left-handed helix to be compacted, with H1 directing the relative positioning of successive nucleosome and the pattern of nucleosome-nucleosome contacts, to form the 30 nm fiber. 2. The histone tails project from the core histones. They can interact with other nucleosomes, helping position the nucleosome to form the highly-compacted 30 nm chromatin structure and higher-order chromatin structures.

Which histone proteins form the core?

1. H2A 2. H2B 3. H3 4. H4

Give some examples of DNA-binding motifs.

1. Helix-Loop-Helix 2. Helix-Turn-Helix 3. Leucine Zipper 4. HMG-Box: contact DNA through the major and minor groove 5. Zinc Finger: form a finger-like structure to make contact with the DNA

What are the two classes of proteins associated with DNA?

1. Histone Proteins 2. Non-Histone Proteins

What are four functional consequences of histone modifications?

1. Histone modifications can help establish global chromatin environments. For example, a hallmark of heterochromatin structure is trimethylation of H3K9. This mark can recruit additional histone modification enzymes to make the same mark on adjacent histone proteins. As a result, the mark can spread along the chromatin structure, establishing the heterochromatin structure along the chromatin. 2. Changes in gene expression and the recruitment of proteins involved in gene expression, including activators and repressors, can result from histone modifications. Proteins can recognize the modification mark and recruit activators and repressors to regulate transcription. 3. Histone modifications can help in the recruitment of proteins involved in DNA repair. 4. Histone modifications can help in the recruitment of proteins required for DNA replication. (CC)

What are the two types of dimers often formed by transcription factors?

1. Homodimers 2. Heterodimers

What are three physiological roles of proteasomes?

1. Housekeeping: Proteasomes are active at all times to destroy misfolded and oxidized proteins. 2. Regulated Protein Destruction: Proteasomes are involved in regulated protein destruction during the cell cycle, transcription, and signal transduction. 3. Immune Response: Modified proteasomes have different enzyme activities that produce peptides that are used in antigen presentation.

Give some examples of ATP-dependent chaperone proteins. Differentiate between each.

1. Hsp70 Family (BiP): folding 2. Hsp90 Family: denature and refold 3. Hsp40 Family: work with other members of the Hsp family to fold proteins (CC)

What two things did comparative genomic studies reveal?

1. Humans and other mammals share most of the same genes. 2. Large blocks of the genome contain genes in the same order. The homeobox genes, for example, are involved in the anterior and posterior segmentation of the embryo. They are organized in the same order from Drosophila to humans.

When is IV contrast not used for CTs?

1. If a patient presents with possible kidney stones, kidney stones are dense without the use of contrast. 2. Subacute blood is very dense. On a CT, it is very visible.

What are two specialized core particles?

1. Immunoproteasome 2. Thymoproteasome: contain specialized β1, β2, and β5 subunits that produce specialized peptides

Differentiate between LINE and SINE translocation.

1. LINE elements contain an RNA polymerase II promoter so RNA polymerase II can recognize the promoter and bind to the promoter, transcribing a large RNA. The large RNA has two open reading frames, where one can make a protein that contains reverse transcriptase and endonuclease activity. Using the reverse transcriptase activity, it will reverse transcribe its RNA into double-stranded DNA. Using the endonuclease activity, it will induce double-strand cleavage and insert itself into the genome. 2. SINE elements have an RNA polymerase III promoter so RNA polymerase III can recognize the promoter, bind to the promoter, and transcribe and small RNA. The RNA does not contain any open reading frames, so it will depend on LINE elements for transposition. It will use the reverse transcriptase encoded by LINE elements to reverse transcribe RNA into double-stranded DNA. It will use the endonuclease activity of the LINE elements to cut and insert itself into the genome.

What are the three classes of retrotransposons? Differentiate between each.

1. LINEs (long-interspersed elements) are transcribed by RNA polymerase II. They are about 6000 bp long and make up about 21% of human DNA. 2. SINEs (short-interspersed elements) are transcribed by RNA polymerase III. They are about 300 bp long and make up about 13% of human DNA. 3. Other, LTR-containing elements make up about 8% of human DNA.

What preganglia form the hypogastric plexus?

1. Lumbar Splanchnics 2. Sacral Splanchnics

What are three functions of lysine acetylation?

1. Lysine acetylation is used in histone regulation. HATs acetylate histones while HDACs deacetylate histones. Histone acetylation plays a role in epigenetics and gene expression. 2. Acetylation of the p53 tumor suppressor is required for its activity. 3. Acetylation stabilizes cytoskeletal microtubules. (CC)

What are the seven histone post-translational modifications that are performed by enzymes on the N-terminal tails?

1. Methylation 2. Citrullination 3. Acetylation 4. SUMOylation 5. Ubiquitination 6. ADP-Ribosylation 7. Phosphorylation

What are the three classifications of neurons? Differentiate between each.

1. Multipolar Neurons: multiple dendrites extending from a polygonal-shaped cell body. Dendrites receive information, and the neuron transmits the signal to the next neuron or effector cell. 2. Unipolar Neurons: large, round cell body that gives rise to a single process that bifurcates shortly after leaving the soma. One process is directed to the PNS while the other is directed to the CNS. They are involved in sensation. 3. Bipolar Neurons: two processes that extend from opposite sides of a round or oval-shaped cell body. They are involved in special senses, such as sight, hearing, and taste.

What are three types of protein glycosylation? Differentiate between each.

1. N-Linked: Sugar is added to the amide of the Asn side chain. 2. O-Linked: Sugar is added to the Ser and Thr OH group. 3. GPI Anchor: A GPI anchor is placed on the end of a protein. Due to the presence of phosphoethanolamine, it makes the protein inserted into the membrane.

How is mannose-6-phosphate formed? Explain each step.

1. N-acetylglucosamine (NAG) phosphate is transferred to mannose. This reaction is catalyzed by N-acetylglucosaminyl-1-phosphotransferase. 2. NAG is removed by a phosphodiesterase. This leaves the phosphate on the 6 position of the mannose residue. (CC)

What are the two types of acetylation?

1. N-terminus 2. Lysine

What are the required structural elements for a chromosome?

1. Origins of Replication 2. Two Telomeres 3. Centromere

What two activities are required for translation elongation?

1. Peptide Bond Formation 2. Translocation

What are the two main components of the peripheral nervous system?

1. Peripheral Nerves 2. Ganglia

What are two physiological roles of poly ADP-ribosylation? Describe each.

1. Poly ADP-ribosylation plays a role in DNA damage and repair. Histone poly ADP-ribosylation acts as a signal of DNA damage. 2. Poly ADP-ribosylation plays a role in apoptosis. PARP-1 is a target of proteolysis during apoptosis.

What are the two requirements for a protein to be recognized by a proteasome?

1. Polyubiquitin Chain (4+) 2. Linkage (K48 typically)

What are the two types of protein targeting? Differentiate between each.

1. Post-Translational: Post-translational targeting refers to proteins destined for the nucleus, mitochondria, and peroxisomes that are synthesized in the cytosol and targeted to the appropriate organelle by interaction with carrier proteins. Once a protein has been translated, the protein can be targeted to its final destination due to a sequence within the protein that binds to a factor that will carry them to the protein's final destination. 2. Co-Translational: Co-translational targeting refers to proteins destined for secretory organelles, such as the ER, Golgi, and lysosome, that are synthesized into the ER and transferred into vesicles to the appropriate destination. Before a protein has completed translation, it enters the secretory pathway and is transferred in vesicles in case it needs to be exported from the ER.

What are the four components of an operon? Describe each.

1. Promoter: RNA polymerase binds to the promoter to initiate transcription. 2. Operator: The operator is the controlling site. The operator is the location that the repressor protein binds, regulating transcription. 3. Coding Sequence: The coding sequence consists of polycistronic coding sequences that are co-transcribed to make a polygenic DNA. 4. Terminator DNA Sequence

What are the two types of protein degradation machinery?

1. Proteasome 2. Autophagy

What are three reasons proteins are degraded?

1. Proteins are degraded to repair or replace damaged proteins. 2. Proteins are degraded to provide an amino acid buffer for protein translation. If amino acid stores are diminished, then new proteins cannot be synthesized. For example, during starvation, the cell cannot synthesize amino acids. Autophagy allows for the break down of proteins to produce amino acids. 3. Proteins are degraded as a regulatory mechanism.

The addition of carbohydrates to a protein can do what six things? Explain each.

1. Provide functional attributes, especially specific interaction/recognition: When proteins are synthesized into the ER are modified by carbohydrates, it affects specific interactions and aids in folding. 2. Affect enzymatic activity 3. Promote proper folding: When proteins are synthesized into the ER are modified by carbohydrates, it affects specific interactions and aids in folding. 4. Improve stability 5. Improve solubility 6. Target protein within cell (CC)

What are the three types of RNA polymerases in eukaryotes? What do each synthesize?

1. RNA Polymerase I: rRNA (excluding 5S rRNA) 2. RNA Polymerase II: mRNAs, miRNAs, and LINEs 3. RNA Polymerase III: tRNAs, 5S rRNA, and SINEs

What three mechanisms by which eukaryotic gene regulatory proteins that require co-repressors repress transcription?

1. Recruitment of Chromatin Remodeling Complexes 2. Recruitment of Histone Deacetylases 3. Recruitment of Histone Methyltransferases

What are two classes of ADP-ribosylation?

1. Reversible poly ADP-ribosylation of many amino acids. 2. Irreversible mono ADP-ribosylation of many amino acids.

What are the seven reactants for protein synthesis?

1. Ribosome (60S/40S in Eukaryotes and 50S/30S in Prokaryotes) 2. mRNA 3. Translation Factors 4. tRNAs 5. Amino Acids 6. tRNA Synthetases 7. GTP

What two things do centromeres require?

1. Secondary/Higher-Order DNA Structure 2. CENP-A

What are the two divisions of the peripheral nervous system? Differentiate between each.

1. Sensory (Afferent) Division: composed of sensory neurons. This division conducts signals from the receptors to the CNS. 2. Motor (Efferent) Division: composed of motor neurons. This division conducts signals from the CNS to its effectors.

What are the two types of spinal nerves based on innervation? Differentiate between each.

1. Somatic: innervate body walls, limbs, skin, skeletal muscle, and joints. Somatic spinal nerves are involved in voluntary movement. 2. Visceral: innervate the viscera of smooth muscle, cardiac muscle, and glands. Visceral spinal nerves are involved in involuntary movement.

What are two key functions of N-glycosylation?

1. Sugars added to the protein are hydrophilic surface features that can help promote proper folding. 2. Sugars added to proteins are recognizable by and can be bound specifically by lectins. (CC)

What are the two divisions of the autonomic nervous system? Differentiate between each.

1. Sympathetic Nervous System: mobilizes body systems. This is the fight or flight response. 2. Parasympathetic Nervous System: conserves energy. This is the rest and digest system.

What are the two components of the 19S regulatory particle? What is the structure and function of each?

1. The base consists of six related AAA+ ATPase subunits in a ring structure. It rests on the core particle and opens the central pore of the 20S core particle, funneling unfolded substrate into protease chamber. 2. The lid is involved in ubiquitin binding and DUB activity.

What were the three major conclusions from Khorana's experiment in mRNAs with specific trinucleotide repeats?

1. The code does not overlap. It is read from triplet to triplet. 2. The start site of translation affects the translation product. For example, the start site affected the emergence of polyPhe, polySer, and polyLeu in Khorana's experiment. 3. Reading frame is maintained from the start site. (CC)

What are two anomalies of the diaphragm on x-rays?

1. The diaphragmatic slips can be irregular rather than smooth. 2. The diaphragm can be lobulated. It is often a developmental abnormality.

What did we learn through the Human Genome Project?

1. The human genome contains 3 billion base pairs. 2. Almost all nucleotide bases (99.9%) are exactly the same in all people. 3. Around 30% of the genome is transcribed into pre-mRNA, around 95% of that mRNA is removed through RNA splicing, and about 5% of those mRNAs encode for proteins. 4. The human genome consist of around 20-30,000 genes. The function is unknown for most (around 50%). 5. The average gene contains about 27,000 base pairs with dystrophin being the largest. 6. The human genome contains pseudogenes, which are genes containing mutations that prevent proper expression. 7. Around 50% of the genome are high-copy repetitive elements.

What are the consequences of mobile genetic elements?

1. The insertion and recombination of mobile genetic elements can contribute to genomic diversity. 2. The insertion of transposable elements into functional genes can inactivate the gene and lead to disease. For example, L1, a LINE, can insert into the blood clotting protein factor VIII, which can inactivate the gene. Then, it cannot be properly expressed and can cause hemophilia A. In another example, L1 insertion in to the APC tumor suppressor gene can inactivate the gene and cause colon cancer.

Why is the genetic code almost universal?

1. The mitochondrial stop codons are AGA and AGG. 2. Selenocysteine is a non-standard amino acid used in specific prokaryotic and eukaryotic proteins. It is encoded by UGA, but only in specific contexts.

What are the two types of E3 regulated protein degradation?

1. The substrate is activated for degradation through phosphorylation and other modifications, targeting the substrate for E3. 2. E3 is activated for protein degradation.

What are the two possible substrates for E3?

1. The substrate of E3 could be the amino group of a Lys residue on a protein substrate. 2. The substrate of E3 could be the amino group of a Lys residue or α-amino group of the N-terminal methionine on ubiquitin, forming polyubiquitinated proteins. Seven lysines and the N-terminal methionine of ubiquitin can be ubiquitylated. (CC)

What are the two conclusions of the Raney Nickel experiment?

1. The tRNA identity, rather than the amino acid it carries, determines which amino acid is incorporated. 2. There is no proofreading of amino acid incorporation during translation. (CC)

Since there are only 20 amino acids in the toolbox to make proteins, what are three limitations on those proteins?

1. There are limitations on catalytic activity and chemistry. 2. There are limitations on protein stability or solubility. 3. There are limitations on temporal control of activity and stability.

At what steps can gene expression be regulated? Differentiate between each.

1. Transcriptional Control: Which genes are transcribed? When and how often is a gene is transcribed? 2. RNA Processing Control: Splicing and processing of mRNA transcripts are controlled. How will the pre-mRNA be processed? 3. RNA Transport and Localization: Which mRNAs are transported out of the nucleus? Where do they go in the cytoplasm? 4. Translational Control: Which mRNAs are translated? How often are the mRNAs translated? 5. mRNA Degradation Control: mRNAs are selectively unstabilized in the cytoplasm. 6. Protein Activity Control: Proteins are selectively activated, deactivated, or located. For example, phosphorylation can either activate or inactivate a protein.

In what two ways does the structure of transcriptionally-active chromatin differ from inactive chromatin?

1. Transcriptionally-active chromatin are typically deficient in H1. When H1 is removed, the DNA wraps loosely around the histone proteins. 2. Core histones are more likely to by acetylated in more transcriptionally-active chromatin. Acetylation negates the positive charge on the histone tails, so the nucleosomes are loosely packed and create more open chromatin structure.

What are the three stages of translation? What are the factors that assist in each step? How many of each factor are found in bacteria?

1. Translation Initiation: Initiation involves the assembly of the complex required for translation onto the mRNA. The initiating methionine enters the ribosome. The factors that regulate this step are the initiation factors (three in bacteria). 2. Translation Elongation: Elongation is the continuation of translation until the stop codon is reached. The factors that regulate this step are the elongation factors (two in bacteria). 3. Translation Termination: The complete peptide is hydrolyzed from the ribosome. The factors that regulate this step are the release factors (three in bacteria).

What three things are required for bacteria to utilize lactose as an energy source? Explain each.

1. Transporter: In order for the bacteria to digest lactose, they must express the proteins to transport lactose. 2. β-galactosidase: β-galactosidase is an enzyme that is required to hydrolyze lactose into galactose and glucose. 3. Enzymes to Convert Galactose into Glucose: Following lactose hydrolysis, the bacteria require enzymes to convert galactose to glucose in order for the bacteria to fully use lactose as an energy source.

What are the three loops found in tRNA? Differentiate between each.

1. TᴪC Loop (Thymidine-Psuedouridine-Cytidine): The TᴪC loops contains these characteristic bases. It binds to the ribosome. 2. DHU (Dihydrouridine) Loop and Stem: The DHU loop bind to the tRNA synthetase. 3. Anticodon Loop and Stem: The anticodon loop binds to the codon of the mRNA. (CC)

What are the three functions of de-ubiquitination (DUB) enzymes?

1. Ubiquitin genes are synthesized as polyproteins of fusions of ubiquitin to a ribosomal protein. The removal of the C-terminal sequence is required to generate the proper ubiquitin C-terminus for function. DUBs release ubiquitin from these polypeptides and form the proper C-terminus. 2. DUBs also play a role in ubiquitin recycling during proteasomal degradation. 3. DUBs are involved in chain editing of ubiquitin modified proteins.

What three functional genes are encoded by the lac operon? What do each encode for?

1. lacZ encodes for β-galactosidase. 2. lacY encodes for the transporter so that bacteria can transport lactose into the cell. 3. lacA is unclear as of now.

How many pairs of cranial nerves are there?

How many standard amino acids are there?

How much of the genome in multicellular organisms are solitary genes?

20-50%

Human cells contain _____ pair(s) of autosomal chromosomes and _____ pair(s) of sex chromosomes.

22; 1

The large subunit ______S/________S rRNA is a ribozyme.

23; 28

Human cells contain ____ pairs of chromosomes for _____ total chromosomes.

23; 46

What is the function of 23S/28S rRNA?

23S/28S rRNA catalyzes peptide bond formation.

How many pairs of spinal nerves are there?

How many spinal segments are there?

How many phosphate bonds are cleaved per amino acid?

If the codon is 5' AUG 3', what is the anticodon?

5' CAU 3'

RNA is translated from ______ to ______.

5' to 3'

The prokaryotic ribosome contains a ______S and a ______S subunit while the eukaryotic ribosome contains a ______S and a _________S subunit.

50S and 30S; 60S and 40S

The twenty standard amino acids encode for _______ sense codons.

What are the divisions of spinal nerves?

8 cervical 12 thoracic 5 lumbar 5 sacral 1 coccygeal

What are the divisions of spinal segments?

8 cervical 12 thoracic 5 lumbar 5 sacral 1 coccygeal

Eukaryotic Ribosome Size _____ Prokaryotic Ribosome Size

How much of the human genome is repetitive DNA?

>50%

What is the DNase I hypersensitive site?

A DNase I hypersensitive site is a nucleosome-free site that is very sensitive to DNase I. These nucleosome-free regions are very accessible to protein factors, but are hypersensitive to DNase I. While the DNA lacks nucleosomes, they are still bound by other proteins factors.

What is a guanine nucleotide exchange factor (GEF)? What is its function?

A GEF is an accessory factor that binds to GTPases and exchanges GDP for GTP, thereby activating the GTPase.

What is a posterior-anterior (PA) radiograph of the chest? Where is the detector and x-ray source in regards to the patient?

A PA radiograph of the chest is taken when the patient stands facing the detector/the x-ray film. The detector is a digital screen. The x-ray source is located behind the patient. The x-rays produced by the source differentially interact with tissues in the chest and hit the detector, producing the final image.

What is chromatin remodeling?

A cell's chromatin must "open" in order for gene expression to occur. This process of "opening" is called chromatin remodeling.

What is a centromere? What is its function?

A centromere is a unique, AT-rich region region on the chromosome that is required for attachment to the mitotic spindle and chromosome segregation. They serve as the primary constriction on chromosomes where two sister chromatids are in contact. They function in lining up and separating the two sister chromatids during mitosis.

What is a co-repressor?

A co-repressor is a molecule that cooperates with a repressor protein to switch an operon off.

A codon must use at least _________ ribonucleotide bases. Why?

A codon must use at least three ribonucleotide bases. This is because one nucleotide per codon can code for four different amino acids. There are 20 standard amino acids, so four codons is not enough codons for each amino acid. Two nucleotides per codon can code for 16 different amino acids. Again, this is not enough codons for each amino acid. Three nucleotides per codon can code for 64 different amino acids, which is enough codons for the 20 standard amino acids.

What is a gene?

A gene is a functional unit of heredity. DNA encodes for a protein or an RNA with a structural or enzymatic function.

What is a genome?

A genome is an organism's complete set of DNA, including all of its genes. Total DNA includes nuclear and mitochondrial genes.

What is required for attenuation to occur in prokaryotes?

A leader sequence is required for attenuation in prokaryotes.

What is a mixing artifact?

A mixing artifact is the mixture of light and dark due to a mixture of the blood with contrast dye and blood without contrast dye.

What is a nerve plexus?

A nerve plexus is a network of intermingling nerves.

How can you diagnose a pneumothorax on a chest x-ray?

A pneumothorax can be diagnosed when there is separation of the parietal and visceral pleura. The parietal pleura makes contact with the ribs while the visceral pleura makes contact with the lungs. When these two layers separate, air is trapped. Dots and dashes of white are normal in the lungs, but when they disappear, there could be a possible pneumothorax.

What is prolyl hydroxylase? How does it work?

A prolyl residue and α-ketoglutarate in the presence of prolyl hydroxylase and oxygen forms 4-hydroxylprolyl residues, succinate, and CO2. Fe2+ in the active site of prolyl hydroxylase is oxidized during the reaction. Vitamin C is required to reduce Fe3+ back to Fe2+ to allow prolyl hydroxylase to be used in subsequent reactions. (CC)

What is a proteasome? Describe its structure and function.

A proteasome is a major site of protein degradation in the nucleus and cytoplasm of all cells. They are abundant, barrel-shaped chambered proteases that consist of two parts: the 20S core and 19S lid.

What is a pseudogene?

A pseudogene are genes that contain mutations that prevent proper expression. However, they are found to be active in some cell types.

How can you tell if a patient has cardiomegaly from a left lateral x-ray?

A radiologist could tell if a patient has cardiomegaly because the space between the left atrial border of the heart and the anterior thoracic vertebrae is reduced. The heart should be less than 50% of the diameter of the thoracic cavity. If the heart exceeds 50% of the thoracic cavity diameter, then a patient has cardiomegaly.

How is a silent mutation possible?

A silent mutation is possible due to the degeneracy of the genetic code.

Describe the structure of a spinal nerve.

A spinal nerve first emerges from the spinal cord into dorsal rootlets and ventral rootlets. Dorsal and ventral rootlets join to form the dorsal root and ventral root respectively. The dorsal root and ventral root join together past the dorsal root ganglion to form spinal nerves.

What is the function of a stop codon?

A stop codon serves to terminate translation.

What is the significance of a terminal glucose resident on an N-linked glycan in the ER? Explain.

A terminal glucose on an N-linked glycan in the ER is an indicator of need for chaperone function. A glucosyl transferase binds hydrophobic regions in context of N-linked glycosylation. The glucosyl transferase recognizes the improperly folded protein and glucosylates them. This is the key that the protein has an exposed hydrophobic region in the ER, so the protein is not ready to be exported out of the ER quite yet. The chaperones calnexin and calreticulin bind specifically to glucosylated proteins and prevent ER exit, promoting proper protein folding in the process. Once the protein properly folded with no exposed hydrophobic regions, glucose can be trimmed by glucosidase and can exit the ER. (CC)

What is a transition mutation?

A transition mutation is a change from a purine to purine or pyrimidine to pyrimidine in DNA.

What is a transversion mutation?

A transversion mutation is a change from a purine to pyrimidine or vice versa.

What type of distribution system moves proteins from the place of synthesis to many proper destinations, excluding the nucleus and mitochondria, in eukaryotic cells?

A vesicle-mediated distribution system moves proteins from the place of synthesis to many proper destinations, excluding the nucleus and mitochondria.

RNA has four ribonucleotide bases. What are those?

A, U, C, G

Match the statements with whether they apply to eukaryotic gene regulation, prokaryotic gene regulation or both: A. Requirement for gene regulatory proteins (trans-regulators) B. Requirement for cis acting sequences C. Importance of weak and reversible protein-protein interactions D. Versatility afforded by DNA looping E. Can have multiple protein encoding genes regulated by one operon F. RNA polymerase always has some access to DNA G. RNA polymerase requires one general transcription factor H. Transcription is not separated from translation I. Promoter access is restricted by chromatin J. Large, multimeric complexes regulate transcription K. Transcription is separated in both space and time from translation

A. Requirement for gene regulatory proteins (trans-regulators) B B. Requirement for cis acting sequences B C. Importance of weak and reversible protein-protein interactions B D. Versatility afforded by DNA looping B E. Can have multiple protein encoding genes regulated by one operon P F. RNA polymerase always has some access to DNA P G. RNA polymerase requires one general transcription factor P H. Transcription is not separated from translation P I. Promoter access is restricted by chromatin E J. Large, multimeric complexes regulate transcription E K. Transcription is separated in both space and time from translation E

What changes in DNA cause it to become DNase sensitive? A. Transcriptionally active chromatin tends to be deficient in Histone H1 and the core histones are more likely to be modified by acetylation. B. DNA that is transcriptionally active tends to be hypermethylated at CpG residues. C. DNA that is transcriptionally active contains single strand nicks due to DNase I. D. DNA that is transcriptionally active is no longer wrapped around histones. E. DNA that is transcriptionally active is more sensitive to DNase I due to the loss of site-specific DNA binding proteins.

A. Transcriptionally active chromatin tends to be deficient in Histone H1 and the core histones are more likely to be modified by acetylation.

How does tryptophan acting on the trp repressor affect the production of the enzymes required for tryptophan synthesis? A. Tryptophan binds to the trp repressor causing it to bind the trp operator and repress RNA synthesis. B. Tryptophan binds to the trp repressor causing it to release from the trp operator and repress RNA synthesis. C. Tryptophan binds to the trp repressor causing it to bind the trp operator and activate RNA synthesis. D. Tryptophan binds to the trp repressor causing it to bind the trp leader sequence and repress ribosome progression. E. Tryptophan binds to the trp repressor causing it to bind the trp leader sequence and stall ribosome progression, which allows a rho independent transcription stop signal to form.

A. Tryptophan binds to the trp repressor causing it to bind the trp operator and repress RNA synthesis.

As a result of wobble pairing, U and C can base pair with ______, and A and G can base pair with _______.

A; U

What is ADP-ribosylation?

ADP-ribosylation is an enigmatic modification where ADP ribose is added to proteins using NAD+ as a substrate.

What is ATF6? How does it work?

ATF6 is a transmembrane protein in the ER involved in the UPR. Unfolded proteins accumulation in the ER lumen, triggering a stress response. ATF6, in response to protein accumulation, binds and transports these proteins to the Golgi, where proteases cleave the N-terminal fragment ATF6 into the cytoplasm. ATF6 enters the nucleus and increases the expression of chaperone-encoding genes. The protein products of this gene expression are transported into the ER lumen to participate in proper protein folding.

What is the translation start site?

AUG, which encodes for methionine, is the typical translation start site.

Which postganglia innervate abdominal organs? Which innervate the hindgut and pelvic organs?

Abdominal Organs: 1. Celiac Ganglion 2. Superior Mesenteric Ganglion 3. Aorticorenal Ganglion Pelvic and Hindgut Organs: 1. Inferior Mesenteric Ganglion

How does acetylation of histone protein tails cause activation of transcription?

Acetylation of K residues on histone protein tails neutralizes the positive charge on K. As a result, the interaction with the DNA phosphate group is eliminated, and the affinity of the nucleosome for the DNA decreases. As a result, the DNA is loosely wrapped around the nucleosome, and transcription is activated.

Why is acetylation of lysine a reversible reaction?

Acetylation of Lys is a reversible reaction because acetylation requires separate acetylases (HATs) and deacetylases (HDACs).

How can chromatin structure be inherited?

After DNA replication, some of the specialized chromatin components, such as the H3K9me3 mark, are passed on to daughter DNA. These components will recruit histone modification enzymes to make the same marks on the new nucleosomes. This is how liver cells remain as liver cells. The liver cells pass down the epigenetic marks to the daughter cells. As a result, the daughter cells express the same genes, maintaining their genetic identity.

Where do N-linked glycoproteins go following core glycosylation, folding, and initial core oligosaccharide processing? What happens there?

After core glycosylation, folding, and initial core oligosaccharide processing, glycoproteins are transported to Golgi for further processing and sorting. Before transport, glucose residues are removed in the ER, and some mannose residues may also be trimmed. The proteins are then transported from the ER in vesicles to the Golgi. In the Golgi, further mannose trimming and the addition of other sugars can take place. Proteins are also sorted in the Golgi, and the glycosylation of the N-linked polypeptide can play a role in protein targeting.

What is a negative contrast agent?

Air is a negative contrast agent.

Where do each of the following fall on the density scale for radiographs? What color will each appear? Air: Soft Tissues: Metal/Contrast: Bone:

Air: Black Soft Tissues: Shades of Grey Metal/Contrast: White Bone: White

How are N-glycosylated proteins formed?

All N-glycosylation has a shared core structure. The N-linked core structure is assembled first. The core N-oligosaccharide is built on dolichol phosphate on the cytoplasmic face of the ER membrane. Dolichol is an intermediate in cholesterol synthesis, and this dolichol phosphate is embedded on the cytoplasmic face of the ER membrane. The core oligosaccharide for N-linked glycosylation is built by glycosyl transferase enzymes that are specific for the sugar added using "activated" nucleotide sugars. Sugars are added one at a time to this core structure. As the core is being built, the precursor will flip from the cytoplasmic face of the ER to the lumen face of the ER to complete the core structure. Any trimming of the core structure is performed by glycosidases as necessary. As the protein is synthesized into ER, sites for N-linked glycosylation are revealed. The site is always Asn-X-Ser/Thr. Once exposed, the site has a chance of being glycosylated, as not all such Asn residues are glycosylated. The core oligosaccharide is transferred to the appropriate Asn side chain en bloc. (CC)

Eukaryotic chromosomes have thousands of origins of replication. What do all of these origins of replication share?

All eukaryotic origins of replication are AT-rich sequences.

What is a consequence of the degeneracy of the genetic code?

Although amino acid sequence can be determined unambiguously from the nucleotide sequence, the nucleotide sequence cannot be determined unambiguously from the amino acid sequence.

Although chromatin restricts access to genes, they provide avenues for regulation. What is that avenue for regulation?

Although chromatin restricts access to genes, they provide avenues for regulation. Most genes are in the "off" position; however, cell can turn "on" necessary genes.

Describe what happens to the lac operon under the following condition: + Glucose + Lactose

Although lactose is able to bind to the repressor protein and inactivate it, glucose is used as the preferential energy source. When glucose is present, the concentration of cAMP is low. When the concentration of cAMP is low, it cannot bind to CAP. As a result, CAP cannot bind to the DNA, thereby inactivating the operon.

What are Alu elements? What can they cause?

Alu elements are SINEs that are the most abundant transposable elements in the human genome. Multiple copies of the Alu sequences can hinder precise chromosomal pairing during meiosis, resulting in unequal crossovers. This is one of the main reasons for chromosome duplication. During meiosis, the homologous chromatids are aligned and exchange their genetic materials through crossing over. However, Alu elements can cause homologous chromosomes to misalign, resulting in one chromatid with a deletion and the other chromatid with a duplication. (CC)

What is the overall tRNA synthetase reaction?

Amino Acid + ATP + tRNA + H2O <----> Aminoacyl-tRNA + AMP + 2 Pi

What are aminoacyl-tRNA synthetases?

Aminoacyl-tRNA synthetases are enzymes that catalyze the formation of aminoacyl-tRNAs, or in other words, catalyze the attachment of amino acids to the 3' ends (CCA acceptor stems) of tRNAs, forming an ester linkage with the amino acid COOH group.

What is an angiogram? How is it performed?

An angiogram is a specialized image that demonstrates vasculature. Intravenous contrast dye is injected to show vessels. An angiogram can be obtained using either CT or MRI techniques.

What is an operon?

An operon is a coordinated unit of gene expression consisting of one or more related genes, the operator, and the promoter sequences that regulate their transcription.

How can you differentiate collapsed lungs and pleural effusion on a chest x-ray?

Another film should be taken. The patient should be turned on his/her side and check for a fluid level. If there is a fluid level, it is PE. If there is no fluid level, then it is collapsed lung.

What does the positive charge of histone proteins and the negative charge of DNA molecules allow them to do?

As a result of their opposite charges, DNA wraps around and interacts tightly the positively-charged histone proteins.

What is the unfolded protein response?

At homeostasis, protein synthesis is balanced with protein degradation. However, under stress, protein aggregation can occur at a level at which protein degradation cannot keep up. The cell, as a result, increases the rate of degradation, induce folding, and reduce protein synthesis through the phosphorylation of E2F.

A 44-year-old man with a diagnosis of human immunodeficiency virus (HIV) comes to consult you in an infectious disease clinic. He has a dramatically decreased CD4+ T-cell count and he has a high viral load. You start him on a nucleoside analog. This class of drugs inhibits viral DNA synthesis because they lack which of the following properties required for normal DNA polymerization? A. A 5' phosphate B. A 3' hydroxyl C. A 7-methyl G cap D. A poly(A) tail E. A consensus sequence

B. A 3' hydroxyl

Which of the following statements about tRNA is TRUE? A. A tRNALeu mischarged with Ile would not be used by the translational machinery. B. Important features of tRNA structure include the anticodon loop, the acceptor stem, and the DHU loop. C. The results of the Raney Nickel experiment demonstrate that there is proofreading of amino acid sequence during translation. D. In the Wobble hypothesis, the first nucleotide of the codon is proposed to base pair in a non-Watson-Crick fashion with the third base of the anticodon.

B. Important features of tRNA structure include the anticodon loop, the acceptor stem, and the DHU loop.

Both quinolones and dideoxynucleotides are drugs that act by blocking DNA replication. Why are these drugs minimally toxic to the patient? A. Neither affects type II topoisomerases in eukaryotes. B. Quinolones are specific to bacterial gyrase and dideoxynucleotides are removed by the proofreading activities of eukaryotic DNA polymerases. C. Quinolones are specific to bacterial topoisomerase I and dideoxynucleotides are only incorporated by RNA dependent DNA polymerases. D. Quinolones are specific to bacterial helicase and dideoxynucleotides are incorporated by RNA dependent RNA polymerases. E. Eukaryotes don't have a cell wall.

B. Quinolones are specific to bacterial gyrase and dideoxynucleotides are removed by the proofreading activities of eukaryotic DNA polymerases.

Which of the following statements regarding protein synthesis is TRUE? A. The genetic code contains one codon for each amino acid. B. The mRNA sequence is read without punctuation. C. Frameshift mutations result from deletion or insertion of multiples of three bases. D. A silent mutation is usually a deletion or insertion of one or two bases.

B. The mRNA sequence is read without punctuation.

A culture of E. coli has been growing on a medium containing glucose and lactose. Once the cells have utilized all of the glucose in the medium, what change occurs in the bacteria to cause the rate of beta-galactosidase synthesis to increase? A. cAMP levels decrease and stimulate the binding of CAP protein to its DNA binding site. B. cAMP levels increase and activate CAP protein, which can then bind its DNA-binding site. C. RNA polymerase binds the operator sequence with high affinity because the repressor is no longer present. D. The inducer binds RNA polymerase, thereby increasing its affinity for the lac operon. E. The lac operon is turned on because lac repressor is bound and CAP is not bound.

B. cAMP levels increase and activate CAP protein, which can then bind its DNA-binding site.

Which of the following elements is only present once on a eukaryotic chromosome? A. origin of replication B. centromere C. gene D. repetitive DNA E. telomere

B. centromere

Describe how heme-regulated kinase acts to balance heme biosynthesis with globin biosynthesis in reticulocytes.

Back in the day, researchers observed that rabbit reticulocyte lysate with the addition of heme produced more globin protein than the rabbit reticulocyte lysate alone. Further experiments showed that heme inactivates an inhibitor of protein synthesis. Heme-regulated protein kinase (HRPK) phosphorylates eIF2. eIF2B, the eIF2 exchange factor, binds very tightly and non-productively to phosphorylated eIF2. eIF2 is unable to perform its function whenever it is phosphorylated and bound to eIF2B and is unable to be regenerated for translation. As a result, the cell has more eIF2 than eIF2B, so eIF2B is rapidly sequestered by phosphorylated eIF2. As a result, translation slows. If the protein synthesis rate is less than the heme synthesis rate, then free heme will bind and inactivate HPRK, thereby increasing the amount of unphosphorylated eIF2 and allowing eIF2 to be regenerated for translation. This allows protein synthesis at a high rate to allow the binding to free heme. On the other hand, if protein synthesis is greater than heme synthesis, then all here is bound to globin, and HRPK is active. When HPRK is active, it phosphorylates eIF2. eIF2 binds tightly and non-productively to eIF2B. As a result, protein synthesis slows until heme synthesis matches its rate. (CC)

Flip card for question. Answer below. A. The lag phase occurs as enzymes for lactose metabolism are expressed.

Bacteria is in a culture of both glucose and lactose. At 1 hour, the amount of glucose is fifty percent reduced; at two hours, it is 75% reduced; and at three hours, it is 99% reduced. The growth curve shows diauxic growth. By this, the curve shows a lag phase at the three hour mark, but then resumes exponential growth. What is the reason for the lag phase at the three hour mark? A. The lag phase occurs as enzymes for lactose metabolism are expressed. B. The lag phase occurs as enzymes for glucose catabolism consume energy that would be used for glucose anabolism. C. The lag phase occurs because glucose metabolites are repressing the lac operon. D. The lag phase occurs because bacteria cannot metabolize lactose at the same rate as glucose.

Why is barium a positive contrast agent?

Barium is a positive contrast agent because it appears white on an x-ray.

What are barrier DNA sequences? What is its function? How does it work?

Barrier sequences, also called insulators, consist of a special DNA sequence and proteins. They function to separate the the chromatin into different domains and prevent the spread of heterochromatin. CTCF proteins recognize and bind to the insulator sequence, recruiting other protein factors to form the barrier function. In the heterochromatin region, the transcription of genes is silent.

What happens if the barrier sequence is removed?

Barrier sequences, also called insulators, consist of a special DNA sequence and proteins. They function to separate the the chromatin into different domains and prevent the spread of heterochromatin. In the heterochromatin region, the transcription of genes is silent. In the euchromatin region, transcription is active. If the barrier sequence is removed or mutated, then the barrier complex cannot be formed, and the heterochromatin structure can spread along the chromatin, silencing the transcription of the euchromatin genes.

What is BiP? What is its function?

BiP, or immunoglobulin binding protein, belongs to the Hsp70 family of chaperones. BiP proteins possess an ATP binding domain and peptide binding domain, which binds hydrophobic peptides. When BiP is associated with proteins, ATP is hydrolyzed, locking BiP onto the protein. ATP exchange causes the protein to dissociate from BiP. While this seems inefficient, BiP allows the protein to be in a partly folded state and gives it the opportunity to fold completely into its native state. If the protein does not fold into its native state, BiP will bind again so the protein can attempt proper folding once more. Cycles of binding and release often are required to achieve proper folding.

How does histone deacetylation alter the expression of the gene being deacetylated? A. It depends on the gene. B. It increases expression. C. It decreases expression. D. It has no effect on expression. E. It slows the progression of RNA polymerase.

C. It decreases expression.

In a study of transcriptional regulation in bacterial cells, it is determined that a chromosomal LacI gene encodes the lac repressor. This lac repressor in turn acts as an inhibitor of the LacZ gene on a plasmid within the same cell. To further clarify how this process occurs, the following cross is made: LacZ-/LacI+ Bacteria X LacZ+/LacI- Bacteria. Which of the following best describes the semi-diploid bacteria that result from this cross? A. Constitutive LacZ expression through cis-regulation B. Constitutive LacZ expression through trans-regulation C. Normal LacZ regulation through trans-regulation D. Normal LacZ regulation through cis-regulation

C. Normal LacZ regulation through trans-regulation

Translation of the synthetic polynucleotide (CAA)n in a cell-free translation system produces three different peptides. Which of the following statements is correct regarding this experiment? A. The three codons used to produce the peptides are CAA, AAA, and AAC. B. There are four codons in the synthetic mRNA, but one of these is a nonsense codon. C. These peptides are produced inefficiently because there is no AUG in the RNA sequence. D. All 20 standard amino acids must be present in the cell-free translation system to produce the three peptides.

C. These peptides are produced inefficiently because there is no AUG in the RNA sequence.

What is the activator protein of the lac operon?

CAP (cAMP)

How does CAP activate transcription of the lac operon?

CAP is a protein that binds to cAMP, undergoing a conformational change that allows it to bind to DNA. CAP then bends the DNA about 90 ° to aid in the formation the open promoter complex and promote RNA polymerase binding to the promoter region in the lac operon. By CAP binding upstream of the DNA promoter, it binds to the RNA polymerase and increases its affinity for the promoter. Without CAP, RNA polymerase does not bind to the promoter, and the lac operon is not expressed.

What is CENP-A? What is its function?

CENP-A, a histone variant of H3, is a structure protein of the centromere, acting as an anchor for the kinetochore so the microtubules can attach to the kinetochore and pull the sister chromatids into the daughter cells while maintaining sister chromatid cohesion. CENP-A is associated with transcription silencing.

What is CFTR ΔF508? What causes it?

CFTR ΔF508 is the most common cystic fibrosis-causing alteration that results from a deletion of phenylalanine. While WT CFTR folds inefficiently in the ER (about 30% subjected to ERAD), CFTR ΔF508 causes misfolding of the N-terminal nucleotide binding domain, leading to the degradation of most CFTR by ERAD. CFTR has many transmembrane domains with two nucleotide binding domains that are associated with its function as a channel. This channel is ATP-gated. The phenylalanine deletion occurs in one of the nucleotide binding domains, causing misfolding of the domain. The misfolding of the domain compounded by the misfolding of the whole CFTR leads to the degradation of most of the protein product produced by CFTR ΔF508. (CC)

How are CTs formed?

CT scanning uses x-ray tubes that rotate around the patient. The large number of positions and angles are calculated into cross-sectional images. CT scans demonstrate better contrast between tissues than plain film x-rays. IV and oral contrast dyes are often used to enhance the contrast between different structures.

What is carboxylation? How does it work?

Carboxylation is a protein modification on Glu residues. It is carried out by a Vitamin K-dependent carboxylase that uses CO2 to produce a carboxylated protein and Vitamin K epoxide. The Vitamin K epoxide is reduced back to Vitamin K by Vitamin K reductase to be used again in the carboxylation reaction. (CC)

What is catabolite repression? What does this look like in the lac operon?

Catabolite repression is a system of gene control in some bacterial operons in which glucose is used preferentially and the metabolism of other sugars is repressed in the presence of glucose. For example, in the lac operon, glucose is the preferred carbon source for most bacteria, and the lac operon allows for effective digestion of lactose only when glucose is not present.

How is Cdk/cyclin E regulated by SCFFbw7? What happens if SCFFbw7 is mutated?

Cdk/cyclin E is a protein kinase that stimulates cells in G1 to proceed into the S-phase. This complex is regulated by SCFFbw7, an E3 that degrades the complex to regulate cell proliferation. However, mutations in SCFFbw7, typically found in patients with breast cancer, result in elevated levels of Cdk/cyclin E, causing rapid and unregulated cell proliferation.

Sympathetic (Thoracolumbar) Division

Cell bodies of preganglionic axons are located in T1 to L2. (CC)

Parasympathetic (Craniosacral) Division

Cell bodies of preganglionic axons are located in the brainstem of cranial nerves III, VII, IX, and X and in the spinal cord from S2 to S4.

What is cell-free translation of mRNAs?

Cell-free translation of mRNAs is a form of translation that does not occur in cells. It takes the cellular components required for translation and combining them extracellularly. The only translation that is completed is with the mRNAs that the cellular extract is programmed with.

If the genome of each somatic cell contains all of the information to make a complete organism, then why do cells differ from one another (i.e. liver cell versus a skin cell)? How?

Cells differ from one another due to differential gene expression. At one time, a cell only expresses a fraction of their genes. As a result, different cell types arise due to differential gene expression.

Why are centromeres called alpha satellite DNA?

Centromeres contain highly repetitive AT-rich sequences that form a satellite band during centrifugation. This band is called the alpha satellite DNA.

How were signal sequences for secretory pathway targeting discovered?

Cesar Milstein and George Brownlee observed that antibodies made in vitro on free ribosomes have extra amino acids on the N-terminus compared to antibodies secreted from cells. This suggested that these secreted proteins were processed, or truncated, in cells but not in vitro. The sequence removed turned out to be a stretch of hydrophobic amino acids following a basic amino acid(s), with a small amino acid (A/G) at the cleavage site. This is now known as the signal sequence. (CC)

What macromolecule prevents the aggregation of proteins in the ER?

Chaperones prevent aggregation in the ER.

Chromatin Structure and Function

What is chromatin?

Chromatin is DNA bound to its associated proteins.

Chromosome and Genome Structure

What are neocentromeres? How do they form?

Chromosome rearrangements can result in the loss of the normal centromere. As a result, a new centromere called the neocentromere forms.

What is cis regulation?

Cis regulation is the regulation of one molecule by a component of the molecule itself, such as a DNA sequence within DNA. In other words, cis regulation occurs when the regulator resides on the same molecule as the target.

What is co-translational targeting? How does it work?

Co-translational targeting refers to proteins destined for secretory organelles, such as the ER, Golgi, and lysosome, that are synthesized into the ER and transferred into vesicles to the appropriate destination. Nearly all cellular protein synthesis begins on cytosolic ribosomes. Proteins that are secreted, plasma membrane-bound, or in or on secretory organelles, such as the ER, Golgi, and lysosomes, are synthesized on ribosomes that become ER-associated. ER association begins with recognition of a hydrophobic N-terminal signal sequence on the nascent protein by the SRP, or the signal recognition particle, during synthesis. Synthesis of the protein pauses while the complex is bound. The SRP is then recognized by an SRP receptor on the ER membrane and is transferred to the receptor. The complex associates with a pore on the membrane called a translocon. Once associated with the translocon, synthesis of the protein then continues into the ER lumen as the SRP dissociates.

How were codons assigned to amino acids? Include and describe each of the three experiments performed.

Codons were assigned to amino acids via cell-free translation of synthetic mRNAs. These synthetic mRNAs can be any sequence. The first experiments used synthetic ribonucleotide polymers (such as poly A or poly U), synthetic copolymers (such as dinucleotide repeats like polyUC), and synthetic mRNAs with trinucleotide repeats. Nirenburg and Matthaei used a cell-free translation system programmed by synthetic polyU mRNAs. They translated their protein product and found the protein was polyPhe. They discovered that UUU encoded for phenylalanine. They performed similar experiments with polyA and polyC mRNAs and found that polyA produced polyLys and polyC produced polyPro, concluding that AAA encodes for Lys while CCC encodes for Pro. Khorana synthesized and translated mRNAs with specific dinucleotide repeats and determined the sequence of the peptide product. For example, polyUG mRNAs contain two codons, UGU and GUG, that formed an alternating Cys and Val polypeptide product. Khorana again synthesized and translated mRNAs, but this time, with specific trinucleotide repeats. For example, polyUUC mRNAs produced polyPhe, polySer, and polyLeu protein products. Khorana's experiment also indicated that there are three different reading frames. Once the reading frame has been established, codons are read three after three, one after another. Khorana concluded that the code does not overlap, the start site affects the translation product, and lastly, reading frame is maintained from the start site.

What happens to collagen when an individual is Vitamin C deficient? Explain using prolyl hydroxylase in your answer.

Collagen is a major extracellular triple helix protein of connective tissue. It contains repeats of the sequence Gly-X-Y, where X is proline and Y is 4-hydroxyproline. 4-hydroxyproline is necessary for the proper folding and assembly of collagen. However, when an individual is Vitamin C deficient, the Fe located in the active site of prolyl hydroxylase would not be able to be reduced, leading to a decrease in the production of 4-hydroxyproline. This results in scurvy.

What are constitutive genes? What kind of genes are regulated?

Constitutive genes are genes who are continuously expressed. These genes include housekeeping genes, such as those required for protein synthesis and glucose metabolism.

Why is contrast used for CT scans?

Contrast is used for most CT scans. For example, where there is inflammation in the body, blood preferentially flows to that area. It heats up the area. If IV contrast is administered, it travels with the blood to that sight and lights up the area on the CT. The same applies for traumas, tumors, and contusions.

Why would contrast be denser in the left brachiocephalic vein rather than the right?

Contrast would be denser in the left brachiocephalic vein than the right brachiocephalic vein because the patient has been injected into left arm with contrast dye.

How should coronal CT images be viewed?

Coronal images should be viewed as if you are standing in front of the patient. Envision the CT scanner moving from the front to the back of the patient. Coronal CT images are in the same frontal orientation as a PA radiograph.

What factor of translation is the target of the diphtheria toxin? Explain.

Corynebacterium diphtheriae affects the upper respiratory tract, where an inflammatory exudate (mainly dead cells and inflammatory cells) forms a fibrous pseudomembrane that causes severe obstruction to the airway, and sometimes, suffocation. The diphtheria toxin catalyzes the ADP-ribosylation of eEF-2, which blocks protein synthesis.

What can cycles of glucosylation and chaperone binding of N-linked glycans result in?

Cycles of glucosylation and chaperone binding can result either in proper folding followed by ER exit or by ER retention followed by ERAD.

During the regulation of metabolism of lactose in bacteria the presence or absent of glucose and lactose regulate whether the operon (LacZ, LacY, LacA) is transcribed. Which of the following conditions in the cell will induce the expression of the operon to give the bacteria ability to metabolize lactose? A. Glucose (+) and Lactose (+) B. Glucose (+) and Lactose (-) C. Glucose (-) and Lactose (-) D. Glucose (-) and Lactose (+)

D. Glucose (-) and Lactose (+)

Eukaryotic and prokaryotic translation share most factors and mechanisms. Which of the following is NOT a shared factor/mechanism? A. Elongation Factor 2 B. Binding of large ribosomal subunit completes translation initiation C. Peptidyl transferase activity is an activity of ribosomal RNA D. Initiation factor 4e, the methylG cap binding factor E. The A, P and E sites are formed by the interface of the small and large ribosomal subunits.

D. Initiation factor 4e, the methylG cap binding factor

Which of the following statements is TRUE regarding translation? A. The action of the ribosome in translation differs between prokaryotes and eukaryotes. B. Puromycin blocks translation elongation only in prokaryotes. C. Prokaryotic ribosomes contain many more RNAs and protein species than do eukaryotic ribosomes. D. Small monomeric G proteins act in all three stages of translation. E. A major target of regulation of translation is the termination stage.

D. Small monomeric G proteins act in all three stages of translation.

Repressors

DNA-binding gene regulatory proteins that inhibit transcription

What are de-ubiquitination (DUBs) enzymes? What is their function?

DUBs are enzymes that are necessary for the process of ubiquitination. Ubiquitin genes are synthesized as polyproteins of fusions of ubiquitin to a ribosomal protein. The removal of the C-terminal sequence is required to generate the proper ubiquitin C-terminus for function. DUBs release ubiquitin from these polypeptides and form the proper C-terminus. DUBs also play a role in ubiquitin recycling during proteasomal degradation as well as chain editing of ubiquitin modified proteins. (CC)

What does degenerate code mean?

Degeneracy of the genetic code refers to more than one codon encoding for a particular amino acid.

What is a degron? Give examples.

Degrons are signals in proteins that are targeted for ubiquitination and degradation. These degrons are recognized by specific E3 ubiquitin ligases. Some result in constitutive ubiquitination degradation while others are heavily regulated. Some examples include PEST, the destruction box, the Ken box, and the N-end rule.

What is the clinical significance of dermatomes?

Dermatomes allow for the identification of a lesion place due to loss of sensation in a cutaneous area.

Chromatin is a highly complex structure with several levels of organization. What are those levels of organization?

Double-stranded DNA wraps around histone proteins to form the nucleosomes. These linker DNA form the beads-on-a-string model, or the 11 nm fiber. This model further wraps to form the left-handed helix to become further compacted and form the 30 nm fiber. The 30 nm fiber can form these loops, forming the 300 nm fiber. The 300 nm fiber can further wrap to form the 700 nm fiber. Eventually, the DNA will be packed fully to produce the chromatid.

What happens to chromatin during interphase?

During interphase, some regions of chromatin are decondensed so that transcription can occur. Chromatin structure must be opened up in some regions in order for the transcription factors to have access to the DNA and transcribe the DNA into mRNA.

What happens to chromatin during mitosis?

During mitosis, the chromatin becomes condensed to form chromosomes. Microtubules bind to the centromere of the chromosomes and pull the sister chromatids apart into the daughter cells. The formation of the chromosome protects the fragile DNA during mitosis.

Which of the following statements concerning the Human Genome Project is not true? A. The human genome contains ~3 billion DNA base pairs (3.2 X 109). B. Almost all (99.9%) nucleotide bases are exactly the same in all people. C. There are only ~30,000 genes--much lower than previous estimates of 80,000 to 140,000. D. Strikingly small amount of DNA encodes proteins (1.5%). E. Almost 5% of the genome is high copy repetitive elements

E. Almost 5% of the genome is high copy repetitive elements

Which of the following is NOT true of mobile genetic elements in the human genome? A. Mobile genetic elements are dispersed in the genomes of higher plants and animals. B. LINE and SINE elements in humans are retrotransposons. C. LINE (L1) transposons are long-interspersed elements that are 6-7 Kb in length and make up ~21% of human DNA. D. Alu elements are the most abundant transposable elements in the human genome with over 106 copies, and comprising 10.7% of human genome. E. Alu elements encode proteins and do not require any other mobile genetic elements to transpose.

E. Alu elements encode proteins and do not require any other mobile genetic elements to transpose.

Which of the following is not true of heterochromatin? A. It is highly condensed. B. Approximately 10% of the genome is in heterochromatin. C. There are two types of heterochromatin: constitutive and facultative. D. The parts of the genome that are not in heterochromatin are in euchromatin. E. Heterochromatin is transcriptionally active.

E. Heterochromatin is transcriptionally active.

Which of the following statements is TRUE regarding aminoacyl tRNA synthetase? A. Aminoacyl tRNA synthetase enzymes have an RNA component. B. The aminoacylation of tRNA requires hydrolysis of ATP to ADP. C. Aminoacyl tRNA synthetases catalyze attachment of an amino acid to the modified base in the DHU loop. D. There is one aminoacyl tRNA synthetase for each tRNA species. E. Hydrolysis of a misacylated amino acid is one of the mechanisms by which some aminoacyl tRNA synthetases contribute to translation fidelity.

E. Hydrolysis of a misacylated amino acid is one of the mechanisms by which some aminoacyl tRNA synthetases contribute to translation fidelity.

Which of the following is NOT a way chromatin is altered during transcriptional activation? A. Remodeling of nucleosomes B. Removal of histones C. Replacement of histones D. Modification of histones E. Proteolytic degradation of histones

E. Proteolytic degradation of histones

How are proteins selected for proteasomal degradation?

E3 ubiquitin ligase recognizes specific sequences, conformations, and modifications of substrates and targets them for degradation.

How is ubiquitin transferred from E2 to the substrate? Explain both possible mechanisms.

E3, or ubiquitin ligase, catalyzes the transfer of ubiquitin from charged E2 to the substrate. 1. E3 is a scaffold protein, bringing E2 close to the substrate. As a result, the ubiquitin is transferred from a Cys residue onto the Lys residue on the substrate, resulting in a ubiquitylated protein. 2. E3 can transfer the ubiquitin from the charged E2 to a Cys residue in its own active site and then transferred from the active Cys of E3 to the Lys residue of the substrate.

How does EF-Tu contributed to translational fidelity?

EF-Tu ensures correct codon-anticodon interaction. This is another contribution to translational fidelity. When the appropriate aminoacylated tRNA is bound, the appropriate conformation of the ribosome stimulates GTP hydrolysis and releases EF-Tu.

What three factors promote molecular mimicry in translation?

EF-Tu, EF-G, and RF-3

What is the one similarity between the two types of acetylation?

Each form of acetylation has the same basic enzymatic mechanism on amino groups.

_____________chromatin is more sensitive to DNase I while _________________chromatin is less sensitive to DNase I.

Eu-; hetero-

What is euchromatin? How does it stain under an electron microscope?

Euchromatin is a less condensed form of chromatin that is transcriptionally active. They appear light under an electron microscope.

Since RNA is synthesized 5' to 3', translation in the 5' to 3' direction allows translation to begin before mRNA synthesis is complete. The resulting ability to couple transcription and translation has potential regulatory implications in bacteria, but not in eukaryotes. Why?

Eukaryotes have compartments. Transcription occurs in the nucleus while translation occurs in the cytoplasm.

Compare and contrast eukaryotic chromosomes with prokaryotic chromosomes.

Eukaryotic chromosomes: 1. are long, linear, duplex DNA molecules arranged into multiple linear chromosomes. 2. are highly-organized and compacted with proteins to form chromatin. 3. are orders of magnitude larger than prokaryotic genomes. 4. are diploid. 5. compartmentalize transcription in the nucleus and translation in the cytoplasm. 6. do not contain plasmids. 7. contain large amounts of noncoding and repetitive DNA. Prokaryotic chromosomes: 1. are singular circular chromosomes. 2. are packaged very differently than eukaryotic genomes. They are condensed in the nucleoid via supercoiling and by architectural proteins. 3. are orders of magnitude smaller than eukaryotic genomes. 4. are haploid 5. allow transcription and translation to happen simultaneously. 6. contain non-essential genes on plasmids. 7. contain little repetitive DNA.

Why is eukaryotic translation so much more complex than prokaryotic translation?

Eukaryotic translation is more complex than prokaryotic translation due to differences between eukaryotic and prokaryotic mRNAs (i.e. eukaryotic mRNAs are monocistronic, do not contain a Shine-Dalgarno sequence, and contain a 7-methylguanosine cap, a polyA tail, and a 5' UTR that contains stable secondary structures). As a result, eukaryotic translation requires more factors.

Describe the effect of the parasympathetic nervous system on the following processes. Eye: Sex:

Eye: pupillary constriction (sphincter pupillae) Sex: sexual arousal

Describe the effect of the sympathetic nervous system on the following processes. Eye: Sex:

Eye: pupillary dilation (dilator pupillae) Sex: orgasm

True or False: All proteins have the same half life.

False

True or False: An N-linked glycoprotein with a terminal glucose residue is welcome to leave the ER.

False

True or False: Bacteria encode a specific initiating tRNAfMet, but eukaryotes just use the tRNAMet to initiate protein synthesis.

False

True or False: Eukaryotic mRNAs differ from prokaryotic mRNAs in 5' untranslated region complexity and the length of the Shine-Dalgarno sequence.

False

True or False: Human artificial chromosomes insert themselves into the human genome.

False

True or False: Small G proteins acting in protein synthesis bind and hydrolyze GTP to drive their translocation along mRNA.

False

True or False: Stop codons encode for an amino acid.

False

True or False: The signal recognition particle (SRP) is a peripheral ER membrane protein that has GTPase activity.

False

True or False: The translocon binds to the SRP.

False

True or False: The ΔF508 mutant CFTR protein is more abundant than is the wild-type CFTR, but is not properly targeted to the plasma membrane.

False

True or False: Vesicular trafficking is used for targeting proteins to mitochondria and nuclei, as well as to secretory compartments.

False

True or False: eIF2 is a GTP exchange protein (GEF) that can be regulated by direct phosphorylation.

False

True or False: eIF4A/B is required in eukaryotes for mRNA cap binding.

False

True or False: A mutation is a change in the mRNA sequence.

False: A mutation is a change in the DNA sequence.

True or False: There is no T1 dermatome.

False: C1

True or False: Glucose residues of N-linked glycoproteins are removed in the Golgi.

False: ER

True or False: Prokaryotic cells are subdivided into functionally-distinct, membrane bound compartments.

False: Eukaryotic

True or False: A GTP-bound signal recognition particle and a GDP-bound signal recognition particle receptor is required for a protein to enter the ER lumen.

False: GTP

True or False: Binding to the signal sequence and ribosome requires a GDP-bound signal recognition particle.

False: GTP

True or False: LacI is the part of the lac operon that encodes for the repressor protein.

False: LacI is not a part of the lac operon.

True or False: All O-linked glycosylation has a shared core structure.

False: N

True or False: The ribosome has proofreading activity that is able to remove misincorporated amino acids.

False: None

True or False: N-linked glycans are usually 80% protein by weight.

False: O-linked glycans are up to 80% carbohydrate by weight: mucins, extended Ser/Thr-rich glycoproteins of the cell surface and extracellular matrix.

True or False: White rami is present at all levels.

False: T1 to L2

True or False: Interphase chromosomes exhibit heterochromatin only.

False: a mixture of heterochromatin and euchromatin

True or False: Methylation of histone tails always represses transcription.

False: activate or repress

True or False: Gray rami is present from T1 to L2.

False: all levels.

True or False: Small monomeric GTPases only act in initiation and elongation of translation.

False: all three steps

True or False: Transcription factories make transcription less efficient, as the transcription factory is a very large protein that must move along the DNA to transcribe it.

False: all wrong

True or False: The genetic code is universal.

False: almost

True or False: The nervous system is asymmetric.

False: bilateral symmetry

True or False: Splanchnic nerves are preganglia for the sympathetic nervous system only.

False: both

True or False: Ribosomes are composed of rRNAs alone.

False: both ribosomes and proteins

True or False: Heterodimers recognize the same DNA sequence, just at different locations.

False: different DNA sequences

True or False: Eukaryotic cells use formylmethionine as well as use a special tRNA for initiation.

False: do not

True or False: If a general somatic afferent fiber detects stimuli in a thoracic skeletal muscle, the signal is directly propagated through the dorsal, lateral, or anterior cutaneous branch depending upon their location.

False: dorsal or ventral primary ramus

True or False: The sequence, function, and the secondary structure of telomeres are conserved in eukaryotes.

False: function and secondary function

True or False: The rate of translation elongation is a major determinant of the overall rate of translation.

False: initiation

True or False: Amino acids with more than one tRNA have more than one aminoacyl-tRNA synthetase.

False: just one

True or False: E. coli has three RNA polymerases: RNA I, II, and III.

False: just one RNA polymerase

True or False: Protein phosphatases are very specific, as there are over 800 encoded by the genome.

False: kinases

True or False: The left atrium is border forming anteriorly on an x-ray.

False: laterally

True or False: Ubiquitination only produces one topology.

False: multiple due to N-terminal methionine and seven Lys residues

True or False: The mediator protein binds to the DNA as a coactivator.

False: never binds to the DNA

True or False: There is a relationship between chromosome number, species complexity, and total genome size.

False: no relationship

True or False: Nonsense mediated mRNA decay is a result of every nonsense mutation.

False: not every

True or False: The peripheral viscera is dual innervated.

False: only sympathetic

True or False: The basic structure of eukaryotic genomes varies; however, their size is the same from organism to organism.

False: opposite

True or False: Splanchnic nerves are postganglia.

False: preganglia

True or False: RNA polymerase can bind to DNA alone.

False: requires TFs

True or False: Ubiquitination is a irreversible reaction.

False: reversible

True or False: tRNAs are large RNAs that act as an adaptor.

False: small

True or False: Final N-glycosylation structures are all the same.

False: vary

True or False: The RNA polymerase core enzyme initiates transcription.

False: σ factor

True or False: The preganglia of the parasympathetic nervous system alone release acetylcholine.

False; both

True or False: The use of a special tRNA as an initiator is not conserved throughout evolution.

False; is

How can carbohydrates affect protein sorting? Use an example to explain your answer.

For example, lysosome targeting requires terminal mannose-6-phosphate on the N-linked glycan. When an N-linked glycan with a terminal mannose-6-phosphate is present, a specific receptor binds to the glycan and includes it as cargo destined for the lysosome. Without mannose-6-phosphate, the glycan would never reach the lysosome.

Gene clusters represent coordinate control. How?

For example, the β globin gene cluster encodes for the β subunit hemoglobin protein. The expression of the five genes is under the control of the same regulatory region. As a result, the cluster of genes can be coordinately regulated.

Why is Foxa1 known as a pioneer transcription factor?

Foxa1 is a pioneer transcription factor because it can bind to condensed chromatin.

What is Foxa1? How does it work in the prostate gland?

Foxa1 is a site-specific gene regulatory protein that can bind to condensed chromatin. It functions to recruit chromatin remodeling machines to open up a local domain of chromatin to allow the entry of other factors. First, Foxa1 recognizes its particular binding sequence (5'-AAAGTAACA-3') and binds to the DNA, even when chromatin is condensed. After Foxa1 binds to the DNA, they recruit chromatin modeling machines and histone modification enzymes to open up the chromatin structure. Now, the DNA is more accessible to other protein factors. For example, the androgen receptor (AR) can bind to DNA and together with Foxa1 can regulate transcription by regulating the general transcription factors along with RNA polymerase II. As a result, transcription will be turned on for the AR downstream target gene, such as PSA.

What is Foxa1? How does it work in the mammary glands?

Foxa1 is a site-specific gene regulatory protein that can bind to condensed chromatin. It functions to recruit chromatin remodeling machines to open up a local domain of chromatin to allow the entry of other factors. First, Foxa1 recognizes its particular binding sequence (5'-AAAGTAACA-3') and binds to the DNA, even when chromatin is condensed. After Foxa1 binds to the DNA, they recruit chromatin modeling machines and histone modification enzymes to open up the chromatin structure. Now, the DNA is more accessible to other protein factors. For example, the estrogen receptor (ER) can bind to DNA and together with Fox1a can regulate the transcription of the downstream ER gene.

What is the wobble hypothesis?

Francis Crick hypothesized that codons differing only by U or C in the third position always encode for the same amino acid. Further, codons differing only by A or G in the third position usually encode for the same amino acid. Crick concluded that physical codon-anticodon interactions determined multiple codon usage. Pairing at the third codon base is likely to be weaker or more flexible, resulting in a "wobble". This "wobble effect" allows for degeneracy.

Gene Expression Q & A

Gene Regulation in Bacteria and Phage I and II

Gene Regulation in Eukaryotes I

What are gene deserts? What is their suspected function?

Gene deserts are gene-poor areas that are devoid of genes. They may contain gene regulatory regions.

What is the correlation between the number of genes in an organism and its apparent complexity?

Generally, as the genome size increases, the number of genes also increase. However, there are some variations in this correlation. For example, some outliers have a large genome size, but not many genes.

Since there is wide range of density in tissues, how should one view a CT scan?

Given the wide range of density of the tissues in the body, one can view a CT scan using various windows to hone in on specific tissue type.

Where does glycosyl modification and protein sorting occur?

Glycosyl modification and protein sorting occur in the Golgi apparatus.

What is the role of histone H1 in the formation of the 30 nm fiber?

H1 is able to bind to the linker DNA and interact with the core histones. H1 controls the direction of the DNA after the DNA emerges from the nucleosome core. It helps position the nucleosome in such an angle that the nucleosome can form the left-handed helix. This allows the left-handed helix to be compacted, with H1 directing the relative positioning of successive nucleosome and the pattern of nucleosome-nucleosome contacts, to form the 30 nm fiber. Each 30 nm fiber contains one molecule of H1 for every nucleosome core.

What is H1? What is its function?

H1 is the linker histone. It is located outside of the nucleosome core and helps stability the nucleosome structure. It seals the DNA wrapping around the histone. Once the DNA emerges from the core, the wrapping is sealed by H1.

What is H2AX? What is its function?

H2AX, a variant of H2A, is involved in DNA damage repair. When DNA damage is detected, H2AX is quickly recruited to replace H2A. H2AX can then recruit other protein factors to repair the DNA damage.

What is H2AZ? What is its function?

H2AZ is always associated with transcription activation and is associated with chromosome segregation.

What is H3K27me3?

H3K27me3 is the trimethylation of K-27 on histone 3. It results in X-chromosomes inactivation. (CC)

What is H3K4me3? What is its function?

H3K4me3 is always associated with transcription activation.

What is the H3K9me3 modification? What is it associated with?

H3K9me3 is the trimethylation of lysine 9 of H3. This mark can recruit additional histone modification enzymes to make the same mark on adjacent histone proteins. As a result, the mark can spread along the chromatin structure, establishing the heterochromatin structure along the chromatin.

What is histone acetyltransferase (HAT)? What is its function?

HATs are enzymes that catalyze the addition of acetyl groups to K residues on histone proteins. This allows localized remodeling of chromatin around target genes, thereby opening chromatin. It facilitates the loading of activators onto the nucleosome, thereby activating transcription.

How does the human papillomavirus (HPV) affect p53 expression?

HPV produces a protein known as HPV-E6. It sequesters another E3 called E6-AP, and they bind together to degrade p53. E6-AP is viral protein that leads to cervical cancer.

Describe whether the parasympathetic nervous system increases or decreases the activity of the following processes. Heart Rate and Contractile Strength: Bronchiole Diameter: Glycogenolysis: Gut Peristalsis and Glandular Secretion: Sweat Glands: Adrenal Medulla:

Heart Rate and Contractile Strength: decreases Bronchiole Diameter: decreases Glycogenolysis: decreases Gut Peristalsis and Glandular Secretion: increases Sweat Glands: no effect Adrenal Medulla: no effect

Describe whether the sympathetic nervous system increases or decreases the activity of the following processes. Heart Rate and Contractile Strength: Bronchiole Diameter: Glycogenolysis: Gut Peristalsis and Glandular Secretion: Sweat Glands: Adrenal Medulla:

Heart Rate and Contractile Strength: increases Bronchiole Diameter: increases Glycogenolysis: increases Gut Peristalsis and Glandular Secretion: decreases Sweat Glands: increases Adrenal Medulla: increases

Since structured 5' untranslated regions and upstream AUG codons decrease translation efficiency in eukaryotes, what is required for translation?

Helicase activity is required for translation.

What is heterochromatin? How does it appear under an electron microscope?

Heterochromatin is a highly-condensed form of chromatin that appears dark under an electron microscope. There are two types of heterochromatin: constitutive and facultative. Heterochromatin is transcriptionally silenced.

What is Hif-1α? How is it regulated?

Hif-1α is a subunit of a heterodimeric transcription factor hypoxia-inducible factor 1 (HIF-1) that is encoded by the HIF1A gene. Under normoxic conditions, the transcription factor, Hif-1α, is prolyl-hydroxylated in the fourth position in the cytoplasm by prolyl hydroxylase. Hydroxyproline creates a degron recognized by the E3, pVHL. Ubiquitinated Hif-1α is degraded by the proteasome. On the other hand, under hypoxic conditions, the prolyl hydroxylase is inactive, allowing Hif-1α to accumulate in the nucleus. Nuclear Hif-1α combines with Hif-1β , and the heterodimer binds to HRE elements upstream of genes induced by hypoxia, producing erythropoietin among other products. Erythropoietin will induce red blood cell production. (CC)

What are histone deacetylases (HDAC)? What is their function?

Histone deacetylases are enzymes that catalyze the removal of acetyl groups from K residues on histone tails. This results in more condensed chromatin, and transcription is repressed.

How does histone modification allow gene regulation?

Histone modification changes histones' interactions with DNA, which affects their function of gene regulation.

What is epigenetic regulation of histone proteins? Describe how it works.

Histone modification of histone tails is a very dynamic process. Writer proteins are enzymes that can add these modification marks. For example, HATs can add acetylation marks to histone tails. Reader proteins recognize the histone marks, bind to the chromatin, and recruit additional protein factors to regulate transcription. For example, bromodomain proteins recognize H3K27 acetylation mark that is associated with cancer. Eraser proteins can remove histone modification marks. This is a highly dynamic process, and the cell will adjust these marks to fit the different needs of the cell under different conditions.

How can histone modifications have different meanings?

Histone modifications can have different meanings. For example, the H3K9me3 is a hallmark for heterochromatin structure. It is always associated with transcriptional silencing. Furthermore, H3K4me3 is always associated with transcription activation. As a result, histone modifications have different meanings. This is known as the histone code.

How do covalent modifications of histone tails function in chromatin remodeling?

Histone tails are involved in the formation of the 30 nm fiber as well as higher-order structures through interactions with other nucleosome tails. Covalent modifications on these histone tails change the chromatin structure by affecting the stability of the 30 nm fiber and higher-order structures. For example, charged lysine residues can undergo a reversible, post-translational addition of acetyl, phosphate, or methyl groups that neutralizes the positive charge on lysine. As a result, the interaction between DNA and histone proteins is reduced. Following covalent modification, these histone marks can be recognized by reader proteins. These reader proteins can bind to these modified histone marks and recruit an activator or repressor protein to regulate transcription.

How can histone variants produced in small amounts in cells make possible different chromatin structures?

Histone variants are encoded by different genes, but share high homology with conventional histone proteins. For example, the conventional H3 can be replaced by H3.3. This particular variant is always associated with transcription activation. CENP-A, another histone variant of H3, is a structure protein of the centromere, acting as an anchor for the kinetochore so the microtubules can attach to the kinetochore to pull the sister chromatids into the daughter cells. CENP-A is associated with transcription silencing. H2AX, a variant of H2A, is involved in DNA damage repair. When DNA damage is detected, H2AX is quickly recruited to replace H2A. H2AX can then recruit other protein factors to repair the DNA damage. H2AZ is always associated with transcription activation and is associated with chromosome segregation. macroH2A, another H2A variant, is involved with transcriptional repression and X-chromosome inactivation.

What are heat shock proteins (Hsps)? What are their functions?

Hsps are molecular chaperone proteins that bind to exposed hydrophobic residues on proteins in the ER lumen or membrane. These proteins protect these hydrophobic residues from interactions with the aqueous phase as well as hydrophobic residues on other proteins. They have slow ATPase activity that is used to promote folding. This ATP to ADP exchange serves as a timer of how long the chaperone binds to the unfolded protein. (CC)

Why are heat shock proteins named as such?

Hsps are so named because these proteins are synthesized following heat stress. They protect cells from heat by aiding in refolding heat-denatured proteins; however, many members of this family are produced constitutively to assist folding in the ER.

What are human artificial chromosomes? What is a possible use of these chromosomes?

Human artificial chromosomes are microchromosomes in human cells that are artificially made. They can be used as gene-therapy vectors to carry larger DNA fragments. As of now, the most common vectors are viral-based transfer systems; however, they can insert into the genome and inactivate genes that cause disease.

What are the requirements for human artificial chromosomes?

Human artificial chromosomes require a functional centromere, two telomeres, and origins of replication. It will also carry the gene of interest for the use of gene therapy.

What is I-cell disease? What causes it?

I-cell (inclusion cell), an autosomal recessive disease, is a rare, lysosomal storage disease with multiple organ system involvement, resulting in problems with skin, skeletal deformities, growth defects, mental disability, cardiac muscle defects, and more. I-cell disease is fatal in early childhood. In I-cell disease, cells have inclusions that contain glycosaminoglycans and glycolipids, inclusions that are derived from lysosomes. These lysosomal derivatives could not be degraded due to the inability to target lysosomal enzymes, such as N-acetylglucosaminyl-1-phosphotransferase. A deficiency of mannose-6-phosphate leads to secretion of lysosomal hydrolases. Lysosomes that lack hydrolytic enzymes accumulate undigested products as inclusions. (CC)

What is IF-2?

IF-2 is a small monomeric GTPase that only binds to the initiator tRNA, which carries fMet-tRNAfMet.

Cranial nerve(s) ____________ innervate(s) the head region.

III, VII, and IX

What is IPTG?

IPTG is a molecular mimic of lactose that is able to inhibit the repressor of the lac operon.

What is IRE1? How does it work?

IRE1 is a transmembrane protein located in the ER membrane. Unfolded proteins cause the autophosphorylation of its kinase domain. Autophosphorylation induces dimerization and oligomerization. Oligomerization activates RNase activity and intron-processing activity. As a result, it is able to excise introns from XBP1 mRNA. This spliced mRNA encodes for a transcription factor. RNase activity induces degradation of the ER associated mRNAs, reducing cellular stress. (CC)

What happens if there is a mutation in an ATP-driven chromatin remodeling machine?

If a mutation occurs in an ATP-drive chromatin remodeling machine, it can lead to the development of diseases, neoplasias, and cancers.

What happens if there is a mutation in the lacI gene upstream of the lac operon?

If there is a mutation in the lacI gene, there will be constitutive expression of the lacZ gene. With mutations in the lacI gene, there is no expression of the repressor protein, so the repressor cannot bind to the operator. As a result, RNA polymerase always has access to the promoter, and transcription of the operon will be constitutive.

What happens if there is a mutation in the operator region of the lac operon (without changing the promoter, of course)?

If there is a mutation in the operator region, there will be constitutive expression of the lacZ gene. With mutations in the operator region, the repressor protein cannot bind to the operator. As a result, RNA polymerase always has access to the promoter, and transcription of the operon will be constitutive.

What happens to the trp operon in the presence of tryptophan?

If tryptophan is available, the bacteria do not synthesize their own tryptophan. Tryptophan functions as a co-repressor protein, binding to and activating the tryptophan repressor protein (trpR). When trpR is activated, it binds to DNA, particularly to the operator region, at a higher affinity than that of RNA polymerase. When trpR binds to the operator, it sterically prevents RNA polymerase from binding to the promoter, thereby decreasing transcription and repressing the gene.

How do we know that proteins are synthesized NH2 to COOH?

In 1961, Dintzis used metabolic pulse labeling of proteins in reticulocytes using 3H-Leucine. Reticulocytes, which are differentiating red blood cells, synthesize globin at high levels to generate hemoglobin. Since Leu is very abundant in hemoglobin, labeled 3H-Leucine was used. Only protein made only after the addition of 3H-Leucine included 3H-Leucine. The globin protein was purified, and the distribution of radioactivity relative to NH2 and COOH termini was mapped. If synthesis was occurring from the amino end of the protein when the protein has already been undergoing synthesis, then 3H-Leucine could not be incorporated into the protein since synthesis has already begun. On the other hand, if synthesis was occuring on the carboxyl end when the protein had already been undergoing synthesis, then 3H-Leucine could not be incorporated into the protein since synthesis has already begun. He found that Label 3H-Leucine was predominantly incorporated in blocks at the COOH terminus. As a result, synthesis must begin at the amino terminus to only have carboxyl terminus labeling when the pulse was added.

Describe Step 1 of initiation of translation in prokaryotes.

In Step 1 of translation in prokaryotes, IF-1 binds to the 30S ribosomal subunit, blocking the A site. In elongation, the charged tRNA binds to the A-site; however, in initiation, the initiator tRNA binds to the P site. IF-3 also binds to the 30S ribosomal subunit, preventing the 50S subunit from binding until all other factors are in place to start translation. Lastly, the Shine-Dalgarno sequence, a purine-rich sequence, of the mRNA binds to a 16S rRNA pyrimidine-rich sequence. This binding positions the AUG near the P-site. (CC)

Describe Step 2 of initiation of translation in prokaryotes.

In Step 2 of translation in prokaryotes, IF-2 bound to GTP brings the initiator tRNA (fMet) with its anticodon to the P site to pair with the AUG start codon.

Describe Step 3 of initiation of translation in prokaryotes.

In Step 3, IF-2 hydrolyzes GTP to GDP once the initiator tRNA is base paired properly to the mRNA start codon. This results in a conformational change in the GTPase that transfers to the small subunit of the ribosome that causes the initiation factors to dissociate and allows the 50S subunit to bind. As a result, the initiation complex is complete. (CC)

How can you diagnose a pleural effusion on a chest x-ray?

In a normal chest x-ray, the costophrenic angles are very sharp. However, in a patient with PE, the costophrenic angles are not sharp, possibly non-existent. There is homogenous capacity in the lungs.

What is a right lateral radiograph of the chest? Where is the detector and x-ray source in regards to the patient?

In a right lateral chest-x-ray, the patient stands with their left side against the film/detector. The detector is a digital screen. The x-ray source is located on the right side of the patient. The x-rays produced by the source differentially interact with tissues in the chest and hit the detector, producing the final image.

How should axial CT images be viewed?

In an axial CT image, the CT scanner moving from the patient's head down toward the patient's feet. These should be viewed as if you are standing at the patient's feet looking toward the head. Just as in viewing an x-ray, the patient's right side is on the left of the image.

Give a basic overview of eukaryotic transcription initiation/activation.

In eukaryotes, DNA is highly compacted, and the chromatin structure must be opened up in order for transcription to occur. First, the activator protein (such as Foxa1) binds to DNA and recruits chromatin remodeling machines and histone modification enzymes to open up chromatin structure. Now, the DNA is accessible to other protein factors. The site-specific transcription factors, such as AR or ER, can bind to DNA and recruit additional co-activator proteins, such as the mediator proteins. They will then recruit general transcription factors followed by RNA polymerase II to form the pre-initiation complex to start trascription. Sometimes, this complex may be rearranged in order for transcription to occur.

What are transcription factories? How does it work?

In eukaryotes, so many proteins are involved in regulating transcription. These proteins assemble into a transcription factory, a unit of proteins that is clustered in a discrete site in the eukaryotic nucleus. This transcription factors includes all five general transcription factors, the site-specific transcription factors, RNA polymerase, the chromatin remodeling machines, and histone remodeling enzymes. Since these protein complexes are so large, DNA moves into the transcription factory for transcription and move out of the factory once complete.

Describe the initiation of translation in eukaryotes.

In eukaryotes, the 5' cap and polyA tail facilitate initiation by recruiting initiation factors. First, eIF3 binds the small subunit and the eIF4F complex. eIF4F is a protein complex containing scaffold protein eIF4G, a 5'-cap binding protein eIF4E, and RNA helicase eIF4A along with its cofactor, eIF4B. The polyA binding protein (PAB) binds eIF4G to bring the 3'-polyA tail to the initiation complex. eIF4A/B uses ATP to unwind the secondary structure in the mRNA and moves the mRNA across the ribosome, scanning the mRNA for the AUG. Once the the start sequence has been found by the eIF4A/B complex, eIF2 brings Met-tRNAimet to bind to the start sequence. Once the start codon is bound, eIF2, a GTPase, is hydrolyzed, and the 60S ribosome is allowed to bind. As a result, initiation is complete. (CC)

Describe the peptide-induced allosteric activation of E3.

In peptide-induced allosteric activation of E3, a substrate is targeted by E3; however, E3 binds with low affinity to the substrate, resulting in slow catalysis of the substrate. A particular dipeptide activator can bind to E3 in order to allosterically activate it for the transfer of ubiquitin onto the substrate, increasing binding affinity of E3 for the substrate as well as increasing the rate of catalysis. (CC)

What is the major mechanism of transcriptional control in prokaryotes? In eukaryotes?

In prokaryotes, the major mechanism of transcriptional control is repression while it is activation in eukaryotes.

What happens to formyl methionine after initiation in prokaryotic cells?

In prokaryotic cells, after initiation, formyl methionine is converted to Met by a peptide deformylase (associated with the ribosome), and NH2-Met is often removed by methionine aminopeptidase.

Describe the N-end rule pathway of protein degradation.

In some cases, the E3 recognizes a specific N-terminal sequence, and this sequence targets the protein for degradation. (CC)

What happens to p53 with MDM2 overexpression?

In some tumors, p53 expression is normal. However, MDM2, an E3, is overexpressed, causing the rapid degradation of lower concentrations of p53. This allows for the rapid proliferation of cells.

What is the Raney Nickel experiment? What are the results?

In the Raney Nickel experiment, the researchers created misacylated tRNA in vitro. They aminoacylated tRNACys with Cys and then treated the charged Cys-tRNACys with Raney Nickel. Raney Nickel causes the chemical removal of the sulfhydryl group from Cys, which converts it to Ala. This treatment created a tRNA specific for Cys codons that is misacylated with Ala (= Ala-tRNACys).They added these misacylated tRNAs to a cell-free translation system and translated the synthetic message, polyUG, with added Ala-tRNACys. The only two possible codons with this synthetic mRNA includes UGU, which encodes of Cys, and GUG, which encodes for Val. Alanine codons contain cytosine, which is not present in the polyUG mRNA. The resulting peptide contained Ala, even though the message contained no Ala codons. Therefore, the tRNA identity, rather than the amino acid it carries, determines which amino acid is incorporated as well as there is no proofreading of amino acid incorporation during translation. (CC)

What happens to the trp operon in the absence of tryptophan?

In the absence of tryptophan, the trp operon is transcribed. The trpR is inactive and is unable to bind to the operator region. As a result, RNA polymerase will bind to the promoter region and transcribe the whole trp mRNA.

What happens to the structure of trpR in the absence of tryptophan?

In the absence of tryptophan, the trpR undergoes a conformational change in which the repressor protein cannot bind within the major groove of the DNA. This conformational change allows RNA polymerase to bind to the promoter and initiate transcription.

What happens to the paravertebral ganglia in the cervical region?

In the cervical region, the ganglia have fused into three ganglia: the superior, middle, and inferior cervical ganglia. The superior cervical ganglion is the largest of the three.

What is the 5'HS4 and 3'HS barrier sequences? What is its function? How is it similar to humans?

In the chicken β-globin locus, the β subunit of hemoglobin protein is encoded. This locus contains an insulator sequence, HS4, at the boundary of the locus. At the 5' end of the DNA, the 5' HS4 barrier sequence is found. This site has the insulator sequence. At the 3' end of the DNA, the 3' HS contains an insulator sequence. The insulator sequences define the boundaries of the β-globin gene locus. This allows the transcription of the β-globin gene locus to not be influenced by the neighboring 5' DNA heterochromatin structure. Similar sequences (HS5 and HS4) can be found in the human β-globin gene locus and serves a similar insulator function.

What is the cis element of the lac operon?

In the lac operon, the cis element if the operator and promoter.

What is the trans factor of the lac operon?

In the lac operon, the trans factor is the lac repressor.

What happens to the structure of trpR in the presence of tryptophan?

In the presence of tryptophan, tryptophan maintains trpR in such a configuration that the trpR dimer is a perfect match to the DNA major groove. It perfectly inserts into the DNA major groove, thereby sterically preventing RNA polymerase from binding to the DNA to initiate transcription.

Describe translation termination in prokaryotes.

In translation termination, release factors (RFs) enter the A site when a termination codon is reached, as there is not tRNA in the A site when the termination codon is reached. RF-1 recognizes UAG and UAA. RF-2 recognizes UGA and UAA. RFs induce the transfer of the peptide to H2O by the peptidyl transferase reaction, releasing the nascent peptide. In other words, hydrolysis occurs rather than the transfer of the peptide to an amino acid by the peptidyl transferase reaction. RF-3, another GTPase, acts with RF-1 and RF-2 to mediate the release of the ribosomal subunits. (CC)

Who has AP x-rays? How does it work?

In very sick hospital patients, portable chest x-rays are taken. The detector is placed under the patient's back, and the x-ray beams cross from front to back. This creates an Anterior-Posterior (AP) x-ray.

How do cells know where proteins should go?

Information regarding the destination of the protein is encoded within the protein itself. Proteins contain a targeting signal sequence that acts as a delivery address by binding to proteins involved in the delivery system. These targeting signals are present in the precursors of all organellar or secreted proteins.

How does the position of the spinal cord change through development?

Initially, the spinal cord occupies the whole length of the vertebral canal. As a result of faster growth of vertebral column, the caudal end of spinal cord shifts gradually to a higher level. After two months and five months of development, the caudal end of the spinal cord is at the level of S1, although the spinal cord does shift vertically from S1 to the L2 level. In a newborn, the caudal end of the spinal cord is at the level of S1 still; however, the spinal cord has shifted to the L1 level. In adults, the spinal cord usually ends at the level of vertebrae L1-L2.

What is the major regulatory step in translation? Why?

Initiation is the major regulatory step in translation because energy conservation dictates the use of regulatory mechanisms early in pathways. Translation has a high energy requirement, so it makes sense to regulate this step of translation.

Give an example of irreversible mono ADP-ribosylation.

Irreversible mono ADP-ribosylation is used by many different bacterial toxins, such as the diphtheria, cholera, and pertussis toxins.

What is the most important thing a tRNA does?

Its identity to the translation machinery is the anticodon, which determines specificity.

What did Jacques Monod and Francois Jacob do? What did they observe?

Jacques Monod and his collaborator, Francois Jacob, discovered the lac operon. They did so by making semi-diploid E. coli strains using a special plasmid called an F plasmid to produce semi-diploid E. coli. Since E. coli cells naturally have only a single chromosome and thereby one copy of each gene, Monod and Francois made use of the F plasmid to carry a region of DNA that included the lac operon. To make these semi-diploid E. coli, the donor bacterium, which included the F plasmid, transferred the F plasmid to the recipient bacterium through conjugation via a sex pilus. The F plasmid carries pilus protein genes as well as antibiotic resistance markers and nutritional markers in the form of the lac operon. Since the bacteria have haploid genomes, E. coli becomes semi-diploid for the genes present on the F plasmid. Previously, they observed biphasic growth for E. coli cultured on lactose and glucose. E. coli preferentially used the glucose stores first as an energy source. After glucose stores are diminished, the bacteria will synthesize enzymes to use lactose as an energy source. Monod named this phenomenon the diauxie growth phase. They observed that mutations that knock out lacI lead to the constitutive expression of the lacZ gene while mutations that knock out the operator also lead to constitutive expression of the lacZ gene.

For a lumbar puncture, CSF is withdrawn between the ________ vertebrae in adults.

L3 and L4

For a lumbar puncture, CSF is withdrawn between the _________ vertebrae in a child.

L4 and L5

What is the most common LINE element?

LINEI (LI)

What is LacI?

LacI is a gene located upstream of the lac operon that encodes for the repressor protein.

What is the function of lactose in the lac operon?

Lactose binds to the repressor protein, inhibiting the repressor from binding to the operator region and allowing transcription of the genes that encode of lactose digestion to occur.

What is lactose? What does it consist of?

Lactose is a disaccharide that consist of galactose and glucose.

What is the function of lipid modifications to proteins?

Lipidation increases hydrophobicity of proteins, thereby targeting proteins to membranes.

What are mediator proteins? What is their function?

Mediator proteins are large protein complexes that mediate protein-protein interactions between the proteins bound to the distal region, the chromatin remodeling machinery, and the proteins bound to the proximal region.

What is mono ADP-ribosylation?

Mono ADP-ribosylation is a type of ADP-ribosylation that targets a single protein at a single residue. This is an irreversible reaction. This protein modification is often seen in pathogenic bacterial toxins.

What is myristoylation?

Myristoylation is a protein modification at the N-terminus of a protein, forming an N-linked thioester bond.

Compare and contrast N-linked and O-linked glycosylation.

N-Linked: 1. Initiation is co-translational, occurring the ER. 2. N-linked sugars are attached to the Asn in the sequence Asn-X-Ser/Thr. 3. Sugars are added as a core structure, then modified one residue at a time. 4. N-linked results in characteristic final structure types. 5. They can function to promote proper protein folding because initiation is co-translational. O-Linked: 1. Initiation is post-translational, occurring in the Golgi. 2. Attachment sites have no consensus sequence. 3. O-linked starts with a single residue (often GlcNAc), then a sequential sugar addition produces a final structure. 4. There are no characteristic final sugar types. Both: 1. Both are processed, where sugars are added and trimmed sequentially in the Golgi. 2. The sugars added to both are "activated," as they are donated from nucleotides. 3. Both contain similar sugars. 4. Both types can serve recognition functions. (CC)

What type of modification is N-terminal methionine acetylation?

N-terminal methionine acetylation is a co-translational modification.

How common is N-terminus acetylation?

N-terminus acetylation is very common in proteins. Up to 80% of proteins are acetylated on their N-terminal methionine, although this methionine is often cleaved.

In N-linked glycans, structures nearer the _____ terminus are often complex while those nearer the _____ terminus are often high in mannose.

N; C

Where are neocentromeres typically found?

Neocentromeres are typically located on marker chromosomes detected in children with developmental delays or congenital abnormalities. They have also been detected in two forms of cancer and experimentally induced in Drosophila.

What is the negative feedback mechanism seen in centromeres?

Neocentromeres can be induced by the removal of the normal centromere. This suggests that the centromere inhibits the formation of other centromeres along the chromosome. If one centromere is removed, another will be induced.

Is N-terminal methionine acetylation reversible?

No, N-terminal methionine acetylation is not reversible; however, proteolysis of the N-terminal methionine can result in N-acetylation by other enzymes.

Do cardiac nerves only innervate the heart?

No, cardiac nerves also innervate the lungs and bronchi.

Are insertions and deletions in the DNA sequence always a problem? Why or why not?

No, deletions and insertions are not always a problem because, if added in multiples of three, they will not cause a frameshift mutation.

What are non-histone proteins? What is their function?

Non-histone proteins are proteins that regulate transcription, telomere stability, mitotic condensation, and more.

What is nonsense mediated mRNA decay?

Nonsense mediated mRNA decay occurs when the presence of an early nonsense codon triggers a cellular mechanism in eukaryotes to degrade the mRNA. This reduces the production of inactive proteins.

Nucleosome tails are rich in what amino acid?

Nucleosome tails are rich in K residues.

Why do O-linked carbohydrates not have a consensus sequence?

O-linked carbohydrates do not have a consensus sequence because the protein is already folded by the time O-linked glycosylation occurs.

What are heterodimers? How can they contribute to combinatorial control? Use an example in your answer.

Often, transcription factors form dimers. These dimers are sometimes heterodimers. The formation of these heterodimers can increase the capacity of the transcription pattern and alter DNA binding specificity. For example, the RXR (retinoid X receptor) and RAR (retinoic acid receptor) often form a heterodimer. Each have different isoforms (both include ⍺, β, and Ɣ isoforms). Through different combinations of these isoforms, a large diversity of transcription factor regulatory mechanisms and binding patterns can be produced. (CC)

What happens after sequence-specific transcription factors (site-specific gene regulatory proteins) bind to DNA?

Once sequence-specific transcription factors bind to DNA, they can recruit the chromatin remodeling machines to open up chromatin structure. Following the opening up of chromatin structure, these sequence-specific factors can then recruit general transcription factors and RNA polymerase. Transcription can then occur.

Why are there gas shadows in the abdominal cavity on x-rays?

One gas shadow is a stomach bubble. Another shadow could be the splenic fissure of the colon.

How was attenuation discovered?

Originally, the regulation of the trp operon was thought to be mediated by simple feedback inhibition, where tryptophan inhibited the production of the enzymes that produces it. However, deletions between the operator and the first gene of the trp operon increased trp mRNA levels. This lead to the discovery of leader sequence and transcription regulation by attenuation.

Overview of the Nervous System

What is PERK? How does it work?

PERK is a transmembrane protein kinase. Normally, PERK is inactive during period of normal folding protein. However, unfolded protein accumulation and other stresses activate PERK, causing it to homodimerize and phosphorylate itself and eIF2α. When eIF2α is phosphorylated, translation initiation slows down; however, synthesis of ATF4, a transcription factor, is increased. ATF4 synthesis induces chaperone and antioxidant response genes to produce more protein product to assist in ER protein folding and to alleviate cellular stress. The GADD34 protein gene is also induced, which encodes for a protein phosphatase that turns off the PERK kinase. This is a feedback loop. Once folding is accomplished and stress has been reduced, eIF2α is dephosphorylated by GADD34. (CC)

What is palmitoylation? What is its function?

Palmitoylation is a protein modification that forms thioester bonds on Cys residues. These bonds are labile and reversible. Palmitoylation results in enhanced membrane association; however, this reaction is often reversed depending if the protein needs to be targeted to the membrane or more soluble in the cytoplasm. (CC)

What parasympathetic nerve runs through the hypogastric plexus?

Pelvic Splanchnics

What are peptidyl proline cis-trans isomerases?

Peptidyl proline cis-trans isomerases are enzymes that catalyze the isomerization of the cis peptide-Pro bonds required for the trans configuration.

What is peptidyl transferase?

Peptidyl transferase is an activity of the 23S/28S rRNA of the large subunit that catalyzes peptide bond formation that transfers the growing peptide to the A site.

What is the function of phosphorylation?

Phosphorylation can change protein activity, location, and stability.

What is poly ADP-ribosylation?

Poly ADP-ribosylation is ADP ribosylation of many different target proteins, forming many different amino acid residues. It is a reversible reaction. Poly ADP-ribose polymerases, or PARPs, add ADP-ribose while other enzymes also hydrolyze poly ADP-riboses.

Give an example of reversible poly ADP-ribosylation.

Poly ADP-ribosylation is a normal physiological response to DNA damage.

What is polynucleotide phosphorylase?

Polynucleotide phosphorylase is an enzyme that is used in cell-free synthetic mRNA systems that catalyzes template-independent synthesis of RNA using ribonucleotide diphosphates.

Identify the neurotransmitters released by the sympathetic nervous system preganglion and postganglion to innervate the sweat glands.

Preganglion: Ach Postganglion: Ach (CC)

Identify the neurotransmitters released by the sympathetic nervous system preganglion and postganglion to innervate the visceral organs.

Preganglion: Ach Postganglion: Nor (CC)

Identify the neurotransmitters released by the sympathetic nervous system preganglion and postganglion to innervate the blood vessels in skeletal muscle.

Preganglion: Ach Postganglion: Nor or Ach

Identify the neurotransmitters released by the parasympathetic nervous system preganglion and postganglion to innervate the visceral organs.

Preganglionic: Ach Postganglion: Ach

What is prenylation? How does it work?

Prenylation is a broad category of lipidation that includes farnesylation and geranylgeranylation. Farnesyl is a 15-carbon unit while geranylgeranyl is a 20-carbon unit. Farnesyl pyrophosphate is intermediate in cholesterol biosynthesis. Farnesyl transferase, in the context of farnesylation, and geranylgeranyl transferase, in the context of geranylgeranylation, recognizes the CAAX box, which is composed of Cys, an aliphatic amino acid, and another random amino acid, and forms a stable thioether bond. Farnesyl transferase will then cleave the last three amino acids of the CAAX box and methylate the Cys residue at the C-terminus. (CC)

How do release factors differ between prokaryotes and eukaryotes?

Prokaryotes: 1. RF-1 recognizes UAA and UAG while RF-2 recognizes UAA and UGA. 2. RF-3 forms a complex with either RF-1 or RF-2 and stimulates its activity. Eukaryotes: 1. eRF-1 recognizes all termination codons. 2. eRF-3 binding to eRF-1-GTP promotes the hydrolytic activity of eRF-3. 3. There is no eRF-2. (CC)

Compare and contrast how genes are organized in prokaryotes and eukaryotes.

Prokaryotes: 1. have operons where pathway genes are together on one promoter so they are under the control of one single regulatory sequence. 2. do not typically contain introns. They are very rare. 3. contain genes that encode for proteins that function together. They are found in polycistronic DNA. Eukaryotes: 1. contain no operons. 2. have introns. They are uncommon in yeast. 3. have pathway genes on different chromosomes. 4. have each gene with a separate promoter. Related genes can be located on different chromosomes.

Contrast prokaryotic and eukaryotic mRNAs.

Prokaryotic: 1. Multicistronic: Prokaryotic mRNAs are multicistronic, meaning that one mRNA can encode for more than one protein. 2. Shine-Dalgarno Sequence: The Shine-Dalgarno sequence recruits the ribosome to the mRNA. At this sequence, the ribosome will find the AUG start codon. Eukaryotic: 1. Monocistronic: Prokaryotic mRNAs are monocistronic, meaning that one mRNA encode one protein. 2. 5' Cap: Eukaryotes have a 7-methyl guanosine cap at the 5' end of the mRNA that recruits translation machinery. 3. PolyA Tail: Eukaryotic mRNAs have a polyA tail at the 3' end. The polyA tail increases translation efficiency. 4. AUG: Translation is often initiated at the first AUG. The ribosome scans for the first AUG in a favorable sequence context.

When does proofreading occur for valyl-tRNA synthetase?

Proofreading occurs following misacylation.

Protein Modification

Protein Synthesis I

Protein Synthesis II

Protein Synthesis III

Protein Targeting and Glycosylation

Protein Ubiquitination and Degradation

What is a key regulatory step in cells and tissues?

Protein degradation is highly regulated in cells and tissues.

What are protein disulfide isomerases?

Protein disulfide isomerases are enzymes that catalyze the formation and cleavage of disulfide bonds in the ER.

What happens after the termination and release of a polypeptide?

Protein folding begins during synthesis. However, the final structure is dictated by intramolecular interactions due to the primary sequence and other factors, including protein-protein interactions and post-translational modifications.

What is protein glycosylation?

Protein glycosylation is the covalent addition of one to thousands of sugar residues to protein. Protein glycosylation is the most common enzymatic protein modification in cells.

What is protein kinase R (PKR)? How does it work?

Protein kinase R (PKR) is a dsRNA-activated protein kinase. PKR is a part of the cellular antiviral response. Virus replication requires cellular protein synthesis. As a result, PKR is activated by dsRNA, which are replicative intermediates of RNA virus genomes, and PKR phosphorylates eIF2. As a result, protein synthesis is slowed in the cell as a whole. Although protein synthesis is slowed as a whole in the cell, it allows the cell time to gather its defenses to fight the virus. PKR is also activated in response to interferon, which is a peptide released by virus-infected cells that binds to cell surface receptors. (CC)

Since nature is stuck with twenty amino acids to produce proteins, how has nature extended the repertoire of protein structure and function?

Protein modifications allow proteins to extend the repertoire of their structure and function.

What is the importance of protein subcellular targeting?

Protein must be correctly localized in order to perform their proper function.

What is pulse labeling?

Pulse labeling is the addition of some particular label for a short period of time, such as 3H-Leucine.

What is puromycin? How does it work?

Puromycin is an analog of aminoacyl tRNA that accepts a peptide from the P-site. It acts as a chain terminator in both prokaryotic and eukaryotic translation. (CC)

_______ recognizes UAG and UAA.

RF-1

_____ recognizes UGA and UAA.

RF-2

What is required for RNA polymerase II to bind to the promoter?

RNA polymerase II is incapable of recognizing promoter sequences alone. RNA polymerase II require general transcription factors to recruit RNA polymerase II to the promoter region. However, access to the promoter is restricted due to the compact heterochromatin. The general transcription factors cannot bind. As a result, site-specific DNA binding transcription factors, such as Foxa1, open chromatin structure to allow the general transcription factors to bind to the DNA and recruit RNA polymerase to the promoter.

Why are activator proteins necessary for RNA polymerase II to bind to the promoter?

How does RNA polymerase find the promoter?

RNA polymerase finds the promoter by loosely binding to DNA in the major groove, scanning the DNA linearly without opening the strands. RNA polymerase detects consensus sequences at -10 and -35 in the major groove. The σ factor binds to the -35 region, allowing RNA polymerase to bind to the promoter.

How is prokaryotic transcription initiated?

RNA polymerase loosely binds to DNA in the major groove, scanning the DNA linearly without opening the strands. RNA polymerase detects consensus sequences at -10 and -35 in the major groove. The σ factor binds to the -35 region, allowing RNA polymerase to bind to the promoter without opening up the DNA complex. This is known as a closed complex, as the DNA is still hydrogen-bonded. However, RNA polymerase will then bend and open the DNA, binding to the single-stranded non-transcribed coding strand of DNA. The complex is now open. RNA polymerase unwinds the DNA approximately two turns (about 17 bp), forming a structure called the transcription bubble.

Why does RNA polymerase require CAP to bind to the promoter region of the lac operon?

RNA polymerase requires CAP to bind to the promoter region because the -10 and -35 regions are not perfect consensus sequence in the lac operon. As a result, the binding affinity of RNA polymerase for the DNA is low. However, CAP stabilizes RNA polymerase and increases its binding affinity for the promoter.

Radiology of the Thorax

What is Raney Nickel?

Raney Nickel is a nickel catalyst that has the interesting property of catalyzing reduction of sulfhydryl groups (-SH) to hydrogen (-H).

What is the redundancy of the genetic code?

Redundancy of the genetic code refers to more than one codon encoding for a particular amino acid.

What are regulated genes? What kind of genes are regulated?

Regulated genes are genes whose expression is regulated by the needs of the cell and the environment as needed. These genes typically control cell growth and cell division.

Describe the structure of the 19S regulatory particle (RP) of the 26S proteasome.

Regulatory particles are located at each end of the 20S core particle. The RPs open the central pore of the core particle and unfold substrate proteins to funnel them into the core particle chamber for degradation. The 19S regulatory particle is divided into the base and the lid. The base consists of six related AAA+ ATPase subunits in a ring structure. It rests on the core particle and opens the central pore of the 20S core particle, funneling unfolded substrate into protease chamber. The lid is involved in ubiquitin binding and DUB activity.

What is a regulatory sequence? What is its function? How does it work?

Regulatory sequences, also known as enhancers, are DNA sequences bound by transcription factors to regulate transcription. Enhancers can be located upstream, downstream, or with the gene they control as well as proximal or distal to promoter. General transcription factors bind to the DNA promoter and recruit RNA polymerase II to the promoter region. Specific transcription factors can recognize the special enhancer sequences, bind to the DNA, and can either activate (activator proteins) or repress (repressor proteins) transcription.

How can release factors perform their function?

Release factors are mimics of tRNA, allowing its entrance into the A-site to induce the transfer of the peptide to water.

How was the Shine-Dalgarno sequence discovered? Why is the Shine-Dalgarno sequence considered necessary and sufficient to direct translation initiation in prokaryotes?

Researchers isolated the initiation complex and cleaved the mRNA showing out of the initiation complex with RNase. However, with protein bound to the sequence, it was untouched by the RNase. This is how the Shine-Dalgarno sequence was discovered. Then, the researchers realized that it was complementary to a mRNA in the ribosome. As a result, it directly directs the ribosome upstream to the start codon. When placed in synthetic mRNA, the ribosome recognized the site and began synthesizing the mRNA. As a result, the Shine-Dalgarno sequence is considered necessary and sufficient to direct translation initiation.

In an adult, the dural sheath terminates at the _______ vertebral level.

The subarachnoid space in adults extends to the caudal border of _______.

The pelvic splanchnics, which emerge from _______ on the vertebral column, innervate ___________.

S2-S4; hindgut and pelvic organs

Why does the signal recognition particle halt translation?

SRP binding halts translation of the mRNA after the signal sequence is exposed because it allows time for bulky ribosome to diffuse to rough endoplasmic reticulum and helps prevent misfolding and aggregation of nascent proteins.

How should sagittal CT images be viewed?

Sagittal CT images should be viewed as if you are standing on the patient's left side, as if you are looking through them to the right. Sagittal CT images are in the same frontal orientation as a lateral radiograph.

Where is satellite DNA typically found?

Satellite DNA is typically found near the centromere.

Compare and contrast prokaryotic and eukaryotic transcription.

Similarities: 1. Both require gene regulatory proteins. Each have trans-regulators in the form of transcription factors that control transcription. 2. Both require cis-acting sequences through the use of proximal and distal promoter sequences. These sequences can be bound by protein factors and, together, they will regulate transcription. 3. Weak and reversible protein-protein interactions are important. For example, both RNA polymerases can interact with general transcription factors. These RNA polymerases cannot bind to DNA by itself, but it can be recruited by the general transcription factors. However, due to weak protein-protein interactions, RNA polymerase can be recycled while the recruitment of these transcription factors can be regulated. 4. Versatility can be afforded through DNA looping. Prokaryotic: 1. Prokaryotes can have multiple protein-encoding genes regulated by one operon. 2. RNA polymerase always have some access to the DNA because the DNA is not highly compacted. Repression is the main method of regulating gene expression in prokaryotes. 3. RNA polymerase requires one general transcription factor (the σ factor). 4. Transcription is not separated from translation. As a result, translation can regulate transcription of the same molecule. Eukaryotic: 1. Each protein is encoded by a gene with its own promoter. However, promoter access is restricted by the promoter. As a result, the chromatin structure must be remodeled in order for RNA polymerase to bind to the DNA promoter for transcription to occur. 2. Chromatin restricts access to eukaryotic promoters. As a result, the main mechanism of eukaryotic transcriptional control is activation. Almost all genes require activation to be transcribed. 3. Large, multimeric complexes regulate transcription (TFIID, TFIIB, TFIIF, TFIIE, TFIIH). They recruit RNA polymerase to the promoter. Chromatin modeling machines also regulate transcription. They contain multiple protein subunits. 4. Transcription is separated in both space and time from translation.

Compare and contrast ATF6, PERK, and IRE1.

Similarities: 1. All three have a transcriptional response, inducing the expression of proteins that increase folding capacity. Differences: 1. PERK blocks translation initiation. 2. IRE1 results in mRNA decay to reduce the concentration of mRNAs.

What is an important implication of transcription occurring in the 5' to 3' direction?

Since RNA is synthesized 5' to 3', translation in the 5' to 3' direction allows translation to begin before mRNA synthesis is complete. However, this only occurs in prokaryotes.

Why are the genes that encode for histone proteins repeated throughout the genome?

Since a human cell contains about 30 million nucleosomes, the gene must be expressed throughout the genome in order to the demand to be met.

How is it known that de-ubiquitination (DUB) enzymes are essential for ubiquitination?

Since ubiquitin is very common, it is possible to identify an E1 that is temperature-sensitive. At 37 °C, E1 cannot charge E2 or E3. At 24 °C, ubiquitin can be produced. If E1 is shut down, all proteins are ubiquitinated. This reveals that DUBs that are constantly active, and the balance between ubiquitination and deubiquitination that allows ubiquitination to occur.

What are small monomeric GTPases? How are they activated? How are they inactivated?

Small monomeric GTPases are proteins that bind to GTP and GDP. These proteins are considered "active" (the protein performs its function when bound to GTP) when bound to GTP. When bound to GTP, GTPases can hydrolyze GTP to GDP, thereby "inactivating" (prevent the protein from performing their function) them. The exchange of GTP for bound GDP requires binding of an accessory factor called a GEF (guanine nucleotide exchange factor). These GEFs bind to the GTPase and exchange GDP for GTP. These accessory factors can also function in accelerating the rate of hydrolysis of GTP.

How can proteasomes be used as a drug target?

Some cancers, such as multiple myeloma, are dependent on very active protein degradation. These cells produce high levels of Bence-Jones proteins, which are antibody proteins that do not fold properly. These antibodies clog the liver, leading to liver disease. These cancers are adapted to a high level of protein degradation. Without ERAD, these cells would not survive. If protein degradation is blocked, these cancer cells could be specifically killed. Proteasome inhibitors are small peptide analogs. MG-132 for example is a proteasome inhibitor used in the laboratory while Bortezomib (Velcade) and Carfilzomib (Kyprolis) are FDA-approved proteasome inhibitors that are used to treat multiple myeloma. (CC)

How do histone variants function in chromatin remodeling?

Sometimes, the conventional core histone proteins are replaced by histone variants by ATP-dependent chromatin remodeling complexes, changing the chromatin structure. For example, the H2A/H2B dimer complex can be removed from the nucleosome and replaced with a variant.

Describe Step 1 of translation elongation in bacteria.

Step 1 of translation elongation is the insertion of aminoacylated tRNA into the A site. Aminoacylated tRNAs are bound by EF-Tu on its acceptor arm. EF-Tu-GTP also binds to the ribosome. Proper base pairing of the anticodon with the codon in the A site stimulates GTP hydrolysis by EF-Tu. EF-Tu-GDP releases the tRNA and the ribosome. EF-Ts, the guanine nucleotide exchange factor for EF-Tu, regenerates EF-Tu-GTP for further cycles. (CC)

Describe Step 2 of translation elongation in bacteria.

Step 2 of translation elongation is the peptidyl transferase reaction. f-Met is displaced from its tRNA by the NH2 of the incoming amino acid. This transfer results in a dipeptidyl tRNA in the A site and an uncharged tRNA in the P site. This reaction is catalyzed by the peptidyl transferase activity demonstrated by 23S rRNA. The transfer also initiates a conformational change in which the tRNAs are shifted across the ribosome with anticodons still in the A and P sites while the dipeptidyl hovers between the A and P site. (CC)

Describe Step 3 of translation elongation in prokaryotes.

Step 3 of translation elongation is translocation. Translocation is a shift of the ribosome along the mRNA by one codon. This process is mediated by EF-G, which is a GTPase translocase. EF-G-GTP binds in the A-site, interacting with both the 50S and 30S subunits. GTP hydrolysis results in a conformational change of EF-G, which causes a shift of the entire ribosome. EF-G displaces peptidyl tRNA to the P site, along with mRNA. Uncharged tRNA moves to E site and is released. EF-G-GDP is then released, leaving the A-site open for the binding of the next charged tRNA. Repeated cycles of tRNA binding, peptidyl transferase activity, and translocation occur until a stop codon is reached.

How are sugars added to sugars in core oligosaccharide formation in N-linked glycosylation?

Sugar are added to sugars in N-linked glycosylation because sugars are activated nucleotide sugars. Energy is added to produce nucleotide sugars, but the energy released by the hydrolysis of the nucleotide sugar bond provides sufficient energy to create sugar-protein or sugar-sugar bonds.

Why dolichol phosphate in core oligosaccharide formation in N-linked glycosylation?

Sugar to protein transfer has a +ΔG and requires energy. Once the core oligosaccharide is built on dolichol, the bond between the sugar phosphate and the dolichol phosphate is cleaved, liberating sufficient energy to create the bond between the core oligosaccharide and the Asn residue. In other words, the oligosaccharide transfer from dolichol pyrophosphate to protein has -ΔG.

Which spinal nerves innervate visceral organs of the head region?

T1-T4

The lesser thoracic splanchnics emerge from ____ and synapse with ______.

T10 and T11; superior mesenteric ganglion

Any preganglia that emerge below ______ innervates the hindgut and pelvic organs.

T12

The least thoracic splanchnics emerge from ____ and synapse with ______.

T12; aorticorenal ganglion

Which spinal nerves innervate visceral organs of the abdominopelvic cavity?

T5-L2

The greater thoracic splanchnics emerge from ____ and synapse with ______.

T5-T9; celiac ganglion

What is a telomere? What is its function?

Telomeres protect the DNA ends from erosion following DNA replication. They consist of hundreds of thousands of repeats of the same short DNA sequence (5'-TTAGGG-3; in humans and other mammals) at the ends of each chromosome. After each round of DNA replication, the telomere is shortened, protecting the DNA sequence.

What regulates glycoprotein exit from the ER? How?

Terminal glucoses on oligosaccharides regulate glycoprotein exit from the ER. A terminal glucose is an indicator that the protein is not folded properly. As a result, if a terminal glucose is present before transport from the ER, then the glycoprotein will be retained in the ER. In the ER, a protein will bind to the glycoprotein and assist in proper folding. When the terminal has been removed, then the glycoprotein is welcome to leave the ER.

What is the beads-on-a-string 11 nm fiber? How does it form?

The 11 nm fiber of chromatin is caused by the double-stranded DNA wrapping around the histone proteins to form a "beads-on-a-string" 11 nm fiber. The linker DNA is the string portions of the fiber.

Describe the structure of the 20S core particle in proteasomes.

The 20S core particle of the 26S proteasome consists of subunits arranged in four, seven-membered rings. The two outer rings contain seven α subunits while the two inner rings contain seven β subunits. However, the only components of these subunits that contain protease activity are subunits β1, β2, and β5. All other subunits do not display protease activity. β1 displays postacidic/caspase-like activity, β2 displays trypsin-like activity, and β5 displays chymotrypsin like activity.

Describe the structure of the 26S proteasome.

The 26S proteasome consist of a core. The core is made of four rings of proteins, with two β rings of proteins in the center with two α rings of proteins on the outside. However, the only components of these subunits that contain protease activity are subunits β1, β2, and β5. All other subunits do not display protease activity. β1 displays caspase-like activity, β2 displays trypsin-like activity, and β5 displays chymotrypsin like activity. Each of these subunits recognize different substrates and sequences in the protein, so, together, they degrade a variety of proteins. On the outer ends of the barrel, the 19S regulatory complex serves as a cap. Without the regulatory complex, the barrel becomes sealed. However, the regulatory complex caps the end, opens the pore, and use ATPase proteins to funnel unfolded proteins into the core. The cap also contains proteins that recognize ubiquitin as well as DUB activity to release ubiquitin for further use.

How are nucleosomes packed to form successively higher-order chromatin structures?

The 30 nm fiber can form loops with the help of the scaffold protein to form the 300 nm fiber. Then, the 300 nm fiber can wrap further to form the 700 nm fiber followed the formation of chromatin.

How are heterochromatin and euchromatin structures dynamic?

The 30 nm fiber, for example, contains more heterochromatin structures than euchromatin structures. As a result, genes located in the heterochromatin regions are silenced. To activate regulation of the genes, an activator protein will bind to the DNA and recruit the chromatin remodeling machines. These enzymes open the chromatin structure. Then, general transcription factors and RNA polymerase can bind and transcribe the DNA. As a result, chromatin structure shifts from mostly heterochromatin to more euchromatin structure. To deactivate transcription of the gene, then a repressor protein will bind to the DNA, recruit the chromatin remodeling machines, which will recruit chromatin remodeling enzymes, and compact the chromatin into the heterochromatin region.

What is the purpose of the 5' UTR in higher-order eukaryotes?

The 5' UTR that exist in higher-order eukaryotic mRNA can form hairpins and stem loops. These structures impede ribosome scanning.

How do ATP-driven chromatin remodeling machines function in chromatin remodeling?

The ATP-driven chromatin remodeling machines are large protein complexes that bind to nucleosomes. Using ATP to provide energy, they push the nucleosome to slide along the DNA to influence the local chromatin structure. Some parts of the local structure can be more condensed while other parts of the local structure can be less condensed. As a result, regulatory DNA sequences can be exposed, becoming accessible to protein factors. Now, the protein factors can bind to the DNA and regulate transcription.

The Autonomic Nervous System

What is the C-value paradox? Does the paradox hold at any point?

The C-value paradox describes the non-equivalence between genome size (C-value) and gene number/complexity in an organism. An individual would expect more complex organisms to require more DNA. However, this is not always the case. Although, at the lower range of complexity, this assumption holds, as bacteria have smaller genomes than eukaryotes, and viruses have smaller genomes than bacteria.

What is The Cancer Genome Atlas (TCGA)?

The Cancer Genome Atlas is a project with the goal of identifying sequence variants and mutations responsible for human cancers.

What could be a potential problem for translocated proteins that fold in the ER? What can overcome this problem?

The ER is a protein factory that contains a very high protein concentration. Translocation through the ER membrane delays protein folding, so exposed hydrophobic areas can lead to protein aggregation, especially at the high concentrations seen in the ER lumen. To overcome this problem when a protein is within the ER membrane or lumen, it is bound by chaperone proteins to protect it from the high concentration of proteins in the ER and give the protein time to fold correctly. N-glycosylation, which occurs before protein synthesis is complete, also can help in folding.

Describe the path of general somatic afferent (GSA) fibers if a stimulus is detected anteriorly.

The GSA's sensory receptors are located near the skin anteriorly. The axon travels through the anterior cutaneous branch to the ventral primary ramus. The signal travels down to the spinal nerve through the dorsal root to the dorsal horn of the spinal cord.

Describe the path of general somatic afferent (GSA) fibers if a stimulus is detected laterally.

The GSA's sensory receptors are located near the skin laterally. The axon travels through the lateral cutaneous branch to the ventral primary ramus. The signal travels down to the spinal nerve through the dorsal root to the dorsal horn of the spinal cord.

Describe the path of general somatic afferent (GSA) fibers if a stimulus is detected posteriorly.

The GSA's sensory receptors are located near the skin posteriorly. The axon travels through the dorsal cutaneous branch to the dorsal primary ramus. The signal travels down to the spinal nerve, through the dorsal root, and then to the dorsal horn of the spinal cord.

Describe the path of general somatic efferent (GSE) fibers if a signal is propagated into the deep back skeletal muscles.

The GSE's receptors are located in the ventral horn. The signal is propagated from the ventral horn through the ventral root to the spinal nerve. From the spinal nerve, the signal is propagated to the dorsal or ventral primary ramus depending on location.

Describe the path of general somatic efferent (GSE) fibers if a signal is propagated into the anterior skeletal muscles.

Describe the path of general somatic efferent (GSE) fibers if a signal is propagated into the lateral skeletal muscles.

What happens when the signal recognition particle (SRP) binds to the SRP receptor on the endoplasmic reticulum membrane?

The GTP-bound SRP protein binds to the signal sequence and ribosome and docks to the GTP-bound SRP-receptor on the ER membrane. The association of the GTP-bound SRP and the GTP-bound SRP receptor results in in GTP hydrolysis. GTP hydrolysis results in a conformational change that causes the dissociation of the SRP and SRP receptor and the opening of the translocon pore. Protein synthesis resumes, with the nascent protein entering the ER through the translocon pore.

Describe the structure of the general visceral efferent (GVE) fibers.

The GVE fibers consist of two neuron connections. The preganglionic axon synapses with the autonomic ganglion. The autonomic ganglion branches into the postganglionic axon synapses with the visceral organs. The cell body of the preganglionic neuron is located in the spinal cord of the CNS while the autonomic ganglion is located in the PNS.

Describe the path of general visceral efferent (GVE) fibers if a signal is propagated to the thoracic viscera.

The GVE's preganglionic cell bodies are located in the lateral horn of T1 to T4. The signal is propagated from the lateral horn through the ventral root (T1-T4) to the spinal nerve (T1-T4) followed by the white ramus. The cell bodies of the postganglionic neurons are located in the superior, middle, and inferior cervical ganglia and the upper four thoracic paravertebral ganglia (T1-T4). The preganglionic neurons synapse with the superior, middle, and inferior cervical ganglia and the upper four thoracic paravertebral ganglia (T1-T4). The signal propagates through the postganglionic neurons (now called cardiac nerves) and form the cardiac plexus to innervate the visceral organs in the thoracic cavity.

Describe the path of general visceral efferent (GVE) fibers if a signal is propagated to the head region.

The GVE's preganglionic cell bodies are located in the lateral horn of T1 to T4. The signal is propagated from the lateral horn through the ventral root (T1-T4) to the spinal nerve (T1-T4) followed by the white ramus. The cell body of the postganglionic neuron is located in the superior cervical ganglion. The preganglionic neuron synapses with the superior cervical ganglion by propagating upwards through the sympathetic chain. The postganglionic neuron follows arteries to innervate visceral organs in the head.

Describe the path of general visceral efferent (GVE) fibers if a signal is propagated into visceral organs.

The GVE's preganglionic cell bodies are located in the lateral horn. The signal is propagated from the lateral horn through the ventral root (T1-L2) to the spinal nerve (T1-L2) followed by the white ramus. The cell body of the postganglionic neuron is located in the paravertebral ganglion. The preganglionic neuron synapses with the postganglionic neuron at the paravertebral ganglion. The postganglionic neuron then innervates the internal visceral organs.

Describe the path of general visceral efferent (GVE) fibers if a signal is propagated into the lateral blood vessels, arrector pili muscles, and sweat glands.

The GVE's preganglionic cell bodies are located in the lateral horn. The signal is propagated from the lateral horn through the ventral root (T1-L2) to the spinal nerve (T1-L2) followed by the white ramus. The cell body of the postganglionic neuron is located in the paravertebral ganglion. The preganglionic neuron synapses with the postganglionic neuron at the paravertebral ganglion. The signal is then propagated through the gray ramus to the spinal nerve to the dorsal or ventral primary ramus depending on the location.

What were the immediate outcomes of the Human Genome Project?

The Human Genome Project described the gross structure of the DNA sequence, the number of, and structure of genes.

What is the Human Genome Project? What was its goal?

The Human Genome Project was a global effort to sequence and map the entire human genome. The project was launched in 1990 and declared complete in 2003.

How are distal enhancer regions able to regulate transcription? Use an example in your answer.

The PSA (prostate-specific antigen) gene is the transcription start site. Proximally upstream of the promoter is the AR, or antigen receptor, that binds transcription factors. Distally upstream from the promoter is the PSA enhancer, which is about 4,000 bp. Within the enhancer regions, AR sites are also found as well as the Foxa1 binding site. Foxa1 is another transcription factor. The DNA can fold over. When the DNA folds over, the protein factors bound to the distal region can bind and interact with the proteins found in the proximal promoter region. They can also interact with the general transcription factors as well as RNA polymerase II. This is how enhancer sequences in the distal promoter region is able to regulate transcription.

Why does the SRP have a hydrophobic binding pocket?

The SRP has a hydrophobic binding pocket because this binding pocket is where the hydrophobic signal sequence binds.

What is the signal recognition particle receptor (SRP receptor)?

The SRP receptor is a membrane-bound receptor located on the ER membrane that is bound to GTP.

What is the Shine-Dalgarno sequence?

The Shine-Dalgarno sequence is a conserved region of mRNA upstream of an AUG. It is a purine-rich region about 10 base pairs from the start site.

Give a basic runthrough of eukaryotic transcription (because why not?).

The TBP (protein found in TFIID) binds to the TATA box on the DNA promoter. TFIID recruits TFIIB and TFIIF. This allows RNA polymerase to be recruited and bind to the promoter through protein-protein interactions. Then, TFIIE and TFIIH bind to RNA polymerase. This causes the formation of the open complex, and transcription will begin. Transcription is terminated at the termination site. RNA polymerase is dephosphorylated and recycled to begin another round of transcription.

What is the acceptor site?

The acceptor site is a 5'-CCA-3' that binds to the amino acid.

Why does the anterior rib seem to stop short of the sternum on an x-ray?

The anterior rib seems to stop short of the sternum because of costal cartilage. Cartilage is soft tissue. As a result, it cannot be seen on an x-ray.

What is the most important factor of fidelity during translation?

The binding of the correct amino acid onto the tRNA is the most important factor.

Why must the biosynthesis of heme be regulated?

The biosynthesis of heme must be regulated because heme is very hydrophobic and could have horrible effects on membranes. Further, the Fe component of heme could be harmful as well. The biosynthesis of heme must be balanced with the biosynthesis of globin to prevent harmful effects.

Where is the cardiac plexus found?

The cardiac plexus is located at the base of the heart.

Where is the caudal end of the spinal cord?

The caudal end of the spinal cord is between L1 and L2.

What is the mode of action of the cholera toxin?

The cholera toxin produced by Vibrio cholerae modifies an Arg residue on Gs. It affects signaling pathways by overactivating adenylate cyclase.

How does the chromosome operate as a distinct structural unit?

The chromosome must function as an independent unit. It must replicate, separate the replicated copies of its genome, and partition those copies correctly into daughter cells.

What is significant about the cleft between two ribosomal subunits?

The cleft between two ribosomal subunits holds mRNA and has sites that bind charged tRNAs.

What is H3.3? What is its function?

The conventional H3 can be replaced by H3.3. This particular variant is always associated with transcription activation.

What is the function of the core enzyme of RNA polymerase?

The core enzyme of RNA polymerase is responsible for polymerization.

How is the 20S core particle of a 26S proteasome formed?

The core particle is formed in a very special way. These are very active proteases, and if these proteases were loose in the cell, they would produce a lot of damage. In the end, the protease proteins are formed as proproteins and are autocatalyzed to form the core particle.

What is the costophrenic angle?

The costophrenic angle is the extreme outermost lower corner of each lung where diaphragm meets the ribs in an x-ray.

The covalent modification of histone tails are involved in what cellular functions?

The covalent modification of histone tails are involved in transcription activation and inactivation, chromosome packaging, and DNA damage and repair.

What is the mode of action of the diphtheria toxin?

The diphtheria toxin produced by the bacteria Corynebacterium diphtheriae modifies a His residue on EF2. It affects protein synthesis.

Why don't we have to worry too much about diphtheria anymore?

The diphtheria toxoid, or an inactive form of the toxin, is used in the DPT vaccination.

Compare and contrast cranial and spinal meninges.

The dura mater of cranial meninges are attached to the skull while it is not attached in the spinal cord. In the cranial meninges, the subarachnoid space is much larger than the subarachnoid space in the spinal meninges.

What enzyme performs ADP-ribosylation? How does it work?

The enzyme that performs ADP-ribosylation is known as poly ADP-ribose polymerase, of PARP. The PARP attaches the ADP-ribose to the end of the protein using NAD+ as a substrate, producing nicotinamide as a side product.

Where can the esophagus be seen on a CT?

The esophagus is usually left to the trachea posteriorly.

What controls eukaryotic gene expression?

The expression of each eukaryotic gene is controlled by cis-acting DNA sites, which include the proximal promoter and the distal enhancer (either 5' or 3' from the gene). When the protein factors bind to the distal enhancer, they open chromosome structure, thereby enhancing the transcription of the gene.Expression is also controlled by many regulatory proteins, such as transcription factors, remodeling machinery, and mediators. Transcription factors recognize specific sequences, bind to the DNA, and regulate transcription through either activation or repression. The remodeling machinery can remodel chromatin structure using ATP. Mediator proteins are large protein complexes that mediate protein-protein interactions between the proteins bound to the distal region, the chromatin remodeling machinery, and the proteins bound to the proximal region. (CC)

What is the function of the filum terminale?

The filum terminale gives longitudinal support to the spinal cord.

What is the first energy input into protein synthesis?

The first energy input into protein synthesis is the binding of the amino acid to the tRNA acceptor site, cleaving two phosphate bonds.

Why are two bonds hydrolyzed on ATP during aminoacylation?

The first step of aminoacylation is proceeding through a high energy intermediate (aminoacyl-AMP). This is why two bonds are hydrolyzed on ATP, as the amino acid is adenylated.

What is the function of DNA proteins as a whole?

The function of DNA proteins as a whole is to regulate transcription, DNA replication and DNA repair as well as control gene activity and the epigenetic inheritance of traits.

What is the function of N-terminus acetylation in proteins?

The function of N-terminus acetylation is protein quality control and degradation. A target of ubiquitylation is the N-terminus. If the N-terminus is acetylated, it is not necessarily targeted for degradation; however, N-terminus acetylation on specific amino acid residues can target a protein for degradation.

What is the function of polyubiquitination?

The function of polyubiquitination is to serve as a target for proteasomes (in most cases). Proteasomes recognize polyubiquitinated proteins, especially those polyubiquitinated on K48 and K11, and target them for degradation. However, polyubiquitination can also serve other functions.

What were the future outcomes of the Human Genome Project?

The future outcome of the Human Genome Project is that the accumulation of basic knowledge is expected to inform therapeutics.

Beginning with the grey matter of the spinal cord, indicate the paths a signal can follow along a spinal nerve.

The grey matter of the spinal cord branches into the dorsal horn, the lateral horn, and the ventral horn. The grey matter is surrounded by white matter, from which emerges the dorsal root and the ventral root. The dorsal root and the ventral root come together to form a spinal nerve. A spinal nerve divides into the dorsal primary ramus and the ventral primary ramus. The dorsal primary ramus innervates the deep back. The anterior primary ramus innervates the lateral and anterior sides of the thoracic cavity. The dorsal primary ramus gives rise to the dorsal cutaneous branch. The ventral primary ramus gives rise to the lateral and anterior cutaneous branch.

What is the hallmark of eukaryotic transcription? How does it work?

The hallmark of eukaryotic transcription is combinatorial control. Combinatorial control is achieved by combinations of different transcription factors. For example, the combination of Foxa1 with the AR can contribute to prostate-specific gene expression while Foxa1 with the ER can contribute to mammary gland-specific gene expression. Through different combinations of limited transcription factors, a large diversity of transcription patterns can emerge. (CC)

What is a helix-turn-helix motif? What is its function?

The helix-turn-helix motif is a DNA-binding motif that is found in many transcription factors used to compact DNA within the major groove.

What is the histone code? What is its function?

The histone code are combinations of modifications and variants that serve as epigenetic marks for the cell. Code reader proteins can recognize these histone marks and bind to the modified histones. They can function as a scaffold protein and recruit activator or repressor proteins to regulate transcription of the adjacent gene.

What are reader proteins? What is their function?

What is the role of the histone tails in the formation of the 30 nm chromatin fiber?

The histone tails project from the core histones. They can interact with other nucleosomes, helping position the nucleosome to form the highly-compacted 30 nm chromatin structure and higher-order chromatin structures.

Describe the structure of the operator region. What are the implications of this structure?

The lac operator contains palindromic sequences that partially overlap with the promoter sequence. As a result, the binding of the lac repressor protein to the operator and the binding of RNA polymerase to the promoter is mutually exclusive.

How is the lac operon organized?

The lac operon contains the promoter region, where RNA polymerase binds. The operator region overlaps with the promoter region, and this is where the repressor protein binds to inhibit transcription. Following the operator region are the genes that encode for lactose metabolism, including LacZ (β-galactosidase), LacY (permease), and LacA.

When is the lac operon on?

The lac operon is only one when the substrate, lactose, is available.

What is the lac operon? What is its function?

The lac operon is the first genetic regulatory mechanism to be fully understood. The lac operon encodes for enzymes that are involved in lactose digestion. When lactose is present, then lactose will bind to the receptor protein, thereby inactivating the repressor and allow transcription of the lac operon to be induced. On the other hand, if lactose is not available, then the lac operon will not synthesize the enzymes required for lactose digestion, as this is energetically unfavorable. The repressor protein will bind to the promoter region, inhibiting transcription. However, bacteria preferentially use glucose as an energy source. In the presence of glucose, even when lactose is available, the bacteria will not transcribe the lac operon and not digest lactose. Glucose, as a result, inhibits the transcription of the lac operon by binding to CAP, an inhibitor protein. Transcription of the lac operon as a result is under the regulation of both glucose and lactose.

Describe the structure of the lac repressor.

The lac repressor is a repressor protein that binds as a tetramer with a two-fold axis of symmetry. However, the binding of the inducer causes a conformational change in which the lac repressor can no longer bind to the operator region.

Describe the structure of the leader sequence.

The leader sequence has different regions. Region 1 contains the codon for tryptophan (UGG). Region 3 can pair with Region 2 as well as Region 4. This is through alternative splicing.

What is the leader sequence?

The leader sequence is the sequence of DNA located between the promoter sequence and the coding sequence.

On a PA x-ray, where does the left atrium lie, although it is not border forming?

The left atrium lies between the pulmonary arteries.

Why do the lungs appear black on an x-ray? What are the white splotches on the lungs?

The lungs appear dark due to their air content. The white tubular densities near the lung roots are the pulmonary vessels.

What is the mediator protein? What is its function?

The mediator protein is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. The protein complex does not directly bind to DNA, which is why it is a coactivator. It acts as a scaffold protein, mediating the protein-protein interactions between the transcription factors bound to the distal region, the chromatin remodeling machines, the transcription factors bound to the proximal region, general transcription factors, and RNA polymerase II. They are required for successful transcription by RNA II in activator-dependent transcription.

What is the structure of the mediator protein?

The mediator protein is complex that contains over 31 subunits. The subunit composition is variable, as some subunits can be absent or replaced by other subunits under certain conditions.

How does the neocentromere compare to a normal centromere?

The neocentromere does not contain the alpha satellite sequence, but the secondary structure and higher-order structure is conserved. They maintain the ability to bind to CENP-A. CENP-A can still function as the anchor for the kinetochore.

Describe the structure of the 11 nm fiber.

The nucleosome beads repeat for about 230 bp. 147 bp are bound tightly around the histone protein core, wrapping approximately 1.7 turns in a left-handed coil. The 83 remaining base pairs form linker DNA. However, this linker DNA is an average number of base pairs and can vary by the how loose or compacted the fiber is at a particular time.

Describe the structure of the nucleosome core.

The nucleosome core consists of an octamer of H2A, H2B, H3, and H4 histones. These histones are basic proteins rich in lysine and arginine. As a result, they are positively-charged in a cellular environment. The nucleosome core is globular; however, unstructured tails project from the nucleosome core.

What is the functional subunit of chromatin?

The nucleosome is the functional subunit of chromatin.

How do valyl-tRNA synthetase and isoleucyl-tRNA synthetase discriminate between these two related amino acids?

The only difference structurally between valine and isoleucine is a methyl group. Valyl-tRNA synthetase has a binding pocket that excludes Ile, using amino acid affinity to its advantage. Valine is included while isoleucine is excluded from the pocket. Isoleucyl-tRNA synthetase cannot exclude Val based on size because a binding pocket large enough to fit isoleucine will also fit valine. As a result, isoleucyl-tRNA synthetase must use a different mechanism. So, if alanine is bound into the active site of isoleucyl-tRNA synthetase, the enzyme realizes that the amino acid fits differently in its binding pocket. As a result, the bond will be hydrolyzed rather than t-RNA being added to the bond. (CC)

What is the paravertebral ganglia?

The paravertebral ganglia are interconnected autonomic ganglia that lie close to the spinal nerves and the vertebrae, from the lower cervical/upper thoracic level to the sacral level of the spinal cord.

How is the paravertebral sympathetic ganglion connected to the spinal nerve?

The paravertebral sympathetic ganglion is connected to the spinal nerve through the white and grey ramus.

What is the mode of action for the pertussis toxin?

The pertussis toxin produced by Bordetella pertussis modifies a Cys residue on Gi. It affects signaling pathways by overactivating adenylate cyclase.

What is the function of the polyA tail in translation?

The polyA tail is recruited to the ribosome. The purpose of this recruitment is to increase translation efficiency. The ribosome is able to hop back onto the 5' end of the mRNA following translation.

Where are the postganglionic fibers located in the parasympathetic nervous system? What is the exception to the rule?

The postganglionic fibers of the parasympathetic nervous system are located in the wall of the target organ. The exception is the head region, where they are located outside of the target organ.

Describe the path of general visceral efferent (GVE) fibers if a signal is propagated through the least thoracic splanchnic nerves to the abdominal organs .

The preganglionic cell bodies of the least splanchnic nerves are located in the lateral horn of T12. The signal is propagated from the lateral horn through the ventral root to the spinal nerve followed by the white ramus. The signal travels through the sympathetic chain. The cell body of the aorticorenal ganglion, the postganglionic neuron, is located in the prevertebral ganglia of the aortic plexus. The least splanchnic nerves synapse with the aorticorenal ganglion. The aorticorenal ganglion follows arteries to innervate abdominal organs.

Describe the path of general visceral efferent (GVE) fibers if a signal is propagated through the lesser thoracic splanchnic nerves to the abdominal organs .

The preganglionic cell bodies of the lesser splanchnic nerves are located in the lateral horn of T10 and T11. The signal is propagated from the lateral horn through the ventral root to the spinal nerve followed by the white ramus. The signal travels through the sympathetic chain. The cell body of the superior mesenteric ganglion, the postganglionic neuron, is located in the prevertebral ganglia of the aortic plexus. The lesser splanchnic nerves synapse with the superior mesenteric ganglion. The superior mesenteric ganglion follows arteries to innervate abdominal organs.

Describe the path of general visceral efferent (GVE) fibers if a signal is propagated through the lumbar splanchnic nerves to the abdominopelvic organs .

The preganglionic cell bodies of the lumbar splanchnic nerves are located in the lateral horn of L1 and L2. The signal is propagated from the lateral horn through the ventral root to the spinal nerve followed by the white ramus. The signal travels through the sympathetic chain. The cell bodies of the postganglionic neurons of the lumbar splanchnics are located in the prevertebral ganglia of the aortic plexus and the hypogastric plexus. In the aortic plexus, the lumbar splanchnic nerves synapse with the inferior mesenteric ganglion. In the hypogastric plexus, the lumbar splanchnic nerves synapse with postganglia of the plexus. The postganglia of the hypogastric plexus follow arteries to innervate the hindgut and pelvic organs while the inferior mesenteric ganglion follows arteries to innervate the abdominal organs.

Describe the path of general visceral efferent (GVE) fibers if a signal is propagated through the sacral splanchnic nerves to the hindgut and pelvic organs .

The preganglionic cell bodies of the sacral splanchnic nerves are located in the lateral horn of S2-S4. The signal is propagated from the lateral horn through the ventral root to the spinal nerve followed by the white ramus. The signal travels through the sympathetic chain. The cell body of the postganglion is located in the hypogastric plexus. The sacral splanchnic nerve synapses with the postganglion. The postganglion innervates the hindgut and pelvic organs.

Describe the path of general visceral efferent (GVE) fibers if a signal is propagated through the greater thoracic splanchnic nerves to the abdominal organs.

The preganglionic greater thoracic splanchnic nerves cell bodies are located in the lateral horn of T5 to T9. The signal is propagated from the lateral horn through the ventral root to the spinal nerve followed by the white ramus. The signal travels through the sympathetic chain. The cell body of the celiac ganglion, the postganglionic neuron, is located in the prevertebral ganglia of the aortic plexus. The greater splanchnic nerves synapse with the celiac ganglion. The celiac ganglion follows arteries to innervate abdominal organs.

Describe the path of general visceral efferent (GVE) fibers if a signal is propagated to the abdominal and pelvic viscera (in general).

The preganglionic splanchnic nerves cell bodies are located in the lateral horn of T5 to L2. The signal is propagated from the lateral horn through the ventral root (T5-L2) to the spinal nerve (T5-L2) followed by the white ramus. The signal travels through the sympathetic chain. The cell bodies of the postganglionic neurons are located in the prevertebral ganglia. The splanchnic nerves synapse with the prevertebral ganglia. The prevertebral ganglia follow arteries to innervate visceral organs in the abdominopelvic cavity.

What is the prevertebral ganglia?

The prevertebral ganglia are associated with the major branches of abdominal aorta. These ganglia are located anterior to the spinal cord. These individual ganglia are not associated with sympathetic trunk.

What is the promoter region?

The promoter region is a sequence of DNA to which RNA polymerase binds and initiates transcription. It controls the initiation of transcription in the adjacent segment of DNA.

What is the purpose of upstream reading frames in eukaryotes?

The purpose of upstream reading frames in eukaryotes is translation regulation. For example, if translation is occurring efficiently, then scanning will occur until an AUG is reached. With upstream reading frames, the reading frame will be translated, and the ribosome will dissociate following translation.

Where is the reaction energy for the peptidyl transferase reaction derived from?

The reaction energy for the peptidyl transferase reaction is derived from the cleavage of the high energy ester linkage formed by the tRNA aminoacylation reaction.

What is a reading frame? Where is the reading frame set?

The reading frame is the starting codon offset by three bases. Reading frame is set at the start of the coding sequence.

How can you tell the right hemidiaphragm from the left hemidiaphragm on a lateral chest x-ray?

The right diaphragm is higher than the left diaphragm.

Describe the path of general visceral afferent (GVA) fibers if a signal is propagated from the visceral organs to the spinal cord.

The sensory receptors in the internal organ sends a pain signal through the white ramus to the spinal nerve. The spinal nerve then propagates the signal to the dorsal root to the spinal cord.

What is the signal recognition particle (SRP)? What is its function?

The signal recognition particle is a cytosolic ribonucleoprotein complex (six proteins and one RNA) that recognizes the signal sequence to direct the nascent polypeptide into the endoplasmic reticulum. The SRP also binds the ribosome. The binding of the ribosome to the SRP directs the ribosome and nascent protein to the ER. The SRP contains a hydrophobic pocket that binds the signal sequence. In addition, the SRP also includes a GTPase, and binding to the signal sequence and the ribosome requires a GTP-bound SRP. When the SRP binds to the polypeptide and the ribosome, translation is halted immediately.

How was the stop codon assigned?

The stop codon was assigned through the translation of specific polytrinucleotide mRNAs. For example, polyGUA translation produced only polyVal and polySer. Thus, one of the three codons does not encode for an amino acid. As a result, UAG, UGA, and UAA (UAG in this particular example) are stop codons, and stop codons do not encode for an amino acid. Rather, they serve to terminate translation.

How was the structure of the nucleosome discovered?

The structural organization of the nucleosome was discovered by isolating them from the beads-on-a-string complex through the addition of nuclease followed by the dissociation of the histone core and DNA by the addition of a high salt solution.

What is the subarachnoid space?

The subarachnoid space is the interval between the arachnoid membrane and the pia mater that contains cerebrospinal fluid.

What is the structure of substrates that undergo γ-carboxylation? Where are they commonly found? What is their typical function?

The substrates of γ-carboxylation contain a conserved protein domain, or GLA. This GLA is a γ-carboxylglutamic acid rich domain. Many of these GLA-containing proteins are found in the clotting cascade, where γ-carboxylation of the GLA domain allows Ca++ binding that facilitates membrane binding.

What is the sympathetic chain?

The sympathetic chain is a chain of paired paravertebral ganglia that lies lateral of the bodies of the vertebrae.

Why must the mRNA move each time an acylated tRNA is moved to the P site?

The tRNA and the acylated tRNA are base paired, so one must move with the other.

How is tRNA identity specified during translation?

The tRNA identity is specified during translation by the codon-anticodon interaction. (CC)

What is the target of Warfarin (Coumadin)?

The target of Warfarin is Vitamin K reductase.

How is the tertiary structure of tRNA stabilized?

The tertiary structure of tRNA is stabilized by non-Watson-Crick interactions between bases distant from one another in primary structure.

What was the first tertiary structure solved?

The tertiary structure of tRNA was the first to be solved by X-ray crystallography.

What is the translocon? What is the translocon in prokaryotes and eukaryotes?

The translocon is a protein-containing pore through which a nascent protein is inserted into the ER lumen. In eukaryotes, the translocon is known as the Sec61 complex while the homologous complex in prokaryotes is known as the SecYEG complex.

What is the trp operon? What is its function?

The trp operon is a well-studied operon in prokaryotes that encodes for five enzymes that synthesize tryptophan. These enzymes are transcribed in a polycistronic fashion, as one trp mRNA molecule encodes for these five enzymes. The transcription of the trp mRNA is under the control of the same promoter and operator. If the tryptophan level is low, then the bacteria will transcribe the trp operon, and these five enzymes will be synthesized. As a result, the bacteria will synthesize its own tryptophan.

What does the upright arrow mean on an x-ray?

The upright arrow on an x-ray means the patient was in the upright position when the x-ray was taken. If the arrow is not present, then the patient was supine.

What explains the degeneracy of the genetic code?

The wobble hypothesis explains the degeneracy of the genetic code without having a tRNA for every position possible.

What is γ-carboxyglutamic acid domain?

The γ-carboxyglutamic acid domain is a common protein domain that is found in proteins of the clotting cascade.

What is the sigma (σ) factor? What is its function?

The σ factor is a separate protein in the RNA polymerase that is required for transcription initiation. The σ factor contributes to RNA polymerase promoter specificity. There are a number of different σ factors, and different σ factors allow for the expression of different genes. For example, starvation and heat shock conditions require a different σ factor to specify the promoter sequence that will be transcribed.

Why do so many antibiotics target translation?

There are enough differences between prokaryotic and eukaryotic translation that antibiotics can be produced to specifically target bacterial translation.

Why do CT scans demonstrate better contrast between tissues than x-rays?

This is because a Hounsfield unit can allow differentiation between different tissues.

What is trans regulation?

Trans regulation is the regulation of one molecule by an external factor, such as a protein or RNA. In other words, trans regulation occurs when the regulator is provided by a different molecule. Trans regulation requires the production of a diffusible factor.

Why is there no evidence for translational control of transcription in eukaryotes?

Transcription and translation occur in different compartments of the cell in eukaryotes, so it is impossible to exert translational control over transcription.

Why is transcription a restrictive ground state in eukaryotes?

Transcription is a restrictive ground state in eukaryotes because chromatin restricts the access of the RNA polymerase and general transcription factors to bind to the DNA. Further, eukaryotic RNA polymerases have little affinity alone for the promoter. RNA polymerase is recruited by general transcription factors through protein-protein interactions. So, if the general transcription factors do not bind, then RNA polymerase is restricted from binding to the DNA promoter.

Why is transcription highly regulated?

Transcription is highly regulated for energy conservation purposes. For example, if tryptophan is at high levels in the cell, then the bacteria will not waste energy and materials to produce their own tryptophan. As a result, transcription is a highly regulated process.

What is the paramount control of gene expression? Why?

Transcriptional regulation is paramount of gene expression because: 1. it is fast and cheap. It limits the energetic and materials cost of aborting expression at subsequent stages. 2. it permits the regulation of multiple genes encoding products with interdependent activities. For example, genes can be transcribed into polycistronic mRNAs that can be translated into multiple proteins. However, these multiple proteins share a regulatory region. In eukaryotes, synchronized transcription regulation can be achieved through transcription factors. For example, NF-κB controls the synchronized transcription of inflammatory cytokines in eukaryotes. (CC)

How are transcriptionally-active chromatin structurally distinct from inactive chromatin? How does it affect their sensitivity to DNase I?

Transcriptionally-active chromatin is structurally distinct from inactive chromatin. Transcriptionally-active chromatin contain more open chromatin structure, so they are more accessible to protein factors and more sensitive to DNase I than inactive chromatin. On the other hand, transcriptionally-inactive chromatin contain more compacted chromatin structure, so they are less accessible to protein factors and less sensitive to DNase I.

Why can DNase I be used as a tool to study chromatin structure?

Flip card for question. Answer below. NH2-Met-Ala-Trp-Ala-Ser-Ser-Gly-Pro-Ala-Ala-Ala-COOH

Translate the following RNA sequence: 5'-AUGGCGUGGGCCUCCUCAGGGCCAGCGGCGGCC-3'.

Does translation have a directional notion? Why or why not?

Translation has no directional notion. Diffusion controls when tRNAs bring amino acid to the growing polypeptide chain.

Describe one way that translation initiation is regulated.

Translation initiation can be regulated by the GTP exchange on eIF2. eIF2 is a GTPase that binds GTP and GDP with similar binding affinities. However, only GTP-bound eIF2 can bind charged initiator tRNA. The hydrolysis of GTP competes with the initiation step of translation, and the hydrolysis of GTP results in GDP-bound eIF2, which is unable to bind charged initiator tRNAs. As a result, the exchange of GTP for bound GDP must occur to allow eIF2 to bind a charged initiator tRNA and act in the next initiation cycle. The exchange of GTP for GDP on eIF2 is promoted by the binding of a GEF. In translation, the GEF is eIF2B.

Why is need high specificity needed when proteins are produced?

Translation requires high specificity because it could produce a dysfunctional protein.

What is translocation? How does it work?

Translocation is a shift of the ribosome along the mRNA by one codon. This process is mediated by EF-G, which is a GTPase translocase. EF-G-GTP binds in the A-site, interacting with both the 50S and 30S subunits. A conformational shift of EF-G upon GTP hydrolysis drives the tRNA-like domain further into A-site, displacing the dipeptidyl tRNA to P site. The mRNA, base paired to dipeptidyl tRNA anticodon, shifts also. The uncharged tRNA is displaced from the P site to the E site, from which it is released.

How is translocation possible?

Translocation is possible because EF-G is a structural mimic of the EF-Tu:tRNA complex. It is able to bind to the A-site and displace the peptidyl tRNA.

How are transmembrane proteins inserted into the endoplasmic reticulum membrane?

Transmembrane proteins require additional signal sequences to insert into the ER membrane. These sequences are often very hydrophobic, resulting in transmembrane domains. Several types of transmembrane proteins exist, including single-pass (cytosolic N- or C-terminus) and multi-pass (cytosolic or luminal N-terminus) transmembrane proteins. However, signal anchor and stop-transfer sequences prevent the entire protein from entering the ER lumen, allowing one to multiple transmembrane domains.

What are transposable elements? What is their function?

Transposable elements, or moderately-repetitive DNA, interspersed repeats, transposons, or jumping genes, are DNA sequences that can change its position within a genome, sometimes creating or reversing mutations. When a transposable element inserts into a gene, it causes a mutation; however, when it pops out of a gene, it can reverse the mutation produced by its original insertion. They make up about 45% of the genome and can be concentrated in specific regions of the chromosome or dispersed between genes.

True or False: Acetylation of histone tails always activates transcription.

True

True or False: Axial, coronal, and sagittal images are used to make a 3D image on a CT.

True

True or False: Cells must change gene expression in response to stimuli.

True

True or False: Centromeres do not require a specific DNA sequence to carry out their function.

True

True or False: Chromatin remodeling is a highly dynamic process.

True

True or False: Co-translational targeting is important for proteins residing in secretory compartments.

True

True or False: E. coli RNA polymerase synthesizes all types of RNA.

True

True or False: E3 are specific to particular E2.

True

True or False: Each amino acid has a corresponding aminoacyl-tRNA synthetase.

True

True or False: Each compartment of a eukaryotic cell has its own distinct set of proteins and distinct functions.

True

True or False: Each genome contains all of the genetic information required to build and maintain the organism.

True

True or False: For many proteins, the signal sequence is cleaved from the nascent polypeptide upon translocation into the membrane.

True

True or False: Glucose represses transcription of the lac operon.

True

True or False: Gray rami are present at all levels.

True

True or False: In eukaryotes, the initiating methionine is often cleaved by an aminopeptidase.

True

True or False: Initiation factor 2 is very similar between prokaryotes and eukaryotes, escorting the aminoacylated initiator tRNA to the ribosome small subunit-mRNA complex.

True

True or False: Initiation is the most heavily regulated step of protein synthesis.

True

True or False: Lysine acetylation is a reversible reaction.

True

True or False: Many diseases are associated with protein misfolding as well as with the loss of ERAD activity.

True

True or False: Mutations in the operator that lead to lower affinity for the repressor and hence less binding allow continued transcription (and thus expression) of the lac operon even in the absence of inducer (constitutive expression).

True

True or False: Mutations in the repressor that prevent its binding to the operator will lead to constitutive expression (no repression in the absence of inducer).

True

True or False: Mutations that prevent binding of the inducer without affecting the ability to bind to the operator lead to a non‑inducible phenotype (no expression in the presence of inducer).

True

True or False: N-glycosylation begins in the ER and continues in the Golgi, whereas O-glycosylation occurs in the Golgi.

True

True or False: One fascicle innervates one region.

True

True or False: Protein kinases are very specific, as there are over 800 encoded by the genome.

True

True or False: Replication and transcription are based on the complementary nature of polynucleotides to generate complementary nucleic acids.

True

True or False: Since sequence 4 is required to form the 3:4 attenuator stem‑loop, in its absence no attenuation would be observed.

True

True or False: Site-specific gene regulatory proteins accelerate the rate of transcription initiation.

True

True or False: The central nervous system is the control and processing center of the body.

True

True or False: The inferior vena cava would be found within the right cardiophrenic angle on an x-ray.

True

True or False: The left atrium on a lateral film is border forming.

True

True or False: The structure of BiP is very conserved all the way to bacteria.

True

True or False: The sympathetic nervous system and parasympathetic nervous system not only have "opposite" actions, but also have a complementary relationship.

True

True or False: There is one paravertebral ganglion per spinal nerve.

True

True or False: There is only one paravertebral ganglia per spinal nerve.

True

True or False: White rami is present from T1 to L2.

True

True or False: Some sympathetic fibers can innervate farther up or down the sympathetic chain to innervate the head region and lower extremities.

True: Preganglionic fibers exit the spinal cord in the ventral roots of spinal cord segments T1 to L2. Some fibers synapse in their corresponding paravertebral ganglia, some fibers synapse in the paravertebral ganglia rostral to T1 and caudal to L2.

What is tunicamycin?

Tunicamycin is a dolichol analog produced from Streptomyces that blocks N-linked glycosylation. (CC)

Give an example of amino acid affinity that increases fidelity.

Tyrosyl-tRNA synthetase binds tyrosine with 104 higher affinity than phenylalanine, which only differs from tyrosine by a hydroxyl group.

What are the termination codons?

UAA, UAG, UGA

What is ubiquitylation? How does it work?

Ubiquitylation is the addition of ubiquitin, a 76 amino acid conserved protein, to lysine residues via the formation of an isopeptide bond. The C-terminus of ubiquitin binds to a lysine residue, forming an isopeptide bond to produce water. (CC)

What parasympathetic nerve runs through the aortic plexus?

Vagus Nerve

What parasympathetic nerve runs through the cardiac plexus?

Vagus Nerve

How does valyl-tRNA synthetase discriminate against polar threonine and nonpolar valine?

Valyl-tRNA synthetase must discriminate between polar Thr and non-polar Val. Valine and threonine are around the same size, so they cannot be differentiated using size exclusion. Once aminoacylation occurs, the tRNA with the amino acid must reposition to remove the amino from the acetylation binding pocket so that the amino acid is subjected to another binding step. Another binding site has a site for threonine. Valine does not fit in this binding site; however, threonine fits into this hydrolytic site. Then, threonine is able to be hydrolyzed off the tRNA.

What happens to DNA when it is under physiological salt conditions?

WHen DNA is placed under physiological salt conditions, it will form the 30 nm fiber, a highly compacted DNA structure.

Flip card for question. Answer below. CFTR ΔF508 does not fold properly and exit the ER. Two species of CFTR ΔF508 are labeled: mature CFTR and nascent CFTR. Mature CFTR (NL) is associated with decreased electrophoretic mobility, as the CFTR is glycosylated. Glycosylation is a part of the maturation process for CFTR. DF508 CFTR (CF) does not achieve this mature state and is present at a lower level.

What does this immunoblot show?

Flip card for question. Answer below. The radiograph is a posterior-anterior (PA) radiograph because the posterior aspect of the patient is struck by x-rays first on their way to the detector.

What type of radiograph is the following picture?

What happens when H1 is removed from the 30 nm fiber?

When H1 is removed from the 30 nm fiber, the DNA loosely wraps around the nucleosome core, unable to form the 30 nm fiber.

What happens when Ras proteins are farnesylated? When they are palmitoylated?

When Ras proteins are farnesylated, they have weak membrane association. However, when they are palmitoylated, they have enhanced membrane association.

Describe what happens to the lac operon in the following semi-diploid E. coli cross: lacZm vs. lacYm and Operatorm.

When a lacZm and a lacYm and Operatorm are present in semi-diploid E. coli, the repressor protein is able to bind to the operator in the lacZm operon, but is unable to bind to the operator in the lacYm and Operatorm operon. As a result, lacZ and lacA can still be expressed by the lacYm and Operatorm, as lacY is mutated and is unable to be expressed.

Describe what happens to the lac operon in the following semi-diploid E. coli cross: Intact Operon vs. lacIm.

When an intact operon and a lacIm are present in semi-diploid E. coli, the repressor protein is still produced by the intact operon. As a result, the repressor protein can diffuse and bind to the operator in both genes. As a result, repression by lacI is dominant and no lac proteins are synthesized.

Describe what happens to the lac operon in the following semi-diploid E. coli cross: Intact Operon vs. Operatorm.

When an intact operon and a operatorm are present in semi-diploid E. coli, the repressor protein is able to bind to the operator of the intact operon, but is unable to bind to the operator in the Operatorm operon. As a result, knockout of the operator is dominant and leads to lac protein synthesis in the Operatorm operon.

What is the catabolite activator protein (CAP)? What is its function in the lac operon?

When glucose concentrations in the cell are low, cAMP levels increase, as adenylyl cyclase is active. CAP is a protein that binds to cAMP, undergoing a conformational change that allows it to bind to DNA. CAP then bends the DNA about 90 ° to aid in the formation the open promoter complex and promote RNA polymerase binding to the promoter region in the lac operon. By CAP binding upstream of the DNA promoter, it binds to the RNA polymerase and increases its affinity for the promoter. Without CAP, RNA polymerase does not bind to the promoter, and the lac operon is not expressed.

Describe what happens to the lac operon under the following condition: + Glucose - Lactose

When glucose is present and lactose is absent, the repressor protein binds to the operator region of the DNA, thereby preventing RNA polymerase from binding to the promoter. Further, when glucose is present, the concentration of cAMP is low. When the concentration of cAMP is low, it cannot bind to CAP. As a result, CAP cannot bind to the DNA. These two factors in combination inactivate the lac operon.

What is the relationship between cAMP and glucose in respect to the lac operon?

When glucose is present, it inhibits adenylyl cyclase, which is an enzyme that converts ATP to cAMP. As a result, cAMP levels are low in the present of glucose. However, during glucose starvation, cAMP levels rise, and this increase in cAMP concentration activates the lac operon by binding to the catabolite activator protein (CAP).

Why is it important to know whether an x-ray is posterior-anterior or anterior-posterior?

When images are acquired AP, the heart is magnified, so without knowing that the image is AP, a physician could diagnose a patient with cardiomegaly. Further, an AP view causes lucency of the lungs, so a pneumothorax may be overlooked.

How do overlapping structures appear on an x-ray?

When structures overlap in an x-ray, the x-ray beam has passed through multiple layers of tissue and thus the resulting image appears more dense. For example, the breasts overlap with the diaphragm, so the diaphragm appears very white.

Describe what happens to the lac operon under the following condition: - Glucose + Lactose

When the concentration of glucose is low, the concentration of cAMP increases. Because the concentration of cAMP increases, cAMP is able to bind to CAP. CAP is able to bind to the DNA, increasing the affinity of RNA polymerase for the promoter region. Further, lactose is able to bind to the repressor protein, thereby inhibiting the repressor protein. The repressor protein is unable to bind to the operator region of the DNA. These two factors in combination activate the lac operon.

Describe what happens to the lac operon under the following condition: - Glucose - Lactose

When the concentration of glucose is low, the concentration of cAMP increases. Because the concentration of cAMP increases, cAMP is able to bind to CAP. CAP is able to bind to the DNA. However, in the absence of lactose, the repressor protein is bound to the DNA, preventing RNA polymerase from transcribing the lac operon. As a result, the lac operon is inactivated.

How does the inducer allosterically regulate the lac repressor?

When the inducer binds to the lac repressor, it induces a conformational change that the repressor can no longer bind to the DNA.

How is translation of the trp mRNA in prokaryotes affected by high tryptophan concentrations?

When the tryptophan concentration is high, the translation machinery quickly passes the tryptophan codon. When they quickly pass Region 1 and reach the space between Region 1 and Region 2, it disrupts how Region 2 base pairs with Region 3. As a result, Region 2 cannot pair with Region 3, and Region 3 base pairs with Region 4 as Region 4 is transcribed. When Region 3 and Region 4 base pair, they form a hairpin structure. Following this hairpin structure, a polyU stretch is present. This is the rho-independent translation termination. As a result, transcription is prematurely terminated. (CC)

How is translation of the trp mRNA in prokaryotes affected by low tryptophan concentrations?

When tryptophan concentration is low, the transcription machinery binds to the mRNA before synthesis is completed and begins to translate the mRNA. When the translation machinery reaches tryptophan in the leader sequence, the translation machinery is paused in the leader sequence. The Region 2 will base pair with Region 3. When Region 3 is translated, Region 3 is unable to base pair with Region 4. As a result, transcription continues. (CC)

Flip card over for question. Answer below. Both blue lines are constitutive genes. All other genes are regulated.

Which genes are constitutively expressed? Which are regulated?

Why do final N-glycosylation structures vary? What is the common thing between them?

While all N-glycosylation products share the same core, structures can vary between molecules of same protein, causing microheterogeneity. This is because synthesis is not templated-directed. As a result, final products can differ from one another.

What happens to the 11 nm fiber with the addition of salt?

With the addition of salt, H1 is removed, as it is on the outside of the bead. Its location makes it easily removed to form the "beads on a string structure". (CC)

Cranial nerve(s) ____________ innervate(s) the thoracic organs.

How are x-rays formed?

X-rays are formed by electrons striking a metallic target (usually tungsten). When the tungsten wire is heated, it produces electrons. The electrons are moving x-rays. The x-ray photons may be absorbed or scattered by tissue or may pass through tissue without interaction. This varying distribution of photons forms the radiographic image by striking photoreceptors on film or digital detector.

How many CENP-A proteins are found in yeast? Humans?

Yeast contain one CENP-A histone per chromosome, as more than one can lead to mitotic instability. On the other hand, human centromeres have multiple CENP-A-containing nucleosomes.

Fascicle

a bundle of axons within a nerve

Inducer

a chemical or environmental agent that initiates transcription of an operon

Neurotransmitter

a chemical substance that is released by neurons to stimulate neighbouring neurons or muscle or gland cells

Cauda Equina

a collection of nerve roots L2 and below that are distal to the end of the spinal cord; are horsetail-like in appearance.

Dermatome

a cutaneous area supplied mainly by a single spinal nerve or spinal segment

Autonomic Nervous System

a division of the peripheral nervous system that acts largely unconsciously and regulates bodily functions such as the heart rate, digestion, respiratory rate, and pupillary response

Point Mutation

a gene mutation in which a single base pair in DNA has been changed

Axon

a long, slender projection of a neuron that functions to transmit information to different neurons, muscles, and glands

Allosteric Molecule

a molecule in which interaction with another molecule causes a conformational change in the active site of that molecule

Silent Mutation

a point mutation that does not alter the translation product; changes the codon to another codon specifying the same amino acid

Missense Mutation

a point mutation that results in an amino acid substitution; can result in the production of a full-length protein that has altered activity

Non-Sense Mutation

a point mutation that substitutes a termination codon for the original codon; results in the premature termination of protein synthesis

Gene Family

a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions

Degeneracy

a situation in which multiple states are equivalent; in protein synthesis, degeneracy means that different codons can specify the same amino acid

Sagittal Section

a slice through the brain parallel to perpendicular to the ground, dividing the brain into left and right portions

Horizontal Section

a slice through the brain parallel to the ground, diving the brain into superior and anterior portions

Coronal Section

a slice through the brain that divides the brain into dorsal and ventral portions

Transverse Section

a slice through the brainstem that divides the brainstem into superior and inferior portions

Angiogram

a specialized image that demonstrates vasculature

The dorsal root and the ventral root come together to form _________.

a spinal nerve

Ganglia

a structure containing a number of nerve cell bodies

Myelin

a white lipoprotein membrane that surrounds some axons of CNS and PNS to increase the conduction velocity of the axon

Superior (Rostral)

above

Protein kinases _______ a phosphate group while protein phosphatases ___________ a phosphate group.

add; remove

The aorticorenal ganglion follows the _________ artery, which perfuses the kidneys.

aorticorenal

The general visceral efferent (GVE) fibers are a part of the _____________ nervous system.

autonomic

The subclavian artery supplies the ________.

axilla and upper extremity

Posterior (Dorsal)

back

Nuclear proteins have a __________ targeting sequence.

basic

Peroxisomal proteins have a ___________ targeting sequence.

basic

Proteins in the endoplasmic reticulum, Golgi, lysosomes, endosomes, plasma membrane, or outside of the cell traveled to these locations via _____.

being synthesized in the ER and transferred by a vesicle to its final destination

Inferior (Caudal)

below

On a CT, hollow structures appear ________ while dense structures appear __________.

blacker; whiter

On a radiograph, hollow structures appear _________ while denser structures appear _________.

blacker; whiter

Cranial nerves originate from the ___________.

brain

Peripheral Nerve

bundles of axons that function to transmit motor signals from the CNS to the rest of the body or to transmit sensory information from the rest of the body to the CNS

The postglangia of the general visceral efferent fibers that innervate the thoracic viscera are known as the ______.

cardiac nerves

The sympathetic nervous system is involved in ___bolic energy-__________ activities. On the other hand, the parasympathetic nervous system is involved in ___bolic energy-___________ activities.

cata; consuming; ana; conserving

The celiac ganglion follows the _________ artery, which perfuses the spleen, stomach, and pancreas.

celiac

N-linked glycosylation occurs _______-translation.

Filum Terminale

coccygeal ligament; a delicate strand of fibrous tissue, about 20 cm in length, proceeding downward from the apex of the conus medullaris and attaching to the coccyx

Fidelity of translation demands _________.

correct aminoacylation of the tRNA

In the CNS, the cell body is located in the __________________ for the brain and ___________________ for the spinal cord.

cortex and nuclei; gray matter

The sympathetic nervous system __________ the activity of the internal visceral organs while the parasympathetic nervous system _____________ the activity of the internal visceral organs.

decreases; increases

The dorsal primary ramus innervates the _____.

deep back

Afferent neurons are associated with the __________ root.

dorsal

If a general somatic afferent fiber detects stimuli in a thoracic skeletal muscle, the signal is directly propagated through the _______.

dorsal or ventral primary ramus

A spinal nerve divides into ______.

dorsal primary ramus and ventral primary ramus

The cell body of general somatic afferent fibers are located in the _____________.

dorsal root ganglion

The cell body of general visceral afferent fibers are located in the _____________.

dorsal root ganglion

What is the largest gene in the human genome?

dystrophin gene

_____________ in eukaryotes is analogous to EF-Tu.

eEF-1α (CC)

_____________ in eukaryotes is analogous to EF-Ts.

eEF-1β (CC)

EF-G in prokaryotes is analogous to _________ in eukaryotes.

eEF-2

What is eIF2? What is its function?

eIF2 is an initiation factor in eukaryotes that brings the initiating tRNA to the start site.

What is eIF2B? What is its function?

eIF2B is the GEF for eukaryotic translation. Its function is to exchange GDP-bound eIF2 for GTP-bound eIF2 to allow charged initiator tRNA to bind to eIF2.

What is eIF4A/B? What is its function?

eIF4A/B is an initiation factor in eukaryotic translation that contains helicase activity. Due to the secondary structure of the mRNA, a helicase is required to unwind those secondary structures.

What is an initiation factor, other than eIF2, that is regulated?

eIF4E, the cap binding factor, and its interaction with eIF4G can be blocked by a binding protein that slows down translation. However, the phosphorylation of the 4eBP in response to growth factor signal, for example, indicates the need for higher translation rates. This causes eIF4e to be released from the 4eBP, increasing initiation rates. (CC)

What is eIF4G? What is its function?

eIF4G is an initiation factor in eukaryotic translation that acts as a scaffold protein. It binds to the cap binding protein to recruit the mRNA. It is bound to the ribosome by eIF3. (CC)

What is eIF4E? What is its function?

eiF4E is an initiation factor in eukaryotic translation that binds to the 5' cap of the mRNA, recruiting the small ribosomal subunit.

The 5'-CCA-3' acceptor site forms an ___________ linkage with the amino acid COOH group.

ester

How is fMet-tRNAfMet formed?

fMet-tRNAfMet is formed on the tRNA in two steps: Step 1: The tRNA is charged with methionine to produce Met-tRNAfMet. Step 2: Transformylase transfers the formyl group onto methionine, forming fMet-tRNAfMet

Anterior (Ventral)

front

In the PNS, the cell body is located in _____________.

ganglia

The central part of the spinal cord contains _____.

grey matter

The common carotid artery supplies the __________.

head and neck

The fidelity of aminoacylation is ______.

high

The more myelin, the ___________ the conduction velocity in an axon.

higher

Proteins that remain in the lumen of the endoplasmic reticulum have a ____________ targeting sequence.

hydrophobic

Transmembrane proteins contain a _______________ signal sequence that leads to the insertion of the protein into the ER membrane.

hydrophobic

The preganglia of the sympathetic nervous system can synapse with the ________________ to innervate the upper limbs.

inferior cervical ganglion

The inferior mesenteric ganglion follows the _________ artery, which perfuses the descending sigmoid colon.

inferior mesenteric

The parasympathetic nervous system innervates _________.

internal visceral organs

The sympathetic nervous system innervates _____.

internal visceral organs and peripheral viscera located in body walls and limbs

The general visceral efferent (GVE) fibers are responsible for _________ movement and innervate three major types of tissue:

involuntary; smooth muscle (blood vessels, gastrointestinal tract, respiratory tract, and urogenital tract), cardiac muscle (heart), and glands (salivary, lacrimal, sweat, mucous, digestive, pancreas, liver)

What is the inducer of the lac operon?

lactose

The cell bodies of the preganglionic neurons of general visceral efferent fibers are located in the _____________.

lateral horn

What is the most posterior part of the heart?

left atrium

The ________ is border forming on lateral and PA films.

left ventricle

The left-most heart border on a PA film is the _____.

left ventricle

The greater the acetylation of histone N-termini, the ________ likely chromatin forms condensed structures.

less

The L2 preganglia of the sympathetic nervous system can synapse with ________________ to innervate the lower limbs.

lower paravertebral ganglia on the sympathetic chain

What is macroH2A? What is its function?

macroH2A, another H2A variant, is involved with transcriptional repression and X-chromosome inactivation.

What is the exception to the wobble hypothesis?

methionine

Polycistronic

multiple genes on a single transcript

General somatic efferent fibers are ___________ neurons.

multipolar

General visceral efferent fibers are ___________ neurons.

multipolar

White Ramus

myelinated axon located distally from the spinal column

White Matter

myelinated axons

In the PNS, a bundle of axons is called a _________.

nerve

What is the functional unit of the nervous system?

neuron

Wobble Pairing

non-traditional Watson-Crick base pairing between the 1st position of anticodon and 3rd position

The lac repressor binds to the ___________ in the absence of the inducer.

operator

Dual Innervation

organs that receive instructions from both sympathetic and parasympathetic divisions

How does p53 regulate the cell cycle? What happens in tumors that knock out p53?

p53 is a tumor suppressor that regulates G1 of the cell cycle. In tumors that knock out the function of p53, the cell cycle continues, and cells proliferate when they should not.

The cell bodies of the postganglionic neurons of general visceral efferent fibers that innervate the thoracic visceral organs are located in the _____________.

paravertebral ganglia

The filum terminale is a modification of the ___________.

pia mater

Translation uses a _____________ to generate a polypeptide sequence.

polynucleotide

O-linked and GPI anchor addition occur _______-translation.

post

Splanchnic Nerves

preganglionic sympathetic and sacral parasympathetic nerves that terminate in abdominopelvic cavity

The cell bodies of the postganglionic general visceral efferent fibers that innervate the abdominal and pelvic viscera are located in the _____________.

prevertebral ganglia

What are tandemly-repeated arrays? Give some examples.

rRNA, tRNAs and histones genes are found in tandemly-repeated arrays, encoding identical proteins or functional RNAs. These genes are tandemly-repeated because they must meet a great cellular demand.

Contrast is called ________.

radiodense

The right-most heart border on a PA film is the _______.

right atrium

Only the ________ and ________ contribute to heart borders on a posterior-anterior x-ray.

right atrium; left ventricle

The right border of the heart on a chest x-ray is formed by the _________ while the left border of the heart is formed by the _______.

right atrium; left ventricle

The anterior-most heart border on the lateral film is the _______.

right ventricle

The glycosylation of proteins mainly occurs in ______________________, although specific modifications may occur.

secretory compartments

What are the most commonly phosphorylated residues?

serine, threonine, tyrosine

Dermatomes are formed by general ___________________ fibers.

somatic afferent

Spinal nerves originate from the _____________.

spinal cord

The cell bodies of the postganglionic general visceral efferent fibers that innervate the head region are located in the _____________.

superior cervical ganglion

The preganglia of the sympathetic nervous system can synapse with the ________________ to innervate the head region.

superior cervical ganglion

The superior mesenteric ganglion follows the _________ artery, which perfuses the small intestine and the first half of the large intestine.

superior mesenteric

The cell bodies of the postganglionic general visceral efferent fibers that innervate the thoracic viscera are located in the _____________.

superior, middle, and inferior cervical ganglia and the upper four thoracic paravertebral ganglia (T1-T4)

The preganglionic neurons of the GVE fibers that will innervate the thoracic viscera synapse with the ______.

superior, middle, and inferior cervical ganglia and the upper four thoracic paravertebral ganglia (T1-T4)

Schwann Cell

supporting cells of the peripheral nervous system that responsible for the formation of myelin

The ______________ nervous system only is responsible for temperature regulation and peripheral blood flow.

sympathetic

Nervous System

system of the body that controls the actions and sensations of all the parts of the body, including thoughts, emotions and memories

Why does glycyl-tRNA synthetase have it easy?

tRNA synthetases that charge amino acids with no close structural relatives can use only differential binding affinities to generate fidelity. For example, glycine is very unique in the fact that it is small. As a result, glycyl-tRNA synthetase can make a binding pocket small enough to include glycine, but exclude all other amino acids.

What special initiator tRNA is used by prokaryotes to begin translation?

tRNAfMet

What is the special tRNA used by eukaryotes for translation?

tRNAi

N-End-Rule

the amino acid at the N terminus determines the stability of a protein

Diauxic Growth

the biphasic curve of a culture growing on two carbon sources; in the case of E. coli and the lac operon, glucose is used as an energy source first followed by lactose when glucose concentrations are low in culture

Dendrites

the branched projections of a neuron that act to propagate the electrochemical stimulation received from other neurons

What is the functional unit of translation?

the codon

General visceral efferent (GVE) fibers are responsible for _____.

the control of body temperature and peripheral blood flow

Foramen Magnum

the division between the brain and the spinal cord

The dorsal primary ramus gives rise to __________.

the dorsal cutaneous branch

Neuron

the fundamental unit of the nervous system composed of a cell body with processes called dendrites and an axon

Frameshift Mutation

the insertion or deletion of one or two bases so that the reading frame is altered; results in the production of protein with new termination codon and totally different amino acid sequence downstream of the frameshift

The ventral primary ramus gives rise to __________.

the lateral cutaneous branch and the anterior cutaneous branch

The anterior primary ramus innervates _____.

the left and anterior side of the thoracic cavity

The small subunit of the ribosome interacts with _____________.

the mRNA and translation factors

Attenuation

the premature termination of transcription

Codon

the sequence in mRNA that specifies a single amino acid

Genomics

the study of an organism's genome

Lumbar Cistern

the subarachnoid space inferior to medullary cone that contains the cauda equina and CSF (CC)

Induction

the synthesis of gene product(s) in response to an inducer

Conus Medullaris

the tapered, caudal end of the spinal cord that occurs near L1 and L2, occasionally lower (CC)

C-Value

the total amount of DNA in the haploid genome

Microheterogeneity

the variability in carbohydrate composition in glycoproteins (CC)

Cranial nerve 10 (the vagus nerve) innervates _________.

thoracic organs and abdominal organs

In the CNS, a bundle of axons is called a ________.

tract

Transposable elements move by ______.

transposition

Describe the structure of trpR. Why is the structure of trpR significant?

trpR forms a homodimer that contains six α helices. Helix 4 and Helix 5 form a helix-turn-helix structure that is a DNA-binding motif. trpR uses this binding motif to insert itself into the major groove of the DNA.

What is the co-repressor in the trp operon?

tryptophan

General Visceral Efferent (GVE) fibers contain a __________ neuron connection into the peripheral nervous system.

two

How many phosphate bonds are cleaved per amino acid joined to the acceptor site?

two

General somatic afferent fibers are ___________ neurons.

unipolar

General visceral afferent fibers are ___________ neurons.

unipolar

Grey Ramus

unmyelinated axon located proximally to the spinal column

Efferent neurons are associated with the ___________ root.

ventral

The cell body of general somatic efferent fibers are located in the _____________.

ventral horn

For a lateral chest radiograph, the side that faces the ____________ is the direction of the radiograph.

x-ray source

Give an example of a gene family.

β-globin genes are an example of a gene family. All five β globin genes encode for the β subunit of hemoglobin. However, these five genes are expressed at different developmental stages. The ε gene is expressed in the embryo. The γ genes are expressed in the fetus. After birth, the δ and β globin genes are expressed.

The ____ factor of the RNA polymerase recognizes the promoter sequence and binds to the DNA, beginning transcription of a downstream gene.

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