Best Biochemistry Set of Quizlet
Give two advantages of the activation of glucose, converting glucose to glucose 6-phosphate
1. Begins the degradation of glucose 2. The plasma membrane is less permeable to the charged Glucose 6-phosphate.
What are the three stages of PCR?
1. Denaturation 2. Annealing 3. Extension
What is the pka of ordinary water?
15.7
What is palmitic acid?
16 carbon fatty acid that is fully saturated
How many of the 20 amino acids are negatively charged (at body pH)?
2
What are the 3 temperatures of PCR?
95 for denaturation 68, some sources say 55 for annealing 72 for elongation
Identify the gene fusion that is found on philadelphia chromosome and the gene fusion's abnormal function?
BCR and ABL gene fusion on chromosome 22 hybrid BCR-ABL encodes constitutively active protein tyrosine kinase BCR-ABL activity triggers expansion in the number of WBCs --> CML
Why is the isoelectric point for amino acids around 5-6.5, and not at neutral?
Because carboxylic acids are stronger acids than amine groups are bases
What allosterically activates and inhibits Acetyl-Coa Carboxylase?
Citrate activates Fatty Acids Inhibit
Which protein is in silk?
Fibroin
What are the components needed for a PCR reaction?
Primer mix DNA template PCR Bead
Which Amino acid has the most steric hindrance?
Proline
Which amino acid has a secondary amine group?
Proline
Species of bacteria that plays a role in acne?
Propioni Bacterium Acnes
IgM
IgM is the largest antibody, and it is the first antibody to appear in the response to initial exposure to an antigen
What drugs are available against chronic myeloid leukemia (CML) and what is their target?
Imatinib: tyrosine kinase inhibitor against BCR-ABL reduces proliferation rate, but does not completely eradicate CML cells resistance is reported in some CML patients (due to acquired mutations within BCR-ABL)
Where is ATP made?
In Eukaryotes, most is made in mitochondria and/or chloroplasts. In prokaryotes, its made in the infolding of the plasma membrane.
Thayer Martin Agar
It is used for culturing and primarily isolating pathogenic Neisseria bacteria, including Neisseria gonorrhoeae and Neisseria meningitidis, as the medium inhibits the growth of most other microorganisms.
What is the difference between an oncogene and a proto oncogene?
Proto oncogenes regulate cell cycle. When a proto-oncogene becomes mutated it becomes a oncogene. This causes the cell to divide in an unregulated manner. An oncogene may contribute to the growth of a tumor, which may be cancerous.
What happens if you inhibit NF-kB in cells then apply a senescent-inducing drug?
Senescence is bypassed.
What is sequence homology?
Sequence homology is the biological homology between protein or DNA sequences
In an operon, what is the operator? what is the repressor?
operator is where the repressor binds to prevent transcription. an operator is a segment of DNA to which a transcription factor binds to regulate gene expression by repressing it. The repressor protein physically obstructs RNA polymerase from transcribing the genes
What is the murine equivalent of p14ARF?
p19ARF
What happens if a mutation or alteration in a selected protein signals inappropriately for entry into the cell cycle?
This is detected by p53 checkpoint, and the cell is usually killed.
What are hypoxic conditions?
This is when O₂ levels are too low
How is p53 activated from UV-induced DNA damage?
UV-radiation activates ATR, CHK-1 and casein kinase-2, which results in the modification of different amino-acid residues on the p53 protein
salmonella typhi
cause typhoid disease, transmitted through shit Typhoid involves fever, rash, headache and abdominal pain Also makes hydrogen sulfide Can check for it using the widal test
What is an apurinic/apyrimidic site?
an AP site (apurinic/apyrimidinic site), also known as an abasic site, is a location in DNA (also in RNA but much less likely) that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage. AP sites can be formed by spontaneous depurination, but also occur as intermediates in base excision repair
Neisseria gonorrhoeae
gram negative catalase positive Thayer-Martin media Oxidase positive
At what pH does carbonic anhydrase II catalyse at its maximum rate?
pH 8
Why pythagoras woudn't eat falafel: Glucose 6-phosphate dehydrogenase deficiency
page 576 lehninger
Give an example of an aspartic protease
renin, chymosin
selective killing of p16INK4a-positive senescent cell has what effects
selective killing of p16INK4a-positive senescent cells extends healthspan in a transgenic mouse model (INK-ATTAC mice) of accelerated aging
What are plasmalogens?
Note: ether carbon 1, ester carbon 2
Natural sources of oleic acid?
Olive oil. up to 85% of the triglyceride in this oil contains oleic acid.
Tell me about the cerebral hemisphere
One of the two halves of the cerebrum of the brain
What are Opioids
Opioids are substances that act on opioid receptors to produce morphine-like effects. Opioids are most often used medically to relieve pain, and for their euphoric effects by people addicted to opioids. Tolerance and dependence will develop with continuous use, requiring increasing doses and leading to a withdrawal syndrome upon abrupt discontinuation. Accidental overdose or concurrent use with other depressant drugs commonly results in death from respiratory depression. Because of opioid drugs' reputation for addiction and fatal overdose, most are controlled substances.
At what ages can you find propionibacterium acnes in humans?
P. acnes is usually barely detectable on skin of healthy preadolescents. But it is present on most healthy adults.
What are cytochromes made of?
(Iron-haem) or (iron-porphyrins) picture is porphyrin
3 ways to get Free Fatty Acids into the blood stream?
1) Diet 2) Adipose Tissue 3) Direct synthesis in the liver from glucose
What two mechanisms are there that ensure that stem cell populations are maintained?
1)Obligatory asymmetric replication: a stem cell divides into one mother cell that is identical to the original stem cell, and another daughter cell that is differentiated. 2) Stochastic differentiation: when one stem cell develops into two differentiated daughter cells, another stem cell undergoes mitosis and produces two stem cells identical to the original.
What are the four Primer Criteria?
1. Always complementary to 3' end 2. Try to avoid multiples of same nucleotide 3. Try to end in a G/C pair at the primer's 3' end 4. Don't cut into the highlighted gene.
What methods can you use to synthesize amino acids?
1. alpha bromination of a carboxylic acid by treatment of bromine and phosphorus (Hell-Volhard-Zelinskii), then nucleophilic substitution with ammonia Or use Gabriel phthalimide method rather than ammonia method. 2. Strecker Synthesis
Approximately what percentage of genomic DNA in humans is 5-methyl cytosine?
1.5%
How many amino acids are essential?
10
How long are okazaki fragments roughly?
100 - 200 nucleotides in eukaryotes and 1000 - 2000 nucleotides in prokaryotes.
What is triose phosphate also known as?
3-phosphoglyceraldehyde
How many different types of proton pumps are there in the Inner mitochondrial membrane?
3. Complex I Complex II Complex III
The sequence of reactions in the citric acid cycle makes chemical sense
638 lehninger
What is the pka of zinc bound water?
7
How many different types of carbonic anhydrases have we currently identified in humans?
7. (each with its own gene)
What are interleukins?
A group of cytokines (secreted proteins and signal molecules)
What is a Homeobox?
A homeobox is a DNA sequence found within genes that are involved in the regulation of patterns of anatomical development morphogenesis in animals, fungi, and plants. A homeobox is about 180 base pairs long. It encodes a protein domain (the homeodomain) which when expressed (i.e. as protein) can bind DNA. They are very well conserved throughout organisms
Tell me about the spliceosome
A spliceosome is a large and complex molecular machine found primarily within the splicing speckles of the cell nucleus of eukaryotic cells. The spliceosome is assembled from snRNAs and protein complexes. The spliceosome removes introns from a transcribed pre-mRNA, a type of primary transcript. This process is generally referred to as splicing. Only eukaryotes have spliceosomes and some organisms have a second spliceosome, the minor spliceosome
What does an amide bond look like?
AMIDE BOND IS A PEPTIDE BOND!!!!
What does aerotolerant mean?
Aerotolerant organims cannot use oxygen for growth but tolerate its presence.
What type of structure should most proteins embedded in the membrane contain?
Alpha helix
What is molecular cloning?
Molecular cloning is a set of experimental methods in molecular biology that are used to assemble recombinant DNA molecules and to direct their replication within host organisms.
What happens to HIF 1alpha during normoxia?
HIF1alpha is unstable during normal oxygen it is hydroxylated by proline hydroxylase --> sent for degradation
What is the formula of Arsenate?
AsO₄³⁻
What enzyme mediates the methylation of H3K27?
Histone methylase EZH2
What molecule phosphorylates RB?
CDK (cyclin dependent kinases)
What is the formula of palmitate?
CH₃(CH₂)₁₄COO⁻ C₁₆H₃₁O₂
Homeobox Genes aka?
Hox genes
What is a common hurdle early tumors face as they begin to grow?
Hypoxia (low oxygen) due to insufficient oxygen supply --> triggers stabilization of Hif-1alpha
Which is more kinked? Cis or trans fatty acids?
Cis is more kinked
What are CpG islands?
Clusters of CpG sites.
Hepatitis A
Diarrhoea Abdominal Pain Jaundice You can test with Anti-HAV IgM It is spread through unsanitary food, causing acute hepatitis.
Diets high in trans fatty acids are associated with which disease?
Diets high in trans fatty acids have been associated with an increased risk of cardiovascular disease and development of the metabolic syndrome and have, therefore, been banned from manufactured food products by most major governments
Digestion, Mobilization and Transport of Fats
Digested fats absorbed in the small intestine Hormones trigger mobilizatin of stored triacylglyercols Fatty acids are activated and transported into mitochondria
What are ganglions?
In anatomy, a ganglion is a nerve cell cluster or a group of nerve cell bodies located in the autonomic nervous system and sensory system.Ganglia house the cell bodies of afferent nerves and efferent nerves.
Tell me about transactivation domains (TADs)
Domains that stimulate transcriptional activation through contacts with general Transcription Factors
Who invented PCR?
Dr. Kary Mullis
What is downregulated during senescence?
Extracellular matrix proteins
What is the charge of ATP?
Negative. Most ATP molecules are 4- charged.
Tzanck test
In dermatopathology, the Tzanck test, also Tzanck smear, is scraping of an ulcer base to look for Tzanck cells. It is sometimes also called the chickenpox skin test and the herpes skin test. Tzanck cells (acantholytic cells) are found in: Herpes simplex Varicella and herpes zoster Pemphigus vulgaris Cytomegalovirus
What is a missense mutation?
In genetics, a missense mutation is a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid. It is a type of nonsynonymous substitution. A nonsynonymous substitution is a nucleotide mutation that alters the amino acid sequence of a protein.
What are postganglionic nerve fibers?
In the autonomic nervous system, fibers from the ganglion to the effector organ are called postganglionic fibers.
where is p53 normally found?
In the cytoplasm
Tell me about the hypothalamus
In vertebrates, region of the brain below the thalamus responsible for the regulation of a variety of bodily functions
Which locus is frequently mutated in cancer?
Ink4a/Arf locus
Escherichia Coli
Ferments Lactose Gram Negative Catalase positive grows on MacConkey Agar Common in urinary tract infections, can cause abdominal abscesses, bacteremia Treat with Azithromycin, trimethoprim-sulfamethoxazole, ciprofloxacin can pick up antibiotic resistance genes very easily
Once activated, what does p53 do?
It can activate DNA repair proteins when DNA has sustained damage. Thus, it may be an important factor in aging. It can arrest growth by holding the cell cycle at the G1/S regulation point on DNA damage recognition (if it holds the cell here for long enough, the DNA repair proteins will have time to fix the damage and the cell will be allowed to continue the cell cycle). It can initiate apoptosis (i.e., programmed cell death) if DNA damage proves to be irreparable. It is essential for the senescence response to short telomeres.
What happens when you treat Ercc1−/∆ mice, a mouse model of a human progeroid syndrome, with the HSP90 inhibitor 17-DMAG
It extended healthspan, delayed the onset of several age-related symptoms and reduced p16INK4a expression.
How to generate a knock-out using CRISPR/Cas9?
Generating a Knock-out Using CRISPR/Cas9 CRISPR Knockout Diagram CRISPR/Cas9 can be used to generate knock-out cells or animals by co-expressing a gRNA specific to the gene to be targeted and the endonuclease Cas9. The genomic target can be any ∼20 nucleotide DNA sequence, provided it meets two conditions: The sequence is unique compared to the rest of the genome. The target is present immediately upstream of a Protospacer Adjacent Motif (PAM). The PAM sequence is absolutely necessary for target binding and the exact sequence is dependent upon the species of Cas9 (5′ NGG 3′ for Streptococcus pyogenes Cas9). We will focus on Cas9 from S. pyogenes as it is currently the most widely used in genome engineering (see additional species of Cas9 and corresponding PAM sequences here). Once expressed, the Cas9 protein and the gRNA form a riboprotein complex through interactions between the gRNA "scaffold" domain and surface-exposed positively-charged grooves on Cas9. Cas9 undergoes a conformational change upon gRNA binding that shifts the molecule from an inactive, non-DNA binding conformation, into an active DNA-binding conformation. Importantly, the "spacer" sequence of the gRNA remains free to interact with target DNA. The Cas9-gRNA complex will bind any genomic sequence with a PAM, but the extent to which the gRNA spacer matches the target DNA determines whether Cas9 will cut. Once the Cas9-gRNA complex binds a putative DNA target, a "seed" sequence at the 3′ end of the gRNA targeting sequence begins to anneal to the target DNA. If the seed and target DNA sequences match, the gRNA will continue to anneal to the target DNA in a 3′ to 5′ direction. Cas9 will only cleave the target if sufficient homology exists between the gRNA spacer and target sequences. The "zipper-like" annealing mechanics may explain why mismatches between the target sequence in the 3′ seed sequence completely abolish target cleavage, whereas mismatches toward the 5′ end are permissive for target cleavage. The Cas9 nuclease has two functional endonuclease domains: RuvC and HNH. Cas9 undergoes a second conformational change upon target binding that positions the nuclease domains to cleave opposite strands of the target DNA. The end result of Cas9-mediated DNA cleavage is a double strand break (DSB) within the target DNA (∼3-4 nucleotides upstream of the PAM sequence). The resulting DSB is then repaired by one of two general repair pathways: The efficient but error-prone Non-Homologous End Joining (NHEJ) pathway The less efficient but high-fidelity Homology Directed Repair (HDR) pathway The NHEJ repair pathway is the most active repair mechanism, capable of rapidly repairing DSBs, but frequently results in small nucleotide insertions or deletions (InDels) at the DSB site. The randomness of NHEJ-mediated DSB repair has important practical implications, because a population of cells expressing Cas9 and a gRNA will result in a diverse array of mutations (for more information, jump to Plan Your Experiment). In most cases, NHEJ gives rise to small InDels in the target DNA which result in in-frame amino acid deletions, insertions, or frameshift mutations leading to premature stop codons within the open reading frame (ORF) of the targeted gene. Ideally, the end result is a loss-of-function mutation within the targeted gene; however, the "strength" of the knock-out phenotype for a given mutant cell is ultimately determined by the amount of residual gene function.
What is the overall equation for glycolysis?
Glucose + 2ADP + 2Pi + 2NAD⁺ → 2Pyruvate + 2ATP + 2NADH + 2H₂O
When is imprinting normally accomplished?
It is normally accomplished during spermatogenesis and oogenesis
What does DNA methyltransferase 1 do?
It maintains DNA methylation patterns
What does the EGF signal transduction pathway result in?
It results in the cell division of epidermal and endothelial cells
What is the non-template strand called?
Its called the coding strand because its sequences are identical to those of mRNA.
trimethoprim-sulfamethoxazole
Kill E coli can cause hemolytic anemia if G6PD Deficient
Azithromycin
Kill E coli, H ducreyl Azithromycin prevents bacteria from growing by interfering with their protein synthesis. It binds to the 50S subunit of the bacterial ribosome, thus inhibiting translation of mRNA. Nucleic acid synthesis is not affected.
Why is the intracellular part of the membrane more negatively charged than the extracellular part of the membrane at resting potential.
K⁺ ion channels are open, whereas Na⁺ ion channels are closed, because there is a higher concentration of K⁺ inside the cell, K⁺ ions move out of the cell into the extracellular fluid, down its concentration gradient, causing the inside of the cell to be more negative than the outside of the cell. Sodium Potassium Pump also contributes to increased negativity on the inside of the membrane.
What is the practical use of cloning?
Large scale production of animals of superior quality. Can also be used to mass produce animals that are genetically identical for drug testing like is done in china.
Enterohemorrhagic E coli or EHEC
Makes Shiga-like toxin and causes bloody diarrhoea. Sometimes, activates the completement system and depletes platelets. Otherwise, just like any other e coli
What is upregulated during senescence?
Matrix metallo proteinases Cytokines
If fatty acid oxidation yields so much ATP, why do cells oxidise glucose?
Glucose is a very common dietary component Fatty acid oxidation is entirely aerobic, whereas glucose → lactate offers an anaerobic energy source. This is important in rapidly contracting skeletal muscle for example.
How is glycerol integrated into respiration process?
Glycerol is modified slightly and can be fed directly into glycolytic sequence.
Which amino acid has the least steric hindrance?
Glycine
Which amino acid is non-chiral?
Glycine
Tell me the basics about glycine as a neurotransmitter and tell me a couple of antagonists of glycine.
Glycine is an inhibitory neurotransmitter in the central nervous system, especially in the spinal cord, brainstem, and retina. When glycine receptors are activated, chloride enters the neuron via ionotropic receptors, causing an Inhibitory postsynaptic potential (IPSP). Strychnine is a strong antagonist at ionotropic glycine receptors, whereas bicuculline is a weak one.
What is glycosylation?
Glycosylation is the reaction in which a carbohydrate, i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor). In biology glycosylation mainly refers in particular to the enzymatic process that attaches glycans to proteins, lipids, or other organic molecules.
Streptococcus pyogenes
Gram positive chains Beta-hemolytic
H4K16
H4K16 is part what should now be a familiar group of lysines on the N-terminal tail of histone H4. If you've been reading about the others, it should come as no surprise that H4K16 also is acetylated and not methylated. But wait; H4K16ac has some unique and interesting properties. Though H4K16ac is associated with transcriptional activation, it can also be linked with repression. The bromodomain of TIP5, part of NoRC, binds to H4K16ac. After binding, the NoRC complex serves to silence rDNA by recruiting HATs and DNMTs.
H4K20
H4K20 if definitely the odd lysine out on the tail of H4. All the other lysines up until this point are acetylated and not methylated. H4K20 likes to go against the grain and is methylated but not acetylated. Like all lysine residues, H4K20 can be mono, di, or tri methylated. In the case of H4K20, these methylation states have different spatial disruptions and functions.
What does TET stand for?
ten-eleven translocation
If an enzyme binds well to a substrate, what will Km be?
the better enzyme bind to substrate, the smaller kdis, thus the smaller kM is. Since kM=(k-1+kcat)/k1 can be broken down into kM = kd + kcat/k1
Tell me about gray matter
the part of the central nervous system that consists of unmyelinated dendrites and cell bodies and is gray in appearance.
glucose vs gluconate?
they are pretty similar, but gluconate is a carboxylic acid, so doesn't form a ring structure.
What is TERC?
- AKA Telomerase RNA component - serves as a template for telomere replication by telomerase.
What is p16Ink4a?
- Functions as a tumor suppressor protein that inhibits CDK4 and CDK6. - has the capacity to arrest cells in the G1-phase of the cell cycle and it's probable physiological role is in the implementation of irreversible growth arrest termed cellular senescence.
List the steps required for molecular cloning
1) Choice of host organism and cloning vector 2) Preparation of vector DNA 3) Preparation of DNA to be cloned 4) Creation of recombinant DNA with DNA ligase 5) Introduction of recombinant DNA into host organism 6) Selection of organisms containing vector sequences 7) Screening for clones with desired DNA inserts and biological properties
How do cells terminate the EGF signal transduction pathway?
1) Using GTPase activity of G-proteins 2) Using phosphatases to reverse the effects of protein kinases 3) By inactivating the receptor of the pathway
How do androgens contribute to the pathogenesis of acne?
1) they cause hyperkeratinization 2) they increased sebum levels
Give 3 ways NADH and FADH₂ are generated.
1. Krebs Cycle 2. Beta oxidation of fatty acids 3. From glycolysis via mitochondrial membrane shuttle systems
Molecular Mechanisms of Senescence
1.p53 pathway -DNA damage -Increased p53 -Increased transcription p21 -Senescent growth arrest 2.pRB pathway -Increased p16 -Increased pRB -Inhibition of cell cycle regulators -Replicative senescence
How many ATP molecules are generated from one molecule of palmitate?
106
How long are PCR primers, typically?
18-24 bases long
Give 2 examples of uncoupling agents
2,4 - dinitrophenol (DNP) Trifluorocarbonylcyanide phenylhydrazone (FCCP)
In which direction is the synthesised strand on the leading strand being created during DNA semi-conservative replication?
5' to 3'
What does Thymine DNA glycosylase do?
5-fC can also be directly excised by thymine DNA glycosylase (TDG) to allow subsequent base excision repair (BER) processing which converts modified cytosine back to its unmodified state.
conversion of glucose 6 phosphate to glucose is the third bypass
573 lehninger
pyruvate is oxidised to acetyl coA and CO2
634 lehninger
What is the estimated amount of time, starting from androgens to showing up in the blood, to the formation of a spot?
8 weeks
What do barbiturates do? Mechanism of action of Barbiturates?
A barbiturate is a drug that acts as a central nervous system depressant, and can therefore produce a wide spectrum of effects, from mild sedation to total anesthesia. They are also effective as anxiolytics, hypnotics, and anticonvulsants. Barbiturates act as positive allosteric modulators, and at higher doses, as agonists of GABA(A) receptors. GABA is the principal inhibitory neurotransmitter in the mammalian central nervous system (CNS). Barbiturates bind to the GABA(A) receptor at multiple homologous transmembrane pockets located at subunit interfaces, which are binding sites distinct from GABA itself and also distinct from the benzodiazepine binding site. Like benzodiazepines, barbiturates potentiate the effect of GABA at this receptor. In addition to this GABAergic effect, barbiturates also block AMPA and kainate receptors, subtypes of ionotropic glutamate receptor. Glutamate is the principal excitatory neurotransmitter in the mammalian CNS.
Give a characteristic of ageing
A characteristic of aging is the loss of homeostatic mechanisms that once acted to offset the macromolecular wear and tear that occurs during an organism's lifetime. There may be random cell-to-cell variation in gene expression.
Chlamydophila pneumoniae
A common cause of mild respiratory infections. It causes pneumonia. It is classified as an obligate intracellular pathogen. Egg Yolk Culture Giemsa Stain azithromycin or doxycycline
Alzherimers disease
A condition in which memory and though processes of the brain become dysfunctional
What is kcat?
A constant that describes the turnover rate of an enzyme-substrate complex to form enzyme and product. It is the rate of catalysis of a particular substrate.
Describe base excision repair.
A damaged DNA base is flipped, removed and replaced, by DNA glycosylase, which breaks an N-glycosidic bond.
What is the myelin sheath?
A fatty layer surrounding the long axons of motor neurones in the peripheral nervous system of vertebrates
What is dihydrofolic acid?
A folic acid(vitamin B9)derivative which is converted to tetrahydrofolic acid by dihydrofolate reductase. Since tetrahydrofolate is needed to make both purines and pyrimidines, which are building blocks of DNA and RNA, dihydrofolate reductase is targeted by various drugs to prevent nucleic acid synthesis.
What is habituation?
A form of learning, a diminishing response to a repeated stimulus
Tell me about node of ranvier
A gap formed at the point where two schwann cells meet and where the axon is in direct contact with the surrounding intercellular fluid.
Tell me about nitric oxide
A gas that acts as a regulatory molecule in the body, in the peripheral nervous system, causes smooth muscle relaxation.
What is an oligodendrocyte?
A neuroglial cell of the central nervous system that produces myelin comparable to the Schwann cell of the peripheral nervous system.
What is enkephalin?
A neuropeptide that when released by axons descending from the brain into the spinal cord, inhibit the passage of pain information back to the brain
petechiae
A petechia, plural petechiae, is a small (1-2 mm) red or purple spot on the skin, caused by a minor bleed from broken capillary blood vessels
What is a phosphatase?
A phosphatase is an enzyme that removes a phosphate group from its substrate by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group phosphorylation and dephosphorylation serve diverse roles in cell signalling and regulation.
What is ergosterol?
A precursor of vitamin D₂ Ergosterol is a sterol found in cell membranes of fungi and protozoa, serving many of the same functions that cholesterol serves in animal cells. Because many fungi and protozoa cannot survive without ergosterol, the enzymes that create it have become important targets for drug discovery
What is a primer?
A primer is a short strand of RNA or DNA (generally about 18-22 bases) that serves as a starting point for DNA synthesis. Transcription does not need a primer
What is a tyrosine kinase
A tyrosine kinase is an enzyme that can transfer a phosphate group from ATP to a protein in a cell. It functions as an "on" or "off" switch in many cellular functions. tyrosine kinase activity is involved in mitogenesis, or the induction of mitosis in a cell; proteins in the cytosol and proteins in the nucleus are phosphorylated at tyrosine residues during this process
Tell me about the 28S rRNA
A unique function of the 28S rRNA of the large ribosomal subunit is catalytic. This rRNA catalyzes the formation of the peptide bond via the ribozyme (RNA-directed catalysis) activity. 28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large component, or large subunit (LSU) of eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells.[1] It is the eukaryotic nuclear homologue of the prokaryotic 23S and mitochondrial 16S ribosomal RNAs
What is vasoactive?
A vasoactive substance is an endogenous agent or pharmaceutical drug that has the effect of either increasing or decreasing blood pressure and/or heart rate through its vasoactivity, that is, vascular activity (effect on blood vessels). By adjusting vascular compliance and vascular resistance, typically through vasodilation and vasoconstriction, it helps the body's homeostatic mechanisms (such as the renin-angiotensin system) to keep hemodynamics under control. For example, angiotensin, bradykinin, histamine, nitric oxide, and vasoactive intestinal peptide are important endogenous vasoactive substances. Vasoactive drug therapy is typically used when a patient has the blood pressure and heart rate monitored constantly. The dosage is typically titrated (adjusted up or down) to achieve a desired effect or range of values as determined by competent clinicians.
What is a western blot?
A western blot is a widely used analytical technique used to detect specific proteins in a sample of tissue homogenate or extract. Electrophoresis separates proteins Transferred to a membrane (nitrocellulose) Stained with antibodies specific to the targeted protein. Antibodies is how you detect the specific protein.
What is the other advantage of possessing this hydroxyl rather than a water in terms of the kinetics of the reaction?
A zinc-bound hydroxide ion is sufficiently nucleophilic to attack carbon dioxide much more readily than water does.
How does p53 activation due to critical telomere shortening occur?
ATM kinase senses short telomeres, and signals p53 P53 is triggered Cellular senescence occurs
Give an example of a coupled reaction
ATP -> ADP + Pi Equilibrium strongly to the right Glucose + Pi -> Glucose-6-phosphate Equilibrium strongly to the left Hexokinase enzymes couples these two reactions, phosphorylating glucose to glucose-6-phosphate
What is aneuploidy?
Abnormal number of chromosomes, ex 45/47 chromosomes instead of 46.
Comment on the turnover of the acetylation of histones
Acetylation of histones has a rapid turnover.
What is glycosylation?
Addition of carbohydrate to an amino acid. An example of post-translational modification
When can amino acids enter the krebs cycle?
After amino acids undergo oxidative deamination to oxo acids. Oxo acids can be converted into pyruvate which goes into the link reaction. Oxo acids can also be converted into oxaloacetate which feeds into the krebs cycle And oxo acids can also be converted into α-oxoglutarate which also feeds into the Krebs cycle
How does one use a CRISPR library?
All of the CRISPR libraries available through Addgene follow the same general experimental protocol. In most cases, the CRISPR library will be shipped at a concentration that is too low to be used in experiments. Thus, the first step in using your library is to "amplify" the library (C in above figure) such that the total amount of DNA is increased but the "representation" (i.e. the relative percentage of each gRNA with the library) is maintained. Once the library has been amplified and the representation checked using next-generation sequencing (NGS), the next step is to generate lentivirus containing the entire CRISPR library D. Mutant cells are then generated by transducing Cas9-expressing cells (or wild-type cells for libraries containing Cas9 and the gRNA) with the lentiviral library E. In screens where you are measuring the loss of gRNAs from a final population (i.e. negative selection survival screens) you need to use NGS to identify the gRNAs present in the initial mutant cell population prior to selection. Alternatively, for positive screens such as drug-screens, you can treat your mutant cells with drug, or control and directly compare the gRNA distribution at the end of the screen F. It is important to remember that analysis of relevant genes ("hits") at the end of your screen requires the use of NGS.
What happens in the second stage of PCR?
Annealing: Temperature is 50°C, and primers bind to the 3' end of DNA template.
What 4 things can antibodies do against pathogens?
Antibodies kill the pathogens by lysis, enhanced phagocytosis, clumping the pathogen together, or neutralizing the toxins from pathogens.
Tell me about tracrRNA of CRISPR
Binds to crRNA and forms an active complex.
Generally, what are lipids?
Biological molecules that are insoluble in aqueous solution and soluble in organic solvents are classified as lipids.
Which cofactor does Acetyl-CoA carboxylase require?
Biotin co-factor
What is linezolid
Blocks protein production, like a lot of drugs that target gram-negatives
the rate of proton diffusion limits the rate of proton release to less than 10⁴ s-1 for a group with pKa= 7. However, carbon dioxide is hydrated at a rate of 10⁶ s⁻¹. How can you explain this?
Buffer concentrations can be higher
Burkitt's lymphoma
Burkitt lymphoma is a cancer of the lymphatic system, particularly B lymphocytes found in the germinal center. All types of Burkitt lymphoma are characterized by dysregulation of the c-myc gene by one of three chromosomal translocations.
What are protospacers
CRISPR loci in a bacterium contain "spacers" (viral DNA inserted into a CRISPR locus) that in type II adaptive immune systems were created from invading viral or plasmid DNA (called "protospacers").
Tell me about CRISPR and disease models
CRISPR simplifies creation of animals for research that mimic disease or show what happens when a gene is knocked down or mutated. CRISPR may be used at the germline level to create animals where the gene is changed everywhere, or it may be targeted at non-germline cells. CRISPR can be utilized to create human cellular models of disease. For instance, applied to human pluripotent stem cells CRISPR introduced targeted mutations in genes relevant to polycystic kidney disease (PKD) and focal segmental glomerulosclerosis (FSG). These CRISPR-modified pluripotent stem cells were subsequently grown into human kidney organoids that exhibited disease-specific phenotypes. Kidney organoids from stem cells with PKD populations formed large, translucent cyst structures from kidney tubules. Kidney organoids with mutations in a gene linked to FSG developed junctional defects between podocytes, the filtering cells affected in that disease. Importantly, these disease phenotypes were absent in control organoids of identical genetic background, but lacking the CRISPR modifications. A similar approach was taken to model long QT syndrome in cardiomyocytes derived from pluripotent stem cells. These CRISPR-generated cellular models, with isogenic controls, provide a new way to study human disease and test drugs.
What was CRISPR originally used for in bacteria?
CRISPR, is a family of DNA sequences in bacteria that contains snippets of DNA from viruses that have attacked the bacterium. These snippets are used by the bacterium to detect and destroy DNA from further attacks by similar viruses. These sequences play a key role in a bacterial defence system.
How would you enhance specificity with Cas9 Nickase?
CRISPR/Cas9 is highly specific when gRNAs are designed correctly, but specificity is still a major concern, particularly as CRISPR is being developed for clinical use. The specificity of the CRISPR system is determined in large part by how specific the gRNA targeting sequence is for the genomic target compared to the rest of the genome. Ideally, a gRNA targeting sequence will have perfect homology to the target DNA with no homology elsewhere in the genome. Realistically, a given gRNA targeting sequence will have additional sites throughout the genome where partial homology exists. These sites are called "off-targets" and need to be considered when designing a gRNA for your experiment In addition to optimizing gRNA design, specificity of the CRISPR system can also be increased through modifications to Cas9 itself. As discussed previously, Cas9 generates double strand breaks (DSBs) through the combined activity of two nuclease domains, RuvC and HNH. The exact amino acid residues within each nuclease domain that are critical for endonuclease activity are known (D10A for RuvC and H840A for HNH in S. pyogenes Cas9) and modified versions of the Cas9 enzyme containing only one active catalytic domain (called "Cas9 nickase") have been generated. Cas9 nickases still bind DNA based on gRNA specificity, but nickases are only capable of cutting one of the DNA strands, resulting in a "nick", or single strand break, instead of a DSB. DNA nicks are rapidly repaired by HDR (homology directed repair) using the intact complementary DNA strand as the template (jump to our HDR section for more details). Thus, two nickases targeting opposite strands are required to generate a DSB within the target DNA (often referred to as a "double nick" or "dual nickase" CRISPR system). This requirement dramatically increases target specificity, since it is unlikely that two off-target nicks will be generated within close enough proximity to cause a DSB. Therefore, if specificity and reduced off-target effects are crucial, consider using the dual nickase approach to create a double nick-induced DSB. The nickase system can also be combined with HDR-mediated gene editing for highly specific gene edits.
What are cajal bodies?
Cajal bodies (CBs) also coiled bodies, are spherical sub-organelles of 0.3-1.0 µm in diameter found in the nucleus of proliferative cells like embryonic cells and tumor cells, or metabolically active cells like neurons. In contrast to cytoplasmic organelles, CBs lack any phospholipid membrane which would separate their content, largely consisting of proteins and RNA, from the surrounding nucleoplasm. Cajal bodies are associated with telomerase assembly and recruitment via a CAB-RNA sequence common in both CB RNAs (scaRNAs) and the RNA component of telomerase (TERC). TCAB1 recognizes the CAB sequence in both and recruits telomerase to the CBs. CBs assemble RNA which is used by telomerase to add nucleotides to the ends of telomeres
Doxycycline
Can be used to treat cholera It inhibits protein synthesis by stopping translation. It binds to the 16S part of the 30S ribosomal subunit and prevents the amino-acyl tRNA from binding to the A site of the ribosome. The binding is reversible in nature.
Which carbonic anhydrase hydrates CO₂ at rates as high as kcat = 10⁶ s⁻¹
Carbonic anhydrase II
Tell me 2 accessory pigments that help absorb light for photosynthesis.
Carotenes and Phycocyanobilins, These accessory pigments trap light energy at wavelengths where chlorophylls do not absorb light, and pass the energy on to chlorophyll.
Yersinia enterocolitica
Causes abdominal pain and diarrhoea Grows well in cold temperatures Dont need to treat, but if you want it to leave faster, use cipro Gram negative
Cefepime
Cefepime is a fourth-generation cephalosporin antibiotic. Cefepime has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both types of organism than third-generation agents.
How is chromatin involved with ageing?
Chromatin, being a macromolecule of the cell, is exposed to stresses that can affect both its structure and function. There is a proposal stating that aging is due to the change from a youthful chromatin configuration to one that helps bring about molecular signatures of aging. Given that there has been both an observed overall decline in heterochromatin, but an increase at specific sites it has been suggested that aging is also associated with remodeling the chromatin structure.
Where do gram-negative enteric rods live?
Colon
What are the two types of heterochromatin?
Constitutive and Facultative Heterochromatin
Tell me about crRNA of CRISPR
Contains the guide RNA that locates the correct section of host DNA along with a region that binds to tracrRNA (generally in a hairpin loop form) forming an active complex.
In which conformation do most carbohydrates exist
D-conformation
Why does amylose adopt a helical shape?
Due to the bulky CH₂OH groups Because of the angle of the 1-4 glycosidic bonds
What is dystonia?
Dystonia is a neurological movement disorder syndrome in which sustained or repetitive muscle contractions result in twisting and repetitive movements or abnormal fixed postures. The movements may resemble a tremor.
what happens to E2F during senescence?
E2F is repressed.
What do you know about the number of ATP molecules each electron from FADH₂ produces, compared to the number of ATP molecules each electron from NADH produced?
Each electron from NADH produces more ATP molecules than each electron from FADH₂
What is receptor tyrosine kinase?
Enzyme-coupled receptor
What does EGF stand for?
Epidermal growth factor
Tell me about Ercc1−/∆ mice
Ercc1−/∆ mice, a mouse model of a human progeroid syndrome,
What is the type of reaction between phosphate and amino acid to produce phosphorylated amino acid?
Esterification
Eukaryotic and Prokaryotic Ribosomes tell me about their rRNA content
Eukaryotic Ribosomes have 5S, 5.8S, 18S, 28S rRNAs Prokaryotic Ribosomes have 5S, 16S, 23S rRNAs
What happens in the third stage of PCR?
Extension: Temperature is 72°C. Taq polymerase binds to primers and copies the DNA.
Describe the steps in the formation of familial adenomatous polyposis (FAP).
FAP patients must have one inherited defective allele of APC Loss of second allele of APC in a colonic epithelial cell --> adenomatous polyp (benign) polyp forms adenoma (genetically unstable) may lead to Ras mutations and loss of tumor suppressors TP53 carcinoma and metastasis occurs at later stages
What is malonyl transacylase a domain of?
Fatty Acid Synthase
What does FAD stand for?
Flavin Adenine Dinucleotide
What are the two primers?
Forward and Reverse Primers
Fructose 2,6 bisphosphate
Fru-2,6-BP strongly activates glucose breakdown in glycolysis through allosteric modulation of phosphofructokinase 1 (PFK-1). Elevated expression of Fru-2,6-BP levels in the liver allosterically activates phosphofructokinase 1 by increasing the enzyme's affinity for fructose 6-phosphate, while decreasing its affinity for inhibitory ATP and citrate. At physiological concentration, PFK-1 is almost completely inactive, but interaction with Fru-2,6-BP activates the enzyme to stimulate glycolysis and enhance breakdown of glucose
What happens if p53 is deactivated in cells with very short telomeres?
Further cell division occurs, resulting in chromosomal fusion, and abnormalities, lots of cell death. Any cell that survives these events has many mutations, is aneuploid and is transformed and immortalized
What are G proteins?
G proteins are proteins who's activities are regulated by binding and hydrolyzing GTP. They bind to GDP and GTP When a G protein is bound to GTP, it is in the active state. When GTP is hydrolyzed to GDP the protein is in the "off" state.
Tell me about the catabolism of GABA
GABA transaminase enzyme catalyzes the conversion of 4-aminobutanoic acid (GABA) and 2-oxoglutarate (α-ketoglutarate) into succinic semialdehyde and glutamate. Succinic semialdehyde is then oxidized into succinic acid by succinic semialdehyde dehydrogenase and as such enters the citric acid cycle as a usable source of energy
Tell me about other molecules similar to ATP that can also be hydrolysed to release energy
GTP - Guanosine triphosphate CTP - Cytidine triphosphate UTP - Uridine triphosphate
How does alcoholic fermentation occur in yeast?
Glycolysis to produce pyruvate. Then decarboxylation of pyruvate to ethanal. Then reduction of ethanal to ethanol.
Between which groups do glycosidic bonds form?
Glycosidic bonds normally occur between the reducing group(aldehyde/ketone) of one monosaccharide and the hydroxylgroup of another
viridans strep
Gram positive chains alpha hemolytic Quellung negative Use penicillin
Tell me about H2A.Bbd
H2A.Bbd (Barr body deficient) is mammal specific, and is the fastest evolving histone gene. It is believed be involved in opening chromatin structure, similar to acetylation
Tell me about H3K27
H3K27 is known for one thing: shutting down transcription. When H3K27 is trimethylated, it is tightly associated with inactive gene promoters. It acts in opposition to H3K4me3. Because of its dramatic and predictable effect on gene expression, H3K27me3 is a favorite of epigenesists looking for inactive genes.
Tell me about H3K36
H3K36 is currently a puzzle to researchers, an active source of interest. Modifications occurring at H3K36 are very diverse and don't share much similarity with each other.
H4K12
H4K12 is yet another lysine on the N-terminal tail of histone H4 that yet again is acetylated and not methylated. Starting to sound familiar? Like H4K8ac, H4K12ac is part of a "backbone" of histone modifications that are associated with active promoters. H4K12ac is localized to the promoter, like other H4 acetylations; however, H4 localizes more to gene bodies than the other acetylations. This suggests that H4K8ac serves to facilitate transcriptional elongation.
What cancers are involved with BRCA1/2 mutations?
Hereditary Breast and Ovarian Cancer syndrome (HBOC) "incompletely dominant": one copy of BRCA1/2 is mutated --> increased risk of cancer loss of second allele of BRCA1/2 results in cancer
What is transformation (cancer)?
Heritable modification of a cell from its normal state to a malignant state.
What enzyme converts glucose to glucose 6-phosphate?
Hexokinase
What are the effects of histone acetylation and deacetylation?
Histone acetylation removes positive charge from lysine residue. This means DNA is less tightly bound to histone because DNA is negatively charged, so less attraction results. Histone acetylation therefore increases gene transcription, as DNA is looser
What are histone chaperones?
Histone chaperones are histone binding proteins involved in the assembly of histones into nucleosomes and their activity has been used for the determination of chromatin structure and function.
Tell me characteristics of Homeobox genes
Homeobox genes are present on every human chromosome, and they often appear in clusters.
Nanog
Homeobox protein Nanog a transcription factor critically involved with self-renewal of undifferentiated embryonic stem cells. NANOG is a transcription factor in embryonic stem cells (ESCs) and is thought to be a key factor in maintaining pluripotency. NANOG is thought to function in concert with other factors such as POU5F1 (Oct-4) and SOX2 to establish ESC identity. These cells offer an important area of study because of their ability to maintain pluripotency. In other words, these cells have the ability to become virtually any cell of any of the three germ layers (endoderm, ectoderm, mesoderm).
Oxygen is the final electron acceptor of the electron transport chain. Do you know any other final electron acceptor molecules?
In anaerobic respiration, in some organisms sulfate exists as the final electron acceptor
What is flow cytometry?
In biotechnology, flow cytometry is a laser- or impedance-based, biophysical technology employed in cell counting, cell sorting, biomarker detection and protein engineering, by suspending cells in a stream of fluid and passing them through an electronic detection apparatus. A flow cytometer allows simultaneous multiparametric analysis of the physical and chemical characteristics of up to thousands of particles per second.
What is processivity?
In molecular biology and biochemistry, processivity is an enzyme's ability to catalyze "consecutive reactions without releasing its substrate"
Where do eosinophils develop and mature?
In the bone marrow
What are the possible effects of senolytics?
Increase Healthspan Improve stem cell function Reduce Frailty
Penicillin
Inhibits Transpeptidase blocks enzymes that cross link peptidoglycan chains to form bacterial cell walls. These enzymes are called penicillin binding proteins
Albendazole
Inhibits microtubule production So Worms can't take up glucose a medication used for the treatment of a variety of parasitic worm infestations
How does Cyanide work?
It blocks cytochrome c oxidase so that electrons cannot be transferred to molecular oxygen. Symptoms: shortness of breath Hydroxocobalamin (vitamin B12a) appears to be useful as an antidote and is generally first-line
What happens to dihydroxy-acetone phosphate?
It is converted to 3-phosphoglyceraldehyde by triose phosphate isomerase.
What are pasteur pipettes?
Just the normal plastic/glass pipettes
What an example of a biological structure that can cause the Gibbs-Donnan effect. Explain it.
Large anionic proteins in the blood that are not permeable to capillary walls.Because small cations are attracted, but are not bound to the proteins, small anions will cross capillary walls away from the anionic proteins more readily than small cations. The presence of a charged impermeant ion (for example, a protein) on one side of a membrane will result in an asymmetric distribution of permeant charged ions.
What are proteins?
Larger chains of amino acids
Wernicke Korsakoff syndrome
Lehninger 580
Leptospirosis
Leptospirosis is an infection caused by corkscrew-shaped bacteria called Leptospira. Signs and symptoms can range from none to mild such as headaches, muscle pains, and fevers; to severe with bleeding from the lungs or meningitis.
What is the coronavirus?
Less common cause of the common cold
How do Detergents kill bacteria?
Lyse cell membranes because detergents are amphipathic/amphiphilic
Which amino acid can be acetylated?
Lysine
What are the names of the ubiquitin ligases that regulate p53 in an autoregulatory manner?
MDM2 Cop-1 Pirh-2
Why is MHC important?
MHC molecules are important components of the immune system because they allow T lymphocytes to detect cells, such as macrophages, that have ingested infectious microorganisms. When a macrophage engulfs a microorganism, it partially digests it and displays peptide fragments of the microbe on its surface, bound to MHC molecules. The T lymphocyte recognizes the foreign fragment attached to the MHC molecule and binds to it, stimulating an immune response. In uninfected healthy cells, the MHC molecule presents peptides from its own cell (self peptides), to which T cells do not normally react.
Draw Malonyl CoA
Malonic Acid on its own is propanedioic acid
What analysis tools can we use to detect DNA methylation?
Mass spectrometry HPLC ELISA
Basics: How does DNA methylation stop gene expression
Methylation blocks the promoter site at which transcription factors bind to, stopping gene expression.
Where does the pathway for fatty acid oxidation occur?
Mitochondria
Klebsiella pneumoniae
More common in alcoholics that aspirate gastric contents. It will have red currant-jelly sputum gram negative ferment lactose rod bacteria Quellung reaction citrate metaboliser has a special capsule that protects it from macrophages can cause pneumonia if you vomit and aspirate it can cause UTIs if you have a catheter, are hospitalized or don't wipe can kill with ceftriaxone, or a third generation cephalosporin
What proportion of CpG sites are methylated?
Most CpG sites ARE methylated.
Which is a better reducing agent? A) NADH B) FADH₂
NADH is a relatively better reducing agent than FADH₂
What is the general reducing agent in fatty acid synthesis?
NADPH
Which nucleotide cofactors are used in the synthesis of fatty acids?
NADPH (which is oxidised to form FA)
Name 3 electron and hydrogen carriers involved in oxidative phosphorylation
NAD⁺ FAD Ubiquinones (Coenzyme Q)
What is the limiting factor when converting TP to 1,3 diphosphoglycerate?
NAD⁺ concentration.
What else is created when pyruvate is converted to lactate?
NAD⁺ is created. Pyruvate is reduced to lactate. so NAD⁺ is regenerated.
Give examples of beta-lactamase resistant penicillins
Nafcillin
Given that the Na+ equilibrium potential is +60 mV and the membrane potential moves from its resting level to 0 mV, in what direction will Na+ now move through any open Na+ channels?
Na⁺ will move inwards because electrical potential difference is zero, only the concentration gradient acts.
What are the two types of control?
Negative and positive
Tell me about the sympathetic nervous system
One of the two divisions of the autonomic nervous system; the sympathetic division utilize norepinephrine as a neurotransmitter in postganglionic neurones. Its actions are antagonistic to those of the parasympathetic division.
In resting nerve and muscle cells, which ion channels are open and which are closed?
Open K⁺ channel Closed Na⁺ channel
Name the compounds that are part of the Krebs Cycle
Oxaloacetate → Citrate Citrate → Isocitrate Isocitrate → α-oxoglutarate α-oxoglutarate → Succinyl-CoA Succinyl-CoA → Succinate Succinate → Fumarate Fumarate → Malate Malate → Oxaloacetate
What is the pathway from DNA damage to cell cycle arrest involving p53?
P53 is a transcription factor encoded by T53
Tell me the equation for pyrophosphate hydrolysis Tell me about the equilibrium of this reaction
PPi + H₂O → 2Pi The equilibrium for this reaction is strongly to the right
What does PRC2 do?
PRC2 first binds to chromatin and its catalytic subunit, EZH2, trimethylates H3K27.
Give the name of a barbiturate that has been used to treat epileptic seizures.
Phenobarbital
Tell me about PBS
Phosphate-buffered saline (abbreviated PBS) is a buffer solution commonly used in biological research. It is a water-based salt solution containing disodium hydrogen phosphate, sodium chloride and, in some formulations, potassium chloride and potassium dihydrogen phosphate. The osmolarity and ion concentrations of the solutions match those of the human body (isotonic).
What does phosphorylated RB do?
Phosphorylated RB is inactive and allows the cell cycle to continue.
What other ways can p53 undergo post translational modification in order to activate it?
Phosphorylation Acetylation methylation ubiquitination sumolation
What is placentomegaly?
Placentomegaly is a term applied to an abnormally enlarged placenta.
What is pleuritic Chest pain?
Pleuritic chest pain is characterized by sudden and intense sharp, stabbing, or burning pain in the chest when inhaling and exhaling.
Tell me about the optic tectum
Portion of the midbrain that receives and processes visual information
What are all 7 reagents needed in a tube to set up a PCR reaction?
Primer mix DNA Template Sterile Water Nucleotides (dNTPs) Taq Polymerase Buffer Mg2+
Tell me about PAM
Protospacer adjacent motif (PAM) is a 2-6 base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system. PAM is a component of the invading virus or plasmid, but is not a component of the bacterial CRISPR locus. Cas9 will not successfully bind to or cleave the target DNA sequence if it is not followed by the PAM sequence. PAM is an essential targeting component (not found in bacterial genome) which distinguishes bacterial self from non-self DNA, thereby preventing the CRISPR locus from being targeted and destroyed by nuclease. PAM basically stops self destruction
What enzyme breaks down Pyruvate into acetylCoA?
Pyruvate Dehydrogenase
What is RNA polymerase I responsible for?
RNA polymerase I is responsible for rRNA synthesis - a type of RNA that accounts for over 50% of the total RNA synthesized in a cell.
which end does RNA polymerase bind to?
RNA polymerase binds to the 3' end
What are Racetams?
Racetams are a class of drugs that share a pyrrolidone nucleus. Some, such as piracetam, are considered nootropics. Some such as oxiracetam and phenylpiracetam are also stimulants. Others such as levetiracetam and seletracetam are anticonvulsants. They affect the nervous system.
Why is Taq polymerase used in PCR?
Regular Polymerase would lose shape and become inactive (denaturation) due to the high temperature. However, Taq polymerase is derived from hot springs bacteria, so it is THERMOSTABLE.
Problem of oral antibiotics?
Resistance can occur.
Give examples of viruses with RNA genomes
Retroviruses (HIV)
Give 3 compounds that are inhibitors of the ETC
Rotenone Antimycin A Cyanide
How does rotenone work?
Rotenone blocks the transfer of electrons from NADH into the electron-transfer chain
Why will a carbonated (fizzy) drink rapidly degas in the mouth?
Saliva contains carbonic anhydrase.
Which amino acids are most commonly phosphorylated?
Serine and Threonine
How does Shiga toxin work?
Shiga toxin is composed of two major subunits, designated A and B. The B subunit forms a pentamer that binds to globotriaosylceramide-3 and this specificity determines where Shiga toxin mediates its pathophysiology. The A subunit exhibits an RNA N-glycosidase activity against the 28S rRNA that inhibits host protein synthesis and induces apotosis
Treponema Palladium
Silver Stain RPR test spirochete Treat with penicillin
Overexpression of what gene results in lifespan increase of 30%?
Sir2
What is the most common genetic alteration found in human cancers?
TP53 coding for p53
Tachycardia
Tachycardia, also called tachyarrhythmia, is a heart rate that exceeds the normal resting rate. In general, a resting heart rate over 100 beats per minute is accepted as tachycardia in adults. Heart rates above the resting rate may be normal (such as with exercise) or abnormal (such as with electrical problems within the heart)
Tell me about Chromodomain
The Chromatin Organization Modifier (Chromo) domain is defined as a 30-70 amino acid residue protein module found in many proteins involved in the assembly of protein complexes on chromatin. In mammals, chromodomain-containing proteins are responsible for aspects of gene regulation related to chromatin remodeling and formation of heterochromatin regions. Examples of Chromo-domain-containing proteins include transcriptional repressors HP1 and Polycomb (Pc), and the human retinoblastoma binding protein (RBP-1). Chromo domains promote protein binding to methylated lysines in the tail region of histone H3. Chromo domains can function individually or in tandem, as with CHD1, to recognize specific methylated Histone tails. Chromodomains also appear in the RNA-induced transcriptional silencing complex Picture: Structure of polycomb chromodomain
ERK1/2 pathway
The ERK1/2 pathway of mammals is probably the best-characterized MAPK system. The most important upstream activators of this pathway are the Raf proteins (A-Raf, B-Raf or c-Raf), the key mediators of response to growth factors (EGF, FGF, PDGF, etc.); but other MAP3Ks such as c-Mos and Tpl2/Cot can also play the same role. All these enzymes phosphorylate and thus activate the MKK1 and/or MKK2 kinases, that are highly specific activators for ERK1 and ERK2. The latter phosphorylate a number of substrates important for cell proliferation, cell cycle progression, cell division and differentiation (RSK kinases, Elk-1 transcription factor, etc.)
What is oxygen debt?
The accumulation of lactate, and lactate needs to be further oxidised to be fully broken down and get rid of lactate. Thus it is called Oxygen Debt. (EXPAND THIS ANSWER)
What is cellulitis?
The affected skin appears swollen and red and is typically painful and warm to the touch. Cellulitis usually affects the skin on the lower legs, but it can occur in the face, arms and other areas. It occurs when a crack or break in your skin allows bacteria to enter. Left untreated, the infection can spread to your lymph nodes and bloodstream and rapidly become life-threatening. It isn't usually spread from person to person.
Tell me about the catalase test
The catalase test is also one of the main three tests used by microbiologists to identify species of bacteria. The presence of catalase enzyme in the test isolate is detected using hydrogen peroxide. If the bacteria possess catalase (i.e., are catalase-positive), when a small amount of bacterial isolate is added to hydrogen peroxide, bubbles of oxygen are observed. The catalase test is done by placing a drop of hydrogen peroxide on a microscope slide. Using an applicator stick, a scientist touches the colony, and then smears a sample into the hydrogen peroxide drop. Catalase is a common enzyme found in nearly all living organisms exposed to oxygen
Why is mapping epitopes challenging?
The challenges in mapping epitopes and identifying its location becomes challenging because different monoclonal antibodies will recognize different or similar epitopes.
Tell me about blackheads
The dark color of blackheads has nothing to do with dirt: They look dark because this kind of blackhead is "open" and the skin pigment melanin reacts with oxygen in the air.
Why is the pKa of lactic acid 1 point lower than the pka of ethanoic acid?
The deprotonated form is favoured due to intramolecular hydrogen bonding.
Tell me about the diencephalon
The division of the forebrain that includes the thalamus and hypothalamus
Why is Acetyl-CoA carboxylase called an ABC enzyme?
The enzyme requires ATP, Biotin, and CO₂
What is ERK1?
The first mitogen-activated protein kinase to be discovered.
What are the health benefits of consumption of oleic acid?
The health benefits of oleic acid are broad and profound. Numerous studies have shown that consumption of MUFAs is important to maintain low levels of LDL in the blood and is also likely to be associated with the potential for elevated HDL. Another physiologically significant effect of oleic acid is the result of its conversion to oleoylethanolamide (OEA) in the small intestine. OEA has demonstrated effects in the CNS related to the control of appetite and feeding behaviors.
What is the nucleosome core formed from?
The nucleosome core is formed of two H2A-H2B dimers and a H3-H4 tetramer.
What is passive DNA demethylation?
The removal of methyl groups from DNA during the de novo synthesis of DNA via DNMT1
Tell me about the spinal cord
The spinal cord is a cable of nerve tissue that passes down the channel in the vertebrae from the hindbrain to the end of the tail. It becomes progressively smaller as paired spinal nerves pass out of the cord to parts of the body. Protective membranes or meninges cover the cord and these enclose cerebral spinal fluid If you cut across the spinal cord you can see that it consists of white matter on the outside and grey matter in the shape of an H or butterfly on the inside.
Tell me about schwann cells
The supporting cells associated withe projecting axons along with all other nerve cells that make yip the peripheral nervous system
Tell me about the Universal H2A Variants
The universal H2A variants H2A.X and H2A.Z are found in almost all organisms. Phosphorylation of H2A.X at serine 139 (termed γ-H2A.X) is an early response to double strand breaks, leading to structural changes and eventually repair. H2A.Z has many roles, including transcriptional activation and repression and heterochromatin formation.
What happens if H3K27 is methylated?
Then genes around histone will be repressed
Tell me about strychnine poisoning
The symptoms of poisoning in humans are generally similar to those as in other animals, because the mechanism of action is apparently similar across species. The toxicity of strychnine in humans is not ethically studied, so most information known comes from cases of strychnine poisoning, both unintentional and deliberate. After injection, inhalation, or ingestion, the first symptoms to appear are generalized muscle spasms. They appear very quickly after inhalation or injection — within as few as five minutes — and take somewhat longer to manifest after ingestion, typically approximately 15 minutes. With a very high dose, the onset of respiratory failure and brain death can occur in 15 to 30 minutes. If a lower dose is ingested, other symptoms begin to develop, including seizures, cramping, stiffness, hypervigilance, and agitation. Seizures caused by strychnine poisoning can start as early as 15 minutes after exposure and last 12 - 24 hours. They are often triggered by sights, sounds, or touch and can cause other adverse symptoms, including hyperthermia, rhabdomyolysis, myoglobinuric kidney failure, metabolic acidosis, and respiratory acidosis. During seizures, mydriasis (abnormal dilation), exophthalmos (protrusion of the eyes), and nystagmus (involuntary eye movements) may occur. As strychnine poisoning progresses, tachycardia (rapid heart beat), hypertension (high blood pressure), tachypnea (rapid breathing), cyanosis (blue discoloration), diaphoresis (sweating), water-electrolyte imbalance, leukocytosis (high number of white blood cells), trismus (lockjaw), risus sardonicus (spasm of the facial muscles), and opisthotonus (dramatic spasm of the back muscles, causing arching of the back and neck) can occur. In rare cases, the affected person may experience nausea or vomiting. The proximate cause of death in strychnine poisoning can be cardiac arrest, respiratory failure, multiple organ failure, or brain damage. The LD50-values estimated from different cases of strychnine poisoning are listed below in table 2.
Tell me about cranial nerves
There are twelve pairs of cranial nerves that come from the brain. Each passes through a hole in the cranium. The most important of these are the olfactory, optic, acoustic and vagus nerves.
What are aminopenicillins?
These are penicillins with an extra aminogroup that helps them get through the outer membrane. Thus Ampicillin does work on some gram-negatives
How does the TET family promote demethylation?
These proteins may promote DNA demethylation by binding to CpG rich regions to prevent unwanted DNA methyltransferase activity, and by converting 5-mC to 5-hmC, 5-hmC to 5-fC (5-formylcytosine), and 5-fC to 5-caC (5-carboxylcytosine) through hydroxylase activity.
What are phosphatases in the EGF signal transduction pathway?
They are tumor suppressing proteins because they inactivate proteins and enzymes that drive signal transduction pathways. For this reason, genes that code for phosphatases are called tumor suppressing genes.
thrombocytopenia
Thrombocytopenia is a condition characterized by abnormally low levels of thrombocytes, also known as platelets, in the blood.
Difference between thymine and thymidine?
Thymidine is a nucleoside, so has a sugar group attached to it.
What is the TET1 protein involved with?
Transcriptional activation and repression
Why do you take isotretinoin with meals?
Vitamin A is fat soluble compound
Is the primer a DNA primer?
Yes, so there's NO NEED for replacement/gap-filling.
significance of hydrogen bond disruptors
You can disrupt secondary structure using hydrogen bond disruptors
Describe the reductive amination process for synthesizing amino acids in the lab.
Your starting compound is an α-keto acid, or a ketone on the alpha carbon of a carboxylic acid. You add ammonia and a reducing agent like NaBH₄ to reduce it.
Scarlet fever
a disease which can occur as a result of a group A streptococcus (group A strep) infectionf
What is peptidoglycan?
a polymer of N-acetyl glucosamine, N-acetyl muramic acid and amino acids.
What pH are aspartic proteases optimally active?
acidic pH
Fluconazole
antifungal medication used for a number of fungal infections
How does APC regulate Wnt signaling pathway?
beta-catenin activates c-Myc and cyclin
What are the two whey proteins present in milk?
beta-lactoglobulin and alpha-lactalbumin.
At low concentrations of α-amanitin, which RNA class's synthesis is affected?
both tRNA and mRNA are affected
Which carbon on cytosine is the methyl group added?
carbon number 5
vibrio parahaemolyticus
causes diarrhoea in people who eat uncooked seafood. Grow well on bile salt plates. Can have vomiting and abdomina pain Gram negative Non-lactose fermentor treat with doxycycline or cipro
Tell me about Rhinovirus
common cold virus ssRNA+
What are retroviruses?
contain RNA genomes in their virus particles but synthesize a DNA copy of their genome in infected cells.
You are confused about the different names assigned to the compounds participating in the calvin cycle. How do you remember which compounds are the same compounds?
glycerATE 3 phosphate, 3-phosphoglyceric ACID. They are the same molecule. They have carboxylic acids. triOSE phosphate, glycerALDEHYDE 3 phosphate. They are the same molecule. They are aldehydes.
In which direction is RNA synthesized?
in the 5' to 3' direction
sporadic retinoblastoma
independent mutations impact both alleles of RB1 gene in the same cell very rare
Gastroenteritis
inflammation of the gastrointestinal tract caused by cholera
What causes Li-Fraumeni syndrome?
inherited defects in TP53 --> disrupts function of p53 --> allows cells with damaged DNA to continue to divide p53 mutations are dominant negative (homotetramer)
What causes cell cycle arrest?
interplay between p53 and RB pathways
What is HPLC
is a technique in analytical chemistry used to separate, identify, and quantify each component in a mixture. It relies on pumps to pass a pressurized liquid solvent containing the sample mixture through a column filled with a solid adsorbent material. Each component in the sample interacts slightly differently with the adsorbent material, causing different flow rates for the different components and leading to the separation of the components as they flow out of the column.
What is Beta-Oxidation?
is the catabolic process by which fatty acid molecules are broken down in the cytosol in prokaryotes and in the mitochondria in eukaryotes to generate acetyl-CoA, which enters the citric acid cycle, and NADH and FADH2, which are co-enzymes used in the electron transport chain. It is named as such because the beta carbon of the fatty acid undergoes oxidation to a carbonyl group.
four beta oxidation steps are repeated to yield acetyl coa and ATP
lehninger 674
acetyl coa can be further oxidized in the citric acid cycle
lehninger 675
fat bears carry out beta oxidation in their sleep
lehninger 676
fatty acid oxidation is tightly regulated
lehninger 678
transcription factors turn on synthesis of proteins for lipid catabolism
lehninger 679
coenzyme B12, a radical solution to a perplexing problem
lehninger 680
genetic defects in fatty acyl coa dehydrogenases cause serious disease
lehninger 682
What are the four classes of RNA?
mRNA tRNA rRNA small RNA
What are the two broad categories of neurotransmitter receptor?
metabotropic or ionotropic receptors
hereditary retinoblastoma
one or two inherited defective copies of RB1 gene (second somatic mutation)
Once dna damage is detected, how is this relayed to activate the p53 pathway?
proteins that detect and repair the DNA lesion contain enzyme activities that communicate to the p53 protein that the DNA is damaged. This is accomplished by post-translational modifications resulting in phosphorylation, acetylation, methylation, ubiquitination or sumolation of the p53 protein
What is the IUPAC name of barbituric acid?
pyrimidine-2,4,6(1H,3H,5H)-trione
What is the name of the ring that proline has?
pyrrolidine ring
Osteomyelitis
rare but serious infection of the bones caused by staphylococcus aureusce
Her1 and Her2 What is the ligand for Her1 and Her2?
receptor tyrosine kinases for EGF Amplification or over-expression of this oncogene has been shown to play an important role in the development and progression of certain aggressive types of breast cancer. Ligand: EGF. EGF binding triggers receptor dimerization and activation of kinase domain activated kinase domain in turn activates MAP kinase cascade --> cell growth and proliferation
SSRI?
selective serotonin reuptake inhibitor. Class: Antidepressant Treat: Major Depressive Disorder, Anxiety Disorders
What activities are small nuclear RNAs and microRNAs involved in?
small nuclear RNAs are involved in RNA splicing and microRNAs are involved in the modulation of gene expression through the alteration of target mRNA activity.
Midpoint of transition from maximum efficiency to minimum efficiency occurs at pH 7. What does this suggest? To see graph, flip card. Answer is below graph so be careful.
suggests that a group with pKa = 7 plays an important role in the activity of carbonic anhydrase and that the deprotonated (high pH) form of this group participates more effectively in catalysis.
Erythema
superficial reddening of the skin, usually in patches, as a result of injury or irritation causing dilatation of the blood capillaries.
Echinococcus Granulosus
tapeworm
Give a marker indicating active DNA demethylation
the detection of the DNA demethylation intermediate 5-fC in various tissues and cells may also be used as a marker to indicate active DNA demethylation.
6-phosphoglucono-δ-lactone
δ because lactonisation, the oxygen attaches to the delta carbon, counting from the carbonyl.
Omega 3 fatty acids in plants are enriched in _____________ Whereas Omega 3 fatty acids from fish are enriched in _____________
Plants : α-linolenic acid Fish: eicosapentaenoic acid and docosahexaenoic acid *Additionally, the conversion of ALA to EPA and DHA is inefficient in individuals consuming a typical Western diet rich in animal fats. (Why?)
What part of the brain is hindered by taking Crystal Meth?
Prefrontal Cortex
What are the effects of heat shock and cold shock conditions on a cell?
RNA aggregation and Denaturation of proteins This triggers p53 pathway
What is replicative Senescence?
Replicative senescence is a cellular program preventing further cell divisions once telomeres become critically short
What type of disorder are barbiturates used to treat?
Seizures
Tell me about serotonin levels and tumors.
Serotonin and 5-HIAA are sometimes produced in excess amounts by certain tumors or cancers, and levels of these substances may be measured in the urine to test for these tumors.
What does mdm2 do?
Serves as an inhibitor of p53 by recognizing the N-terminal TAD and ubiquitinylating it for degradation. HDM2 complex + ubiquitination breaks down p53
What is the base sequence that is repeated in telomeres?
TTAGGG
What is formed from fatty acid oxidation?
The acetyl groups that are the products of fatty acid oxidation are linked to CoASH.
angiopoietins?
The angiopoietins, Ang1 and Ang2, are required for the formation of mature blood vessels, as demonstrated by mouse knock out studies
Which chair conformation of glucose is more stable?
The conformation where hydroxyl groups point in the equatorial direction http://www.chem.ucla.edu/~harding/ec_tutorials/tutorial15.pdf
Dihydrolipoyl dehydrogenase (E3) of PDH complex
The dihydrolipoate, still bound to a lysine residue of the complex, then migrates to the dihydrolipoyl dehydrogenase (E3) active site where it undergoes a flavin-mediated oxidation, identical in chemistry to disulfide isomerase. First, FAD oxidizes dihydrolipoate back to its lipoate resting state, producing FADH2. Then, a NAD+ cofactor oxidizes FADH2 back to its FAD resting state, producing NADH. 2 cofactors: FAD and NAD+
What happens to the energy that would have been used to form ATP from ADP and Pi when uncoupling agents are used?
The energy is released as heat.
Tell me about the cerebellum
The hindbrain region of the vertebrate brain that lies above the medulla(brain stem) and behind the forebrain; it integrates information about body position and motion, coordinates muscular activities and maintains equilibrium
Tell me about the limbic system
The hypothalamus together with the network of neurones that link the hypothalamus to some areas of the cerebral cortex responsible for many of the most deep seated drives and emotions of vertebrates, including pain, anger, sex hunger thirst and pleasure.
What is the autonomic nervous system?
The involuntary neurons and ganglia of the peripheral nervous system of vertebrates; regulates the heart, glands, visceral organs and smooth muscle.
Tell me about "White matter"
The part of the central nervous system that consists of myelinated axons; the myelin is responsible for its white appearance.
Tell me about the ventral root
The portion of a spinal nerve composed of axons of motor neurons
What is the advantage of adding co-enzyme A to fatty acids?
The resulting compound can be fed into Krebs cycle. It also makes the fatty acid "safe" so there are no free fatty acids.
Basics: What is the mechanism by which Telomeres are extended?
The telomerase enzyme has an RNA template that partially attaches to the shortened end of the DNA strand. New nucleic acids then attach to the template, extending the DNA strand. Once the telomerase leaves, the double stranded DNA is completed with the DNA polymerase.
What does omega refer to regarding fatty acids?
The term omega, as it relates to fatty acids, refers to the terminal carbon atom farthest from the functional carboxylic acid group (-COOH).The designation of a polyunsaturated fatty acid (PUFA) as an omega-3 fatty acid, for example, defines the position of the first site of unsaturation relative to the omega end of that fatty acid.
Tell me about the corpus callosum
The tract that connects the right and left hemispheres of the brain
How many polymerases exist in prokaryotic cells?
There is a single polymerase in prokaryotic cells.
Bacitracin
These peptides disrupt gram positive bacteria by interfering with cell wall and peptidoglycan synthesis.
How have researchers mitigated the decreased efficiency of serial cloning on success rate of viable embryos?
They limited the accumulation of epigenetic abnormalities in clones by using a histone deacetylase inhibitor, trichostatin A.
What are uncoupling agents?
They prevent the formation of a proton gradient across the inner mitochondrial membrane. Hence, ATP cannot be formed. They interfere with oxidative phosphorylation.
Draw Thiol
Thiol with a blue-highlighted sulfhydryl group.
Comment on the stability of DNA methylation
Though DNA methylation is very stable, the reaction can be reversed by enzymes.
Why is a buffer necessary in PCR?
To prevent pH changes, b/c polymerase is an enzyme.
How do you measure SA-ß-Gal activity
To quantify senescence, SA-ß-Gal activity was measured using the colorimetric substrate X-gal (5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside) and the fluorescent substrate C12FDG (5-dodecanoylaminofluorescein-di-b-D-galactopyranoside)39. X-gal-positive cells were counted using a light microscope, whereas C12FDG-positive cells were quantified via flow analysis and with an IN Cell Analyzer 6000 confocal imager
List 4 different experimental methods that can be used to get DNA into host cells
Transformation Transduction Transfection Electroporation
How is the Philadelphia chromosome formed?
Translocation between chromosomes 9 and 22 in hematopoietic stem cells forms fusion of 2 genes (BCR and ABL)
What is the Krebs cycle also known as?
Tricarboxylic acid cycle or Citric Acid cycle
Trimethoprim - Mechanism of Action
Trimethoprim binds to dihydrofolate reductase and inhibits the reduction of dihydrofolic acid (DHF) to tetrahydrofolic acid (THF).v THF is an essential precursor in the thymidine synthesis pathway and interference with this pathway inhibits bacterial DNA synthesis. Trimethoprim's affinity for bacterial dihydrofolate reductase is several thousand times greater than its affinity for human dihydrofolate reductase. Sulfamethoxazole inhibits dihydropteroate synthase, an enzyme involved further upstream in the same pathway. Trimethoprim and sulfamethoxazole are commonly used in combination due to possible synergistic effects, and reduced development of resistance. This benefit has been questioned.
Describe neurofibromatosis 1 (NF1)
Tumor disorder caused by mutations in NF1 that encodes neurofibromin Loss of NF1 function --> no longer controls Ras --> leads to uncontrolled cell division NF1 follows the two hit mechanism symptoms: scoliosis, cafe au lait spots, neurofibromas, Iris lisch nodules
What is Rb (retinoblastoma) protein? What happens to Rb when the cell is ready to divide?
Tumor suppressor, pocket protein when the cell is ready to divide, Rb is inactivated (phosphorylated) --> liberates E2F (transcriptional activators of cell cycle)
What is the TET2 protein involved with?
Tumour suppression
Which type of CRISPR system is used for genome editing?
Type II
What does EGFR contain?
Tyrosine protein kinase domains
West nile virus
Viral Culture ssRNA+ virus
Tell me about Histone H3K4
When you see H3K4, think activation. Whether its methylated or acetylated, this site will turn genes faster that you can say PRDM9. Acylation of all histone residues are activating, and H3K4 is no exception. The real interest in H3K4 lies in its methylation.
What are the biological functions of introns?
While introns do not encode protein products, they are integral to gene expression regulation. Some introns themselves encode functional RNAs through further processing after splicing to generate noncoding RNA molecules. Alternative splicing is widely used to generate multiple proteins from a single gene. Furthermore, some introns play essential roles in a wide range of gene expression regulatory functions such as non-sense mediated decay and mRNA export.
Which pathways does p53 communicate with?
Wnt-beta-catenin IGF-1-AKT Rb-E2F p38 MAP kinase cyclin-cdk p14/19 ARF
Do you wanna see a cool diagram about the activation of p53?
YES!
What is Negative control
You leave out any one component - this tells you that each component is needed to form a product.
Aspergillus fumigatus
a fungus
List penicillin based antibiotics
ampicillin nafcillin piperacillin-tazobactam Meropenem
What's an afferent neurone? What's an efferent neurone?
an afferent nerve fiber is the axon of a sensory neuron. an efferent nerve fiber is the axon of a motor neuron.
In pharmacology, what is an antagonist?
an antagonist is a substance that binds to a receptor but does not activate and can block the activity of other agonists an agonist is a substance that fully activates the receptor that it binds to
What is X-gal?
an organic compound consisting of galactose linked to a substituted indole. X-gal is often used in molecular biology to test for the presence of an enzyme, β-galactosidase. It is also used to detect activity of this enzyme in histochemistry and bacteriology. X-gal is one of many indoxyl glycosides and esters that yield insoluble blue compounds similar to indigo as a result of enzyme-catalyzed hydrolysis.
Hyperkerantinization
believed to start occuring due to hormones Too many cells that contain keratin Shedding doesn't occur perfectly. Hyperkerantization causes a problem at the pores
Argyll Robertson pupils
bilateral small pupils that reduce in size on a near object (i.e., they accommodate), but do not constrict when exposed to bright light (i.e., they do not react to light). They are a highly specific sign of neurosyphilis; however, Argyll Robertson pupils may also be a sign of diabetic neuropathy.
What does RB do?
binds and inhibits the transcription factors of the E2F
staph epidermidis
catalase positive coagulase negative sensitive to novobiocin lives on skin surfaces, but especially targets people with prosthetic devices like heart valves. Resistant to a lot of antibiotics, so vancomycin works best
chandelier sign?
cervical motion tenderness or cervical excitation is a sign found on pelvic examination suggestive of pelvic pathology. It is also known by the colloquial name "chandelier sign" due to the pain being so excruciating upon bimanual pelvic exam (a part of a woman's physical examination where two hands are used to feel the anatomy of the pelvis) that it is as if the patient reaches up to motion the grabbing of a ceiling-mounted chandelier
Describe the functional groups present in carbohydrates
contain large quantities of hydroxyl groups contain either an aldehyde or ketone group
salmonella enterica
doesnt ferment lactose makes hydrogen sulfide has a protective capsule multiply in intestines, weak against cipro
What is telomerase?
enzyme prevents shortening of DNA strand by adding a small DNA sequence (TTAGGG) to telemore structures (shorter linear chromosomes, that if not fixed can lead to chromosomal instability)
Coagulase
enzyme produced by several microorganisms that enables the conversion of fibrinogen to fibrin.
Tell me 5 broad categories of lipids
fats, sterols, fat soluble vitamins, phospholipids, and triglycerides
How is the p53 pathway activated from gamma-induced DNA damage?
gamma-radiation activates the ATM kinase and the CHK-2 kinase, both of which can phosphorylate the p53 protein,
Gatekeeper genes
gatekeeper genes encode gene products that act to prevent growth of potential cancer cells and prevent accumulation of mutations that directly lead to increased cellular proliferation. Rb1 is a gatekeeper gene p53 is a gatekeeper and caretaker gene CDKN1B is a gatekeeper APC is a gatekeeper STK11 is a gatekeeper CDH1 is a gatekeeper
Stochastic
having a random probability distribution or pattern that may be analysed statistically but may not be predicted precisely.
How telomerase contributes to the limitless replicative potential of the cancer cells?
highly expressed telomerase in 85-95% of cancers important for DNA replication prevents shortening of DNA strand by adding small DNA sequence to telomeres
What does zwitter mean in german?
hybrid
Ciprofloxacin
inhibits DNA gyrase Used to kill vibrio Cholerae, y. enterocolitica
oxidation of fatty acid
lehninger 672
myasthenia gravis
most commonly affected muscles are those of the eyes, face, and swallowing. autoimmune disease long term neuromuscular disease
Methicillin-resistant staph aureus
some staph aureus strains have altered penicillin binding proteins, so nothing in the penicillin or cephalosporin families work on them Use vancomycin to treat them
Draw a rough diagram showing fatty acid synthase and describe it
Fatty acid synthetase is a large complex of enzymatic activities which are responsible for the reactions of FA synthesis.
How are fatty acid integrated into respiration?
Fatty acids are split into 2-carbon units and converted into acetyl-CoA by the process of β-oxidation.
What does propionibacterium acnes feast on?
Fatty acids in sebum secreted by sebaceous glands in follicles.
How does sample preparation occur in SOLiD sequencing?
DNA is broken into fragments by one of three methods: Nebulization - compressed nitrogen/air forces DNA through holes, making fragments Sonication - ultrasonic waves create gas bubbles in sample, and shear DNA by resonance vibration Restriction Enzymes P1 and P2 adapter sequences are ligated to the DNA fragments P1 attaches to 5' position, P2 attaches to 3' position
Which DNA methyltransferases are responsible for de novo methylation of DNA?
DNA methyltransferase3a and 3b
What does methylated H3K27 bind to?
chromodomain-containing complex (PRC1)
thiamine pyrophosphate
cofactor. This cofactor is used by transketolase. Thiamine pyrophosphate stabilizes a two carbon carbanion. is produced by the enzyme thiamine diphosphokinase.
Explain SOLiD sequencing to me
https://www.youtube.com/watch?v=YLT-DUeaLms
toxic shock syndrome
is a condition caused by bacterial toxins. Symptoms may include fever, rash, skin peeling, and low blood pressure TSS is caused by bacteria of either the Streptococcus pyogenes or Staphylococcus aureus type.
allopurinol
is a medication used to decrease high blood uric acid levels. It is specifically used to prevent gout, prevent specific types of kidney stones, and for the high uric acid levels that can occur with chemotherapy.
Give a potent inhibitor of aspartyl proteases
pepstatin
Φ how to pronounce?
phi
What are the general names of the groups of molecules that deactivate p53?
phosphatases, histone deacetylases, ubiquitinases, inhibitors of ubiquitin ligases.
What is a common problem in PCR?
Unwanted amplification products.
What is stearic acid
octadecanoic acid. saturated
why are some bond angles prohibited in a protein
stearic hindrance
Non-oxidative phase of pentose phosphate cycle?
page 577 lehninger
Legionella
Gram negative, silver stain, Charcoal Yeast Extract Causes Legionnaire's Disease
What is an Operon
In genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter
What is a nucleosome?
A basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. H2A in yellow, H2B is red, H3 is blue and H4 is green. DNA is gray.
Tell me about the dorsal root ganglia
A collection of cell bodies of sensory neurones grouped together dorsal root ganglia occur outside each level of the spinal cord
Tell me about Blue White Screen
A screening technique that allows for the rapid and convenient detection of recombinant bacteria in vector-based molecular cloning experiments. DNA of interest is ligated into a vector. The vector is then inserted into a competent host cell viable for transformation, which are then grown in the presence of X-gal. Cells transformed with vectors containing recombinant DNA will produce white colonies; cells transformed with non-recombinant plasmids (i.e. only the vector) grow into blue colonies. This method of screening is usually performed using a suitable bacterial strain, but other organisms such as yeast may also be used.
Spinal interneuron
A spinal interneuron, found in the spinal cord, relays signals between (afferent) sensory neurons, and (efferent) motor neurons. Different classes of spinal interneurons are involved in the process of sensory-motor integration. Most interneurons are found in the grey column, a region of grey matter in the spinal cord.
What's an anomeric carbon?
A stereocenter made from the cyclization of a previous acyclic carbohydrate.
What are neuropeptides?
Any class of neurotransmitters consisting of polypeptides
Why can the amide(peptide) bond not rotate?
As it is a partial double bond. Resonance occurs between C=O and C-N.
Tell me about the relative concentration of ADP compared to ATP
At pH 7.4 (pH in a cell) and 25⁰C, there is about 10 000 000 times more ADP than ATP present in solution.
Dihydrolipoyl transacetylase (E2) of PDH complex
At this point, the lipoate-thioester functionality is translocated into the dihydrolipoyl transacetylase (E2) active site, where a transacylation reaction transfers the acetyl from the "swinging arm" of lipoyl to the thiol of coenzyme A. This produces acetyl-CoA, which is released from the enzyme complex and subsequently enters the citric acid cycle. E2 can also be known as lipoamide reductase-transacetylase. 2 cofactors of Dihydrolipoyl transacetylase: lipoate and coenzyme A
Why is it good to end in a G/C pair on the primer in PCR
B/c G/C is a triple bond, so it's a tighter seal.
Overall reaction for one cycle of beta oxidation?
C(n)-acyl CoA + FAD + NAD⁺ + H₂O + CoA → C(n-2)-acyl CoA + FADH₂ + NADH + H⁺ + acetyl CoA
Give an example of a protein in oxidative phosphorylation that has copper in its structure.
Cytochrome c Oxidase
What are sirtuins?
Deacetylases
What is DPBS
Dulbecos' PBS
Where do absorbed amino acids go?
To Liver
Extravasation
Tumor cell must exit blood stream
metronidazole
an antibiotic and antiprotozoal medication
What is hTERT?
- AKA human Telomerase reverse transcriptase. - the catalytic subunit of the enzyme telomerase.
What are the steps in doing cryopreservation
1) Count cells using a hemocytometer to determine their viability. Cell viability should be at least 75% for cryopreservation. 2)Centrifuge for 5 min at 1,000 rpm at room temperature. 3) Remove the supernatant (keep this; it is needed for the freezing media, see Table 1) and loosen the pellet gently. 4)Add freezing media to the required cell density. For mammalian cells this is usually 1,000,000/mL of freezing media. Cells should not be at room temperature in freezing media for more than 10 min. 5)Aliquot 1 mL into cryovials and secure the lids. 6) Transfer the cryovials into a CoolCell (at room temperature) and put into a -80°C freezer. The CoolCell will ensure that the temperature decreases steadily by 1°C/minute. 7)After approximately 24 h, remove the cryovials from the CoolCell and transfer into liquid nitrogen for long term storage.
Tell me about the Ligation and Imaging (Data collection) step of SOLiD sequencing
1) Primer binds to template strands Fragment being sequenced has a primer and primer corresponds to P1 adapter sequence 2) Probe hybridization and ligation After primer attaches, probe will attach next to the first primer, and ligase will bind to annealed probe by joining backbones. After dye end is cleaved in step 4, the next probes will bind to the probe before it, and so on. 3) Fluorescence measured Laser excites fluorescent dye. Dye releases a lower energy photon, and hits detector. Detector measures and records fluorescence. 4) Dye-end (3) nucleotides cleaved Last 3 nucleotides are cleaved, removing fluorescent bases, leaving a free 5' phosphate available for the next round of probe attachment, and allowing ligase to attach. 5) Steps 1-4 repeated 6+ times This entire process is completed 5 times, each time primer is offset by 1 base. This is because after one round, you only have information for every fifth base, you need to repeat to get the 4 remaining bases per section.
What are the 4 levels of the ladder in the treatment of acne?
1) Topical Retinoids (Adapalene, Tazarotene) 2) Topical Benzoyl Peroxide 3) Tetracycline + Erythromicine (macrolide antibiotics) 4) Oral Retinoid (Isotretinoin)
Tell me about Thawing frozen cell lines
1)Remove cryovial from liquid nitrogen storage and place in a 37°C water bath until only about 80% defrosted. This should take no longer than 1 minute. 2)Using a pipette transfer the contents of the vial into a 15 mL Falcon tube containing about 10 mL of pre-warmed culture media. 3)Centrifuge at 500-1,000 rpm for 5 min, discard supernatant and resuspend in the appropriate amount of cell culture media. 4)Transfer cells into a culture vessel and transfer into a 37°C incubator.
What is 1,3-Bisphosphoglycerate
1,3BPG is a transitional stage between glycerate 3-phosphate and glyceraldehyde 3-phosphate during the fixation/reduction of CO₂. It is a 3-carbon organic molecule present in most, if not all, living organisms. It primarily exists as a metabolic intermediate in both glycolysis during respiration and the Calvin cycle during photosynthesis.
If pka = 7, what must Ka equal to?
10⁻⁷
How many ATP molecules does each acetyl-CoA make?
12
How many of the 20 amino acids have neutral side chains?
15
How does EGF bind to its receptor?
2 EGF molecules bind to each domain, binding causes the 2 monomers to form a dimer, changing the shape of the EGFR, causing cross phosphorylation, carboxyl terminal ends are phosphorylation by kinases.
What are oligosaccarides?
2 to 10 monosaccharide units linked by glycosidic bonds
How long does it take for cells from the bottom of the dermis to rise to the top?
2 weeks
Which oxidation state does Zinc exist in, in Biological Systems?
2+
What is the pKa of glycine's COOH and NH₂?
2.34 and 9.60 roughly
How many cycles of PCR are done?
25-30 cycles
Formula for the total number of stereoisomers in a compound with more than 1 chiral centre?
2ⁿ where n is the number of chiral centres (formula is a maximum, some molecules, depending on their structure, have less)
How many of the 20 amino acids are positively charged (at body pH)?
3
What is the zinc bound to in carbonic anhydrase?
3 imidazole rings of 3 histidines and a water molecule(or hydroxide depending on pH)
What are furanoses
5 membered ring structures that are hemiacetals or hemiketals. A furanose is a collective term for carbohydrates that have a chemical structure that includes a five-membered ring system consisting of four carbon atoms and one oxygen atom.
conversion of fructose 1,6 bisphosphate to fructose 6-phosphate is the second bypass.
572 Lehninger
citric acid cycle intermediates and some amino acids are glucogenic
574 lehninger
mammals cannot convert fatty acids to glucose...
574 lehninger
Tell me about absorption of dietary fats in the small intestine
668 lehninger
Tell me about epinephrine and what are epinephrines effects on the body in the fight or flight response
A biogenic amine that is a hormone, neurotransmitter and medication. It is released into the blood as a hormonal secretion from the adrenal medulla, but is also produced by certain neurones; It increases blood flow to muscles, heart rate and stroke volume, pupil dilation and blood glucose in preparation for flight-or-fight Epinephrine is made from norepinephrine via Phenylethanolamine N-methyltransferase It is given intravenously, by injection into a muscle, by inhalation, or by injection just under the skin.
Wht are Catecholamines?
A catecholamine is a monoamine, an organic compound that has a catechol (benzene with two hydroxyl side groups at carbons 1 and 2) and a side-chain amine. Catecholamines are derived from the amino acid tyrosine, which is derived from dietary sources as well as synthesis of phenylalanine. Catecholamines are water-soluble and are 50%-bound to plasma proteins in circulation. Included among catecholamines are epinephrine (adrenaline), norepinephrine (noradrenaline), and dopamine.
What does the combination of the drugs dasatinib and quercetin do
A combination of the drugs dasatinib and quercetin, which target several of these pro-survival pathways, induce death specifically in senescent murine and human cells in vitro, as well as enhance cardiovascular function in aged mice, treadmill endurance in radiation-exposed mice, and decrease frailty, neurologic dysfunction and bone loss in progeroid mice. Furthermore, dasatinib and quercetin reduce senescent cell burden and aortic calcification in the aortae of atherosclerotic apoE−/− mice and improve lung function in the mouse model of idiopathic pulmonary fibrosis
What is an inhibitory post synaptic potential?
A hyperpolarization of the postsynaptic cell membrane in response to the release of a neurotransmitter, acts to move the membrane potential away from initiation of an action potential
Tell me about laminar flow system
A laminar flow system is a vital concept in the control of particulate contamination. Laminar airflow is defined as air moving at the same speed and in the same direction, with no or minimal cross-over of air streams (or "lamina"). By contrast, turbulent flow creates swirls and eddies that deposit particles on surfaces randomly and unpredictably. Most contamination-sensitive environments such as dust-free hoods require laminar flow because it predictably sweeps particles in a uniform direction, from the cleanest area under the hood (the filter face) to the exit area, which is generally the sash opening or vents along the back or bottom of the hood. This design ensures that the cleanest (and most germ-free) area will always be the upstream area closest to the filter face. Work is generally done in that clean zone, as far as possible from obstructions that create turbulence.
Tell me about mast cells
A mast cell (also known as a mastocyte or a labrocyte) is a type of white blood cell. Specifically, it is a type of granulocyte derived from the myeloid stem cell that is a part of the immune and neuroimmune systems and contains many granules rich in histamine and heparin. Although best known for their role in allergy and anaphylaxis, mast cells play an important protective role as well, being intimately involved in wound healing, angiogenesis, immune tolerance, defense against pathogens, and blood-brain barrier function. The mast cell is very similar in both appearance and function to the basophil, another type of white blood cell. Although mast cells were once thought to be tissue resident basophils, it has been shown that the two cells develop from different hematopoietic lineages and thus cannot be the same cells.
What is AMP-activated protein kinase?
A master regulatory enzyme. plays a role in cellular energy homeostasis, largely to activate glucose and fatty acid uptake and oxidation when cellular energy is low. When AMPK phosphorylates acetyl-CoA carboxylase 1 (ACC1) or sterol regulatory element-binding protein 1c (SREBP1c), it inhibits synthesis of fatty acids, cholesterol, and triglycerides, and activates fatty acid uptake and β-oxidation AMPK stimulates glucose uptake in skeletal muscle by phosphorylating Rab-GTPase-activating protein TBC1D1, which ultimately induces fusion of GLUT4 vesicles with the plasma membrane. AMPK stimulates glycolysis by activating phosphorylation of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2/3 and activating phosphorylation of glycogen phosphorylase, and it inhibits glycogen synthesis through inhibitory phosphorylation of glycogen synthase Makes sense because the protein kinase is activated by AMP. You only get AMP when energy is low.
What are metabotropic receptors
A metabotropic receptor is a type of membrane receptor of eukaryotic cells that acts through a second messenger. It may be located at the surface of the cell or in vesicles. Metabotropic receptors are indirectly linked with ion channels on the plasma membrane of the cell through signal transduction mechanisms, often G proteins. Hence, G protein-coupled receptors are inherently metabotropic. Other examples of metabotropic receptors include tyrosine kinases and guanylyl cyclase receptors. Both ionotropic receptors and metabotropic receptors are activated by specific neurotransmitters. When an ionotropic receptor is activated, it opens a channel that allows ions such as Na+, K+, or Cl− to flow. In contrast, when a metabotropic receptor is activated, a series of intracellular events are triggered that can also result in ion channels opening but must involve a range of second messenger chemicals.
What is substance P?
A neurotransmitter released at synapses in the central nervous system by neurones stimulated by painful stimuli
Tell me about norepinephrine Tell me about from what and where it is synthesised
A neurotransmitter released by postganglionic neurones of the sympathetic nervous system. It is synthesised from dopamine by dopamine beta hydroxylase After synthesis, norepinephrine is transported from the cytosol into synaptic vesicles by the vesicular monoamine transporter (VMAT). They are then absorbed back into the presynaptic cell, via reuptake mediated primarily by the norepinephrine transporter (NET). Once back in the cytosol, norepinephrine can either be broken down by monoamine oxidase or repackaged into vesicles by VMAT, making it available for future release. It is synthesised from the amino acid tyrosine in the adrenal medulla and postganglionic neurones of the sympathetic nervous system.
Tell me the basics of organismal cloning. What is it?
A new individual grown from a single somatic cell of its parent and is genetically identical to it. Organismal cloning arises from the technique called somatic cell nuclear transfer.
What is a nucleoside?
A nucleotide without a phosphate group
perinate
A perinate is a member of a viviparous species from approximately one month before birth to one month after it.
What is a protein domain?
A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. One domain may appear in a variety of different proteins. The picture shows pyruvate kinase, a protein with three domains.
What is CDK?
A protein kinase. Cell cycle regulator in all eukaryotes. When CDK is activated, it phosphorylates different proteins that initiate M phase.
Tell me about ADP-ribosylation Can you draw ADP ribose for me?
ADP-ribosylation is the addition of one or more ADP-ribose moieties to a protein.[1][2] It is a reversible post-translational modification that is involved in many cellular processes, including cell signaling, DNA repair, gene regulation and apoptosis.[3][4] Improper ADP-ribosylation has been implicated in some forms of cancer.[5] It is also the basis for the toxicity of bacterial compounds such as cholera toxin, diphtheria toxin, and others. Picture shows ADP ribose
Tell me the equation of the hydrolysis of ATP including the charge
ATP⁴⁻ + H₂O → ADP³⁻ + Pi²⁻ + H⁺ Recombining ADP³⁻ and Pi²⁻ is unfavourable because both are negatively charged.
What is acid fastness
Acid-fastness is a physical property of certain bacterial and eukaryotic cells, as well as some sub-cellular structures, specifically their resistance to decolorization by acids during laboratory staining procedures. Once stained as part of a sample, these organisms can resist the acid and/or ethanol-based decolorization procedures common in many staining protocols, hence the name acid-fast. The mechanisms of acid-fastness vary by species, although the most well-known example is in the genus Mycobacterium, which includes the species responsible for tuberculosis and leprosy. The acid-fastness of Mycobacteria is due to the high mycolic acid content of their cell walls, which is responsible for the staining pattern of poor absorption followed by high retention. Some bacteria may also be partially acid-fast.
What is active DNA methylation?
Active DNA demethylation mainly occurs by the removal of 5-methylcytosine via the sequential modification of cytosine bases that have been converted by TET enzyme-mediated oxidation
How do you convert pyruvic acid to alanine?
Add NaBH₄ and NH₃
Tell me the different classes of oxygen tolerance of microorganisms and explain them.
Aerobic and anaerobic bacteria can be identified by growing them in test tubes of thioglycollate broth: 1: Obligate aerobes need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest. 2: Obligate anaerobes are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest. 3: Facultative anaerobes can grow with or without oxygen because they can metabolise energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more ATP than either fermentation or anaerobic respiration. 4: Microaerophiles need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube but not the very top. 5: Aerotolerant organisms do not require oxygen as they metabolise energy anaerobically. Unlike obligate anaerobes however, they are not poisoned by oxygen. They can be found evenly spread throughout the test tube.
Aflatoxin
Aflatoxins are poisonous carcinogens that are produced by certain molds (Aspergillus flavus and Aspergillus parasiticus) which grow in soil, decaying vegetation, hay, and grains Aflatoxins damage the liver
Tell me about heterotrimeric G proteins
All G proteins that associate with GPCR are heterotrimeric meaning they have 3 different subunits (alpha, beta and gamma subunits)
3 subclasses of sphingolipids?
All subclasses of sphingolipid are derivatives of ceramide, but differing in their head groups: sphingomyelins, neutral (uncharged) glycolipids, and gangliosides.
Tell me about Hay Fever
Allergic rhinitis, also known as hay fever, is a type of inflammation in the nose which occurs when the immune system overreacts to allergens in the air. Signs and symptoms include a runny or stuffy nose, sneezing, red, itchy, and watery eyes, and swelling around the eyes. The fluid from the nose is usually clear. The underlying mechanism involves IgE antibodies attaching to the allergen and causing the release of inflammatory chemicals such as histamine from mast cells.
Tell me about alternative splicing
Alternative splicing, or differential splicing, is a regulated process during gene expression that results in a single gene coding for multiple proteins. Notably, alternative splicing allows the human genome to direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes.
Tell me about the choice of host organism and cloning vector in molecular cloning
Although a very large number of host organisms and molecular cloning vectors are in use, the great majority of molecular cloning experiments begin with a laboratory strain of the bacterium E. coli (Escherichia coli) and a plasmid cloning vector. E. coli and plasmid vectors are in common use because they are technically sophisticated, versatile, widely available, and offer rapid growth of recombinant organisms with minimal equipment.[3] If the DNA to be cloned is exceptionally large (hundreds of thousands to millions of base pairs), then a bacterial artificial chromosome[9] or yeast artificial chromosome vector is often chosen. Specialized applications may call for specialized host-vector systems. For example, if the experimentalists wish to harvest a particular protein from the recombinant organism, then an expression vector is chosen that contains appropriate signals for transcription and translation in the desired host organism. Alternatively, if replication of the DNA in different species is desired (for example, transfer of DNA from bacteria to plants), then a multiple host range vector (also termed shuttle vector) may be selected. In practice, however, specialized molecular cloning experiments usually begin with cloning into a bacterial plasmid, followed by subcloning into a specialized vector. Whatever combination of host and vector are used, the vector almost always contains four DNA segments that are critically important to its function and experimental utility: 1. DNA replication origin is necessary for the vector (and its linked recombinant sequences) to replicate inside the host organism 2. one or more unique restriction endonuclease recognition sites to serves as sites where foreign DNA may be introduced 3. a selectable genetic marker gene that can be used to enable the survival of cells that have taken up vector sequences 4. a tag gene that can be used to screen for cells containing the foreign DNA
Tell me about horizontal laminar air flow
Although both airflow designs provide effective sweeping action near the filter face, their respective flow patterns eventually encounter disruptions that often tip the scale in favor of one or the other configuration. In a vertical-flow hood, the obvious obstacle is the work surface. A perforated or rod-top work surface allows the laminar air stream to pass through the hood with minimal obstruction, but these tops can be a problem in operations involving liquids or small parts. If you're working with these materials and want to avoid picking up parts off the floor, a horizontal flow design may be preferable. Yet even a solid top may not rule out vertical flow if work is performed above the work surface. If sterile or particle-sensitive processes are performed in a clean, sterile zone midway between the work surface and the filter face, a vertical flow hood is generally acceptable. One such operation is sterile compounding, in which injectables or sterile packages are prepared above, not on, the work surface. As long as hands and other contamination sources move up and down, not sideways above a sample, sensitive materials will remain clean. Finally, consider the effects on operators of air exiting the laminar flow hood. Although horizontal laminar flow, with air traveling from the rear of the hood and exiting the front opening, may not encounter large obstructions inside the hood, it does eventually encounter the person performing the work. Any annoying substances, such as soldering fumes or fine powders, may be blown into the operator's face. While this collision may not compromise the laminar flow where work is performed, it may pose a health risk. In such cases, vertical flow is probably preferable.
Which group is actually responsible for the decrease in efficiency of Carbonic Anhydrase II as pH decreases?
Although some amino acids, notably histidine, have pKa values near 7, a variety of evidence suggests that the group responsible for this transition is not an amino acid but is the zinc-bound water molecule.
What is the key role that the pre-frontal cortex regulates and is determined to be altered by crystal meth?
Amygdala responsible for emotion
Tell me about ganglia
An aggregation of nerve cell bodies in invertebrates ganglia are the integrative centres in vertebrates the term is restricted to aggregations of nerve cell bodies located outside the central nervous system
What is an Anhydrase?
An enzyme that catalyses the removal of water
What is an ewe
An ewe is an adult female sheep
What is Positive control
An ideal reaction - becomes your reference to compare your result to.
What is an intron
An intron is any nucleotide sequence within a gene that is removed by RNA splicing during maturation of the final RNA product. The term intron refers to both the DNA sequence within a gene and the corresponding sequence in RNA transcripts.
What is an oncogene?
An oncogene is a gene that has sustained some genetic damage and, therefore, produces a protein capable of cellular transformation. It produces a PROTEIN
What is vancomycin?
Antibiotic that works by binding the subunits that bacteria use to make cell walls. So it still works against bacteria with altered penicillin-binding-proteins. Although it doesn't work against gram-negatives. It binds to D-ala D-ala subunits
Warfarin
Anticoagulant It is commonly used to treat blood clots such as deep vein thrombosis and pulmonary embolism and to prevent stroke in people who have atrial fibrillation, valvular heart disease or artificial heart valves
Tell me about antihistamine sprays
Antihistamines work by competing for receptor sites to block the function of histamine, thereby reducing the inflammatory effect. Antihistamine nasal sprays include: Azelastine hydrocholoride Levocabastine hydrocholoride Olopatadine hydrochloride ============== Antihistamine drugs can have undesirable side-effects, the most notable one being drowsiness in the case of oral antihistamine tablets. First-generation antihistamine drugs such as diphenhydramine cause drowsiness, but second- and third-generation antihistamines such as cetirizine and loratadine are less likely to cause this problem.
What are biogenic amines? Can you give examples of biogenic amines?
Any group of neurotransmitters based on amino acids; includes epinephrine, norepinephrine, dopamine and serotonin
Tell me about Zinc Finger (ZnF) proteins
Are a massive, diverse family of proteins that serve a wide variety of biological functions.The zinc ion serves to stabilize the integration of the protein itself, and is generally not involved in binding targets. The "finger" refers to the secondary structures (α-helix and β-sheet) that are held together by the Zn ion. Zinc fingers typically serve as interactors, binding DNA, RNA, proteins or small molecules
Tell me about Polycomb group Proteins
Are responsible for cellular differentiation during development via transcriptional repression. These proteins have been the subject of intense study as it is clear that they are vital for maintenance of cell-type identity, differentiation, and disease by creating and maintaining repressive chromatin environments by forming one of two major polycomb repressive complexes (PRC): PRC1, and PRC2.
Histone deacetylases (HDACs)
Are responsible for removing the acetyl groups put on histones (and other proteins) by the histone acetyltransferases (HATs). This process is a vital aspect of epigenetic regulation of gene expression and more generally for the control of cellular stability.
Which of these can pass through the blood-brain barrier? A) Dopamine B) L-DOPA C) Both
B) L-DOPA can cross the protective BBB, whereas Dopamine itself cannot.
By convention, peptide sequences are written __ to __ terminus A) C to N B) N to C
B) N to C. Peptide sequences are written N-terminus to C-terminus The N-terminus is the start of a protein.
Why is it pointless to keep increasing the number of cycles? (PCR)
B/c after about 40 cycles, the product amount reaches its maximum because reaction components run out and polymerase stops working.
How do mutations in BRCA1 and BRCA2 genes contribute to the development of cancer?
BRCA1/2 regulated repair of double stranded DNA breaks by delivering effector proteins (BRCA1 also regulates G1/S and G2/M checkpoints) without BRCA1/2 --> homologous recombination is impeded --> mutations accumulate
Tell me about BamH I
BamH I (from Bacillus amyloliquefaciens) is a type II restriction endonuclease, having the capacity for recognizing short sequences (6 b.p.) of DNA and specifically cleaving them at a target site. This exhibit focuses on the structure-function relations of BamH I as described by Newman, et al. (1995). BamH I binds at the recognition sequence 5'-GGATCC-3', and cleaves these sequences just after the 5'-guanine on each strand. This cleavage results in sticky ends which are 4 b.p. long.
What compound are barbiturates derived from? Can you draw this compound?
Barbituric Acid
Tell me about Bcl-2
Bcl-2 (B-cell lymphoma 2), encoded in humans by the BCL2 gene, regulate apoptosis, Bcl-2 is specifically considered an important anti-apoptotic protein but it is NOT considered a proto-oncogene because it is not a growth signal transducer. BCL-2 is localized to the outer membrane of mitochondria,
What must be done to fatty acids before they are broken down? Describe these 2 Stages.
Before being broken down, fatty acids must be activated. ATP is hydrolysed to AMP, allowing the addition of Coenzyme A. Coenzyme A is added to carboxy groups to form 'acyl-coenzyme A' derivatives.
What is a catechol?
Benzene with two hydroxyl side groups at carbons 1 and 2
What does Benzoyl Peroxide do?
Benzoyl Peroxide is a Keratolytic. It causes skin cells to shed faster.
What are β-Lactamase inhibitors?
Beta-lactamases are a family of enzymes involved in bacterial resistance to beta-lactam antibiotics. They act by breaking the beta-lactam ring that allows penicillin-like antibiotics to work. Strategies for combating this form of resistance have included the development of new beta-lactam antibiotics that are more resistant to cleavage and the development of the class of enzyme inhibitors called beta-lactamase inhibitors. Although β-lactamase inhibitors have little antibiotic activity of their own, they prevent bacterial degradation of beta-lactam antibiotics and thus extend the range of bacteria the drugs are effective against. The picture is Tazobactam, a β-Lactamase inhibitor.
What is Biotin? Can you draw Biotin
Biotin is the cofactor required of enzymes that are involved in carboxylation, decarboxylation, or transcarboxylation reactions in prokaryotes and eukaryotes. Biotin is sometimes referred to as vitamin H. Biotin, produced by intestinal bacteria, as well as that found in the diet, is bound to lysine residues in protein forming a complex that is called biocytin. Biotin is a water soluble B vitamin.
Bordet Gengou
Bordet-Gengou agar is a type of agar plate optimized to isolate Bordetella, containing blood, potato extract, and glycerol, with an antibiotic such as cephalexin or penicillin and sometimes nicotinamide
Difference between afferent and efferent nerve fibers?
Both afferent and efferent nerve fibres are axons. The difference is shown in the picture.
What is the main function of peroxisomes?
Break down long and branched fatty acid chains, D-amino acids, and polyamines. They also help in synthesizing plasmalogens and etherphospholipids that are necessary for proper brain and lung function.
Tell me about BrdU
Bromodeoxyuridine BrdU looks exactly like thymidine except it has a Bromine atom replacing the methyl group It is a synthetic nucleoside, an analog of thymidine. BrdU is commonly used in the detection of proliferating cells in living tissues. BrdU can be incorporated into newly synthesised DNA of replicating cells, substituting for thymidine during DNA replication. Antibodies specific for BrdU can then be used to detect the incorporated chemical, thus indicating cells that were actively replicating their DNA.
Tell me about the Buffer systems of Culture media
Buffering systems Regulating pH is critical for optimum culture conditions and is generally achieved by one of the two buffering systems: Natural buffering system In a natural buffering system, gaseous CO2 balances with the CO3/HCO3 content of the culture medium. Cultures with a natural buffering system need to be maintained in an air atmosphere with 5-10% CO2, usually maintained by an CO2 incubator. Natural buffering system is low cost and non-toxic. HEPES Chemical buffering using a zwitterion, HEPES, has a superior buffering capacity in the pH range 7.2-7.4 and does not require a controlled gaseous atmosphere. HEPES is relatively expensive and toxic at a higher concentration for some cell types. HEPES has also been shown to greatly increase the sensitivity of media to phototoxic effects induced by exposure to fluorescent light. Phenol red Most of the commercially available culture media include phenol red as a pH indicator, which allows constant monitoring of pH [24]. During the cell growth, the medium changes color as pH is changed due to the metabolites released by the cells. At low pH levels, phenol red turns the medium yellow, while at higher pH levels it turns the medium purple. Medium is bright red for pH 7.4, the optimum pH value for cell culture. However, there are certain disadvantages of using phenol red as described below: 1) Phenol red mimics the action of some steroid hormones, particularly estrogen. Thus it is advisable to use media without phenol red for studies using estrogen-sensitive cells like mammary tissue. 2) Presence of phenol red in some serum-free formulations interferes with the sodium-potassium homeostasis. This effect can be neutralized by the inclusion of serum or bovine pituitary hormone in the medium. 3) Phenol red interferes with detection in flow cytometric studies.
What is C4 carbon fixation
C4 carbon fixation or the Hatch-Slack pathway is a photosynthetic process in some plants. It is the first step in extracting carbon from carbon dioxide to be able to use it in sugar and other biomolecules. It is one of three known processes for carbon fixation. The C4 in one of the names refers to the 4-carbon molecule that is the first product of this type of carbon fixation. C4 fixation is an elaboration of the more common C3 carbon fixation and is believed to have evolved more recently. C4 overcomes the tendency of the enzyme RuBisCO to wastefully fix oxygen rather than carbon dioxide in the process of photorespiration. This is achieved by ensuring that RuBisCo works in an environment where there is a lot of carbon dioxide and very little oxygen. CO2 is shuttled via malate or aspartate from mesophyll cells to bundle-sheath cells. In these bundle-sheath cells CO2 is released by decarboxylation of the malate. C4 plants use PEP carboxylase to capture more CO2 in the mesophyll cells. PEP Carboxylase (3 carbons) binds to CO2 to make oxaloacetic acid (OAA). The OAA then makes malate (4 carbons). Malate enters bundle sheath cells and releases the CO2. These additional steps, however, require more energy in the form of ATP. Using this extra energy, C4 plants are able to more efficiently fix carbon in drought, high temperatures, and limitations of nitrogen or CO2. Since the more common C3 pathway does not require this extra energy, it is more efficient in the other conditions.
Name 3 substances that inhibit cytochrome c oxidase, and where do they attack cytochrome c oxidase?
CO azide or N₃⁻ cyanide or CN⁻ These compounds bind to haem groups, and are therefore extremely poisonous
Why are carbonic anhydrases required?
CO₂ hydration and HCO₃⁻ dehydration are often coupled to rapid processes, particularly transport processes. For example, HCO₃⁻ in the blood must be dehydrated to form CO₂ for exhalation as the blood passes through the lungs. Conversely, CO₂ must be converted into HCO₃⁻ for the generation of the aqueous humor of the eye and other secretions. Furthermore, both CO2 and HCO3- are substrates and products for a variety of enzymes, and the rapid interconversion of these species may be necessary to ensure appropriate substrate levels.
Tell me about Cas9
Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease enzyme associated with the CRISPR (Clustered Regularly Interspersed Palindromic Repeats) adaptive immunity system in Streptococcus pyogenes, among other bacteria. S. pyogenes utilizes Cas9 to memorize and later interrogate and cleave foreign DNA, such as invading bacteriophage DNA or plasmid DNA. Cas9 performs this interrogation by unwinding foreign DNA and checking for sites complementary to the 20 basepair spacer region of the guide RNA. If the DNA substrate is complementary to the guide RNA, Cas9 cleaves the invading DNA. In this sense, the CRISPR-Cas9 mechanism has a number of parallels with the RNA interference (RNAi) mechanism in eukaryotes.
P-type ATPases
Cation transporters (y?) that are reversibly phosphorylated by ATP (hence P-type) as part of the transport cycle. Phosphorylation forces a conformational change that is central to movement of the cation across the membrane. 70 P-type ATPases in the human genome, have similar sequence and topology. Especially near the Asp residue that undergoes phosphorylation. All are integral proteins with 8 or 10 predicted membrane-spanning regions in a single polypeptide (Type III integral protein) P-type ATPases are sensitive to inhibition by vanadate. This is because vanadate is a phosphate analog (structurally looks very similar) Examples of P-Type ATPases - Na+ K+ pump, H+ ATPase of plants and fungi. SERCA is also a P-type ATPase. Plasma membrane Ca2+ ATPase is also a P-type ATPase (its a uniporter, and maintains cytosolic [Ca2+] below 1µm. Parietal cells in the lining of the mammalian stomach have a P-type ATPase that pumps protons and potassium ions across the plasma membrane, acidifying stomach contents. Lipid Flippases are structurally and functionally similar to P-type transporters. Bacteria and eukaryotes use P-type ATPases to pump out toxic heavy metal ions such as Cd²⁺ and Cu²⁺.
Proteus mirabilis
Cause wound infections and UTI especially in immunocompromised or hospitalized people. Doesn't ferment lactose Proteus m. is gram negative Ampicillin works best on it This rod-shaped bacterium has the ability to produce high levels of urease, which hydrolyzes urea to ammonia (NH3), so makes the urine more alkaline. If left untreated, the increased alkalinity can lead to the formation of crystals of struvite, calcium carbonate, and/or apatite, which can result in kidney stones. The bacteria can be found throughout the stones, and these bacteria lurking in the kidney stones can reinitiate infection after antibiotic treatment. Once the stones develop, over time they may grow large enough to cause obstruction and renal failure. Proteus species can also cause wound infections, septicemia, and pneumonia, mostly in hospitalized patients. P. mirabilis is generally susceptible to most antibiotics apart from tetracycline and nitrofurantoin picture is Proteus mirabilis on an XLD agar plate
Ceftriaxone
Ceftriaxone is a third-generation antibiotic from the cephalosporin family of antibiotics.[7] It is within the β-lactam family of antibiotics. Ceftriaxone selectively and irreversibly inhibits bacterial cell wall synthesis by binding to transpeptidases, also called transamidases, which are penicillin-binding proteins (PBPs) that catalyze the cross-linking of the peptidoglycan polymers forming the bacterial cell wall
What is cell polarity?
Cell polarity is the asymmetric organisation of several cellular components, including its plasma membrane, cytoskeleton or organelles. This asymmetry can be used for specialised functions, such as maintaining a barrier within an epithelium or transmitting signals in neurons.
Tell me how dolly the sheep was created.
Cells taken from the udder of a Finn Dorset ewe, are placed in a culture with very low concentrations of nutrients. Thus starved, the cells stop dividing and switch off their active genes. Meanwhile, an unfertilised egg cell is taken from a Scottish blackface ewe. The nucleus is sucked out, leaving an empty egg cell containing all the cellular machinery necessary to produce an embryo. The two cells are placed next to each other and an electric pulse causes them to fuse together like soap bubbles. A second pulse mimics the burst of energy at natural fertilisation, jump starting cell division. After about 6 days, the resulting embryo is implanted in the uterus of another Blackface ewe. After a gestation period, the pregnant Blackface ewe gives birth to a baby Finn Dorset lamb, named Dolly, that is genetically identical to the original donor.
What are ceramides?
Ceramides are a family of waxy lipid molecules. A ceramide is composed of sphingosine and a fatty acid. Ceramides are found in high concentrations within the cell membrane of cells, since they are component lipids that make up sphingomyelin, one of the major lipids in the lipid bilayer. Contrary to previous assumptions that ceramides and other sphingolipids found in cell membrane were purely supporting structural elements, ceramide can participate in a variety of cellular signaling: examples include regulating differentiation, proliferation, and programmed cell death (PCD) of cells. ceramides are the most basic sphingolipid
Tell me about the cerebral cortex
Cerebral cortex is the thin surface layer of neurones and glial cells covering the cerebrum; well developed only in mammals and particularly prominent in humans. The cerebral cortex is the seat of conscious sensations and voluntary muscular activity
What are peptides?
Chains with fewer than 50 amino acids
What are ethanolamides?
Chemical compounds which are amides formed from carboxylic acids and ethanolamine. Some ethanolamides are naturally occurring, such as anandamide, palmitoylethanolamide and prostamides, which play physiological roles as lipid neurotransmitters and autacoids. Ethanolamides can be prepared synthetically by heating esters with ethanolamine picture is anandamide
What are retinoids?
Chemicals derived from vitamin A
Examples of Bile acids
Cholic Acid and Chenodeoxycholic acid are primary bile acids that are formed by the liver. Their dehydroxylation at C-7 by microorganisms from the intestinal flora gives rise to the secondary bile acids lithocholic acid and deoxycholic acid
Tell me about ChIP/Chromatin Immunoprecipitation
Chromatin immunoprecipitation, or ChIP, refers to a procedure used to determine whether a given protein binds to or is localized to a specific DNA sequence in vivo. 1) DNA-binding proteins are crosslinked to DNA with formaldehyde in vivo. 2) Isolate the chromatin. Shear DNA along with bound proteins into small fragments. 3) Bind antibodies specific to the DNA-binding protein to isolate the complex by precipitation. Reverse the cross-linking to release the DNA and digest the proteins. 4) Use PCR to amplify specific DNA sequences, and sequence DNA.
Tell me about Chromatin Modifiers: Basics
Chromatin modifiers are a large and varied group of proteins that conduct a wide range of epigenetic functions. The ability to bind DNA, adjust chromatin conformation and modify histones allows them to influence gene expression making them powerful targets for epigenomic research and potential therapeutic targets.
What other conditions can propionibacterium acnes cause?
Chronic blepharitis
What is the purpose of acylthioesterase?
Cleaves off the growing FA chain from the acyl carrier protein once it reaches a certain length.
What group does CoA contain?
CoA contains a phosphopantetheine group coupled to AMP.
What is cognitive flexibility?
Cognitive flexibility has been described as the mental ability to switch between thinking about two different concepts, and to think about multiple concepts simultaneously
What is cognitive inhibition?
Cognitive inhibition refers to the mind's ability to tune out stimuli that are irrelevant to the task/process at hand or to the mind's current state.
What are colony stimulating factors
Colony-stimulating factors (CSFs) are secreted glycoproteins that bind to receptor proteins on the surfaces of hemopoietic stem cells, thereby activating intracellular signaling pathways that can cause the cells to proliferate and differentiate into a specific kind of blood cell (usually white blood cells. CSF travels to bone marrow once released by immune cells. CSFs are released in response to a bacterial infection The colony-stimulating factors (CSFs) are the master regulators of granulocyte and macrophage populations. CSFs are cytokines When in the circulation, the CSFs can resemble hormones with highly specific actions on appropriate target cells. In other situations the CSFs can be produced and act in quite localized regions. Unlike hormones, the CSFs are not the products of a single cell type and can, when needed, be produced by virtually any organ or cell type in the body
What is cation exchange chromatography?
Column of negatively charged beads Charged proteins pass through column, the positive proteins attach to beads, negative proteins pass through, negative proteins come out of column first, its a separation technique. Sodium ions are flooded through the column
Side effects of Isotretinoin?
Common: Completely dry skin (shuts down sebaceous glands) Completely dry eyes Very Dry Lips Extremely Teratogenic (damage developing babies and vitamin A in general) Uncommon: Associated with depression IBS IBD(inflammatory bowel disease) idiopathic intracranial hypertension Permanent Blindness
Sphingomyelins
Contain phosphocholine or phosphoethanolamine as their polar headgroup. Therefore, are classified along with glycerophospholipids as phospholipids. Sphingomyelins resemble phosphatidylcholines in their general properties and three-dimensional structure, and in having no net charge on their head groups. Where are sphingomyelins found? In the plasma membrane of animal cells and are especially prominent in myelin, a membranous sheath that surrounds and insulates the axons of some neurones - thus the name "sphingomyelins".
What are long terminal repeats?
Contained within the sequences at the ends of the retroviral genome, sequence that repeats hundreds/thousands of times, are powerful transcriptional promoter sequences termed long terminal repeats (LTRs). The LTRs promote the transcription of the viral DNA leading to the production of new virus particles.
Under what conditions are CpG islands not methylated?
CpG islands of Germ line tissues are unmethylated. CpG islands near promoters of normal somatic cells are unmethylated.
What is the purpose of cryopreservation. When is it best to cryopreserve cells?
Cryopreservation is a method whereby cells are frozen, maintaining their viability, until they are defrosted months or years later. Cells are cryopreserved to minimize genetic change and avoid loss through contamination. It is best to cryopreserve cells when they are at their optimal rate of growth.
What food should you cut out to reduce symptoms if you are suffering from crohn's disease?
Cut out yeast. But a lot of foods contain yeast that you wouldn't expect, like milk. So you need to substitute milk for soy milk, etc. S. cerevisiae cannot break down purines that accumulate in the intestinal tract and transition to another compound called uric acid. Uric acid exacerbates inflammation, which may worsen IBD symptoms.
What are the four classes of cyclins?
Cyclins can be divided into four classes based on their behavior in the cell cycle of vertebrate somatic cells and yeast cells: G1 cyclins, G1/S cyclins, S cyclins, and M cyclins. This division is useful when talking about most cell cycles, but it is not universal as some cyclins have different functions or timing in different cell types.
Where does the pathway for fatty acid synthesis occur?
Cytoplasm
Dehydroepiandrosterone (DHEA)
DHEA is produced in the adrenal glands, the gonads and the brain It functions as a metabolic intermediate in the biosynthesis of the androgen and estrogen sex steroids both in the gonads and in various other tissues. However, DHEA also has a variety of potential biological effects in its own right, binding to an array of nuclear and cell surface receptors, and acting as a neurosteroid and modulator of neurotrophic factor receptors DHEA and other adrenal androgens such as androstenedione, although relatively weak androgens, are responsible for the androgenic effects of adrenarche, such as early pubic and axillary hair growth, adult-type body odor, increased oiliness of hair and skin, and mild acne.
What is DMEM?
DMEM (Dulbecco's Modified Eagle's medium). DMEM contains approximately four times as much of the vitamins and amino acids present in the original formula and two to four times as much glucose. Additionally, it contains iron and phenol red. DMEM is suitable for most types of cells, including human, monkey, hamster, rat, mouse, chicken and fish[1] cells. The original DMEM formula contains 1000 mg/L of glucose and was first reported for culturing embryonic mouse cells. A further alteration with 4500 mg/L glucose has proved to be optimal for cultivation of certain cell types.
What is DMSO
DMSO may also be used as a cryoprotectant, added to cell media to reduce ice formation and thereby prevent cell death during the freezing process.[17] Approximately 10% may be used with a slow-freeze method, and the cells may be frozen at −80 °C (−112 °F) or stored in liquid nitrogen safely. Dimethyl sulfoxide
What is the name of the family of enzymes that control DNA methylation?
DNA MethylTransferases (DNMTs)
Give examples of the different processes that cause DNA damage
DNA alkylation. DNA depurination (hydrolysis to remove the nitrogenous base from deoxyribose) Gamma/UV irradiation Reaction with oxidative free radicals
What must occur after okazaki fragments are formed to form a continuous strand?
DNA ligase must ligate the fragments together.
What is the TET3 protein involved with?
DNA methylation reprogramming
What is DNA mismatch repair?
DNA mismatch repair is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage Utilises MutS, MutL and MutH proteins.
In what direction on the DNA does DNA polymerase move?
DNA polymerase only travels in 3-5 direction on existing strands. Imagine DNA being 'scanned' and 'cloned' in opposite direction, the 5-3 direction. Thus DNA only 'cloned' in 5-3 direction.
Tell me about the Repair Template of CRISPR
DNA that guides the cellular repair process allowing insertion of a specific DNA sequence
What is hemimethylation?
DNA-hemimethylation is when only one of two (complementary) strands is methylated. A hemi-methylated site is a single CpG that is methylated on one strand, but not on the other. (hemi means half)
Tell me about Dapsone's mechanism of action:
Dapsone inhibits bacterial synthesis of dihydrofolic acid
What do De novo DNMT enzymes do? What do Maintenance DNMTs do?
De novo DNMT enzymes initially attaches the methyl group to a DNA strand. Maintenance DNMTs copy the methylation from an existing DNA strand onto the complimentary strand after replication.
What are the two types of DNMT?
De novo DNMTs and Maintenance DNMTs. De novo methyltransferases recognize something in the DNA that allows them to newly methylate cytosines. These are expressed mainly in early embryo development and they set up the pattern of methylation. Maintenance methyltransferases add methylation to DNA when one strand is already methylated. These work throughout the life of the organism to maintain the methylation pattern that had been established by the de novo methyltransferases.
What is the first step common to all amino acids that occurs before amino acid degradation.
Deamination/Transamination occurs. Toxic ammonia is converted into non-toxic urea.
What happens in the first stage of PCR?
Denaturation: Temperature is 94°C, to break the H bonds between bases and separate the strands.
What does ninhydrin do?
Detects ammonia/amines producing a deep blue/purple colour
What is the Giemsa stain?
Detects intracellular pathogens (bacteria, fungi, protozoans)
Tell me about the variation of MHC proteins. Why is there variation of MHC proteins between people? And how does this affect organ transplants?
Different forms of MHC proteins are present in different people. This variation aids in the prevention of a widespread epidemic, since if all people had the same MHC proteins and a pathogen mutated to avoid being presented by MHC proteins, the entire population would be susceptible to the pathogen. This variation is also why a "match" is needed for a successful organ transplant. That is, rejections of transplanted organs by the immune system are often caused by too much variation in the MHC genotypes of the organ donor and acceptor. The hereditary nature of MHC structure reveals why immediate family members are the best candidates for an organ donor.
Na⁺ K⁺ P-type Pump Mechanism?
Differs from the SERCA mechanism. Na⁺ K⁺ ATPase is a co-transporter, that couples phosphorylation and dephosphorylation of the critical Asp residue to the simultaneous movement of both Na⁺ and K⁺ against their electrochemical gradients. For each molecule of ATP hydrolysed, 2 K⁺ moves in and 3 Na⁺ moves out. Co-transport is therefore electrogenic- it creates a net separation of charge across the membrane. The central role of the sodium-potassium ATPase is reflected in the energy investment in this single reaction: about 25% of the total energy consumption of a human at rest.
dimorphic fungus
Dimorphic fungi are fungi that can exist in the form of both mold and yeast. An example is Penicillium marneffei, a human pathogen that grows as a mold at room temperature, and as a yeast at human body temperature Picture: Candida albicans growing as yeast cells and filamentous (hypha) cells
Diphenhydramine
Diphenhydramine is an antihistamine mainly used to treat allergies.[6] It is also used for insomnia, symptoms of the common cold, tremor in parkinsonism, and nausea.[6] It is used by mouth, injection into a vein, and injection into a muscle.[6] Maximal effect is typically around two hours after a dose, and effects can last for up to seven hours.
Tell me about Diptheria
Diphtheria is an infection caused by the bacterium Corynebacterium diphtheriae.[1] Signs and symptoms may vary from mild to severe.[2] They usually start two to five days after exposure.[1] Symptoms often come on fairly gradually, beginning with a sore throat and fever.[2] In severe cases, a grey or white patch develops in the throat.[1][2] This can block the airway and create a barking cough as in croup.[2] The neck may swell in part due to large lymph nodes.[1] A form of diphtheria that involves the skin, eyes, or genitals also exists.[1][2] Complications may include myocarditis, inflammation of nerves, kidney problems, and bleeding problems due to low blood platelets. Myocarditis may result in an abnormal heart rate and inflammation of the nerves may result in paralysis.[1] Diphtheria is usually spread between people by direct contact or through the air.[1][5] It may also be spread by contaminated objects. Some people carry the bacteria without having symptoms, but can still spread the disease to others. The three main types of C. diphtheriae cause different severities of disease.[1] The symptoms are due to a toxin produced by the bacteria. Diagnosis can often be made based on the appearance of the throat with confirmation by microbiological culture. Previous infection may not prevent against future infection.[2] A diphtheria vaccine is effective for prevention
Tell me about Diptheria toxin
Diphtheria toxin is an exotoxin secreted by Corynebacterium diphtheriae, the pathogenic bacterium that causes diphtheria. Unusually, the toxin gene is encoded by a bacteriophage (a virus that infects bacteria).[1] The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis.
In cancer, what does histone methylase EZH2 recruit?
Dnmt3a and Dnmt3b
Shigella
Does not ferment lactose, don't make hydrogen sulfide. But produces a toxin that blocks ribosomes and protein synthesis, killing intestinal cells and causing bloody diarrhoea Can also invade intestinal mucosa via Peyer's patches. Use cipro to kill it
Tell me about dopamine
Dopamine (DA, contracted from 3,4-dihydroxyphenethylamine) is an organic chemical of the catecholamine and phenethylamine families that plays several important roles in the brain and body. It is an amine synthesized by removing a carboxyl group from a molecule of its precursor chemical L-DOPA, which is synthesized in the brain and kidneys. Dopamine is also synthesized in plants and most animals. It is implicated in parkinson disease. It is a neurotransmitter that controls movement, among other things
What happens to the brain, teeth, skin, liver, pancreas and heart when you eat sugar?
Dopamine and opioids are released in the brain. Rats on high sugar diets behave like drug addicts. Teeth - Bacteria like Streptococcus mutans eat leftover sugar in mouth and ferment it into lactic acid. This dissolves the minerals in tooth enamel. Skin - Glucose and fructose form bonds between amino acids that convert collagen and elastin into substances that cause wrinkles. Liver - Liver uses fructose to create fat via a process called lipogenesis. Too much sugar causes a build up of fat globules called non-alcoholic liver disease. Pancreas - Rising blood sugar levels stimulate beta cells to secrete insulin. This signals the liver and muscles to start converting glucose into glycogen for storage. Heart - High insulin levels in the blood cause smooth muscle cells around artery walls to grow faster. This raises blood pressure, eventually leading to heart disease.
Tell me about Dopamine receptors
Dopamine receptors are a class of G protein-coupled receptors that are prominent in the vertebrate central nervous system (CNS). The neurotransmitter dopamine is the primary endogenous ligand for dopamine receptors.
What is the purpose of EDTA in trypsin
EDTA + trypsin is a method for detaching cells. Trypsin cuts the adhesion proteins in cell-cell and cell-matrix interactions, and EDTA is a calcium chelator, which integrins needs to interact with other proteins for cell adhesion-- no calcium, no cell adhesion. And that's why EDTA treatment is gentler than trypsin.
What does Epidermal growth factor do?
EGF is a growth factor that stimulates cell growth, proliferation and differentiation by binding to its receptor EGFR.
What can ERKS do?
ERKS are kinases. ERKs can move into the nucleus of the cell and activate transcription factors that activate genes involved with cell division
Tell me about Eagle's minimal essential Medium
Eagle's minimal essential medium (EMEM) is a cell culture medium developed by Harry Eagle that can be used to maintain cells in tissue culture. It contains: amino acids salts (calcium chloride, potassium chloride, magnesium sulfate, sodium chloride, and monosodium phosphate) glucose vitamins (folic acid, nicotinamide, riboflavin, B12)
What is Egg Yolk Agar?
Egg Yolk Agar (EYA) is an enriched non-selective and differential medium for the presumptive identification of certain anaerobic isolates. Egg Yolk Agar medium contains a suspension of egg yolk for the presumptive identification of various Clostridium, Fusobacterium and Prevotella spp Used for the detection of lecithinase and lipase production
In molecular cloning, what is electroporation?What is transduction?
Electroporation uses high voltage electrical pulses to translocate DNA across the cell membrane (and cell wall, if present). In contrast, transduction involves the packaging of DNA into virus-derived particles, and using these virus-like particles to introduce the encapsulated DNA into the cell through a process resembling viral infection. Although electroporation and transduction are highly specialized methods, they may be the most efficient methods to move DNA into cells.
Ampicillin
Enhanced version of Penicillin that kills some gram negative bacteria. Can treat respiratory tract infections, urinary tract infections.
Pyruvate dehydrogenase complex consists of 3 distinct enzymes
Enzyme Complex 1 : Pyruvate Dehydrogenase. Cofactor is Thiamine Pyrophosphate Dihydrolipoyl Transacetylase has 2 cofactors: lipoic acid and coenzyme A Dihydrolipoyl Dehydrogenase has 2 cofactors: FAD and NAD
How to you detect global DNA methylation?
Enzyme Linked Immunosorbent Assay (ELISA) A 5-methylcytosine antibody can also be deployed in an ELISA-based technique to detect global DNA methylation in DNA samples. Wells in a microplate are treated to have high DNA affinity and the methylated fractions of the input DNA are detected using capture and detection antibodies, followed by an absorbance reading with a spectrophotometer.
Eosinophils
Eosinophils are a type of disease-fighting white blood cell. one of the immune system components responsible for combating multicellular parasites and certain infections in vertebrates Eosinophil counts rise during parasitic infections
What is epigenetic bookmarking?
Epigenetic bookmarking the name given to a proposed process that allows gene expression patterns to be faithfully passed to daughter cells through mitosis. Important cell-type specific genes are marked in some way that prevents them from being compacted during mitosis and ensures their rapid transcription.
Other names of epinephrine and norepinephrine?
Epinephrine is also known as adrenaline, norepinephrine is also known as noradrenaline
What is an epitope?
Epitope, or antigenic determinant, is a small, specific portion of an antigen recognized by the immune system such as antibodies. A single antigen usually has several different epitopes. The region on an antibody which recognizes the epitope is called a paratope. Antibodies fit precisely and bind to specific epitopes.
Which part of lysine often undergoes post-translational modification?
Epsilon amine group
What does NF-kB suppression cause?
Escape from immune recognition by natural killer cells.
What is executive function?
Executive functions (collectively referred to as executive function and cognitive control) are a set of cognitive processes that are necessary for the cognitive control of behavior: selecting and successfully monitoring behaviors that facilitate the attainment of chosen goals. Executive functions include basic cognitive processes such as attentional control, cognitive inhibition, inhibitory control, working memory, and cognitive flexibility.Higher order executive functions require the simultaneous use of multiple basic executive functions and include planning and fluid intelligence (i.e., reasoning and problem solving). Executive functions gradually develop and change across the lifespan of an individual and can be improved at any time over the course of a person's life. Similarly, these cognitive processes can be adversely affected by a variety of events which affect an individual
Tell me about the biosynthesis of GABA
Exogenous GABA does not penetrate the blood-brain barrier; it is synthesized in the brain. It is synthesized from glutamate using the enzyme glutamate decarboxylase (GAD) and pyridoxal phosphate (which is the active form of vitamin B6) as a cofactor. This process converts glutamate, the principal excitatory neurotransmitter, into the principal inhibitory neurotransmitter (GABA). GABA is converted back to glutamate by a metabolic pathway called the GABA shunt
What happens if a CpG island in the promoter region of a gene is methylated?
Expression of the gene is repressed
F-Type ATPase
F-type ATPase active transporters catalyze the uphill transmembrane passage of protons driver by ATP hydrolysis. The "F Type" designation derives from the identification of these ATPases as energy-coupling factors. The F₀ integral membrane protein complex (subscript ₀ denotes its inhibition by the drug oligomycin) provides transmembrane pathway for protons, and peripheral protein F₁ (subscript 1 indicating this was the first of several factors isolated from mitochondria) uses the energy of ATP to drive protons uphill (into a region of higher H⁺ concentration). The F₀F₁ organization of proton-pumping transporters must have developed very early in evolution. BECAUSE Bacteria such as E coli use an F₀F₁ ATPase complex, in their plasma membrane to pump protons outward, and archaea have a closely homologous proton pump, the A₀A₁ ATPase. Like all enzymes, F-type ATPases catalyze their reactions in both directions. Therefore, a sufficiently large proton gradient can supply the energy to drive the reverse reaction, ATP synthesis. When functioning in this direction, the F-type ATPases are more appropriately named ATP synthases. ATP synthases are central to ATP production in the mitochondria during oxidative phosphorylation and in chloroplasts during photophosphorylation, as well as in bacteria and archaea. The proton gradient needed to drive ATP synthesis is produced by other types of proton pumps powered by substrate oxidation( such as the different complexes in respiratory ETC oxidising NADH/FADH₂) or sunlight.
Which nucleotide cofactors are used to oxidise fatty acids?
FAD and NAD⁺ (which will be reduced when oxidising FA)
Tell me about fetal bovine serum
Fetal bovine serum (FBS) or fetal calf serum (spelled foetal in Commonwealth English) is the blood fraction remaining after the natural coagulation of blood, followed by centrifugation to remove any remaining red blood cells.[1] Fetal bovine serum comes from the blood drawn from a bovine fetus via a closed system of collection at the slaughterhouse. Fetal bovine serum is the most widely used serum-supplement for the in vitro cell culture of eukaryotic cells. This is due to it having a very low level of antibodies and containing more growth factors, allowing for versatility in many different cell culture applications. The globular protein, bovine serum albumin (BSA), is a major component of fetal bovine serum. The rich variety of proteins in fetal bovine serum maintains cultured cells in a medium in which they can survive, grow, and divide. FBS is not a fully defined media component, and as such may vary in composition between batches. As a result, some seek to develop serum-free alternatives as a matter of good laboratory practice.[2]
In molecular cloning, tell me about preparation of DNA to be cloned
For cloning of genomic DNA, the DNA to be cloned is extracted from the organism of interest. The DNA is then purified using simple methods to remove contaminating proteins (extraction with phenol), RNA (ribonuclease) and smaller molecules (precipitation and/or chromatography). Polymerase chain reaction (PCR) methods are often used for amplification of specific DNA or RNA (RT-PCR) sequences prior to molecular cloning. DNA for cloning experiments may also be obtained from RNA using reverse transcriptase (complementary DNA or cDNA cloning), or in the form of synthetic DNA (artificial gene synthesis). cDNA cloning is usually used to obtain clones representative of the mRNA population of the cells of interest, while synthetic DNA is used to obtain any precise sequence defined by the designer. The purified DNA is then treated with a restriction enzyme to generate fragments with ends capable of being linked to those of the vector. If necessary, short double-stranded segments of DNA (linkers) containing desired restriction sites may be added to create end structures that are compatible with the vector.
What research processes can PCR be used in?
Forensics Paternity/kinship testing Identification of human remains
Tell me about Fragile X syndrome
Fragile X Syndrome is a developmental disease that eventually causes mental retardation. This disease occurs when abnormal de novo methylation causes the repression of the FMR1 gene early in development. Abnormal de novo methylation is believed to be the cause of Fragile X syndrome due to the fact that inactivation of the FMR1 gene is observed to occur alongside a process known as H3K9me3 heterochromatinization. From these studies, scientists believe that the programming of all abnormal modifications may proceed through a single mechanism in which histone methylases mediate random DNA methylation and repression.
Why are free fatty acids harmful?
Free fatty acids can disorganise the membranes by acting as detergents. Fatty acid breakdown occurs in mitochondria, so it is v. possible that free fatty acids can interfere with the membrane .
What are GPCRs?
G-protein coupled receptors Have 7 transmembrane alpha helices There are two principal signal transduction pathways involving the G protein-coupled receptors: the cAMP signal pathway and the phosphatidylinositol signal pathway
How can one check the length of their PCR products?
Gel electrophoresis
In morphogen, what does the "gen" part mean?
Gen means creating something (generate)
Homeobox genes
Genes involved in development Direct the formation of limbs and organs along the anterior-posterior axis and regulate the process by which cells mature to carry out specific functions (differentiation). Some homeobox genes act as tumor suppressors. A homeobox is a DNA sequence, around 180 base pairs long encode homeodomain protein products that are transcription factors sharing a characteristic protein fold structure that binds DNA. Homeoprotein transcription factors typically switch on cascades of other genes
Tell me about Glucocorticoids
Glucocorticoids (GCs) are a class of corticosteroids, which are a class of steroid hormones. Glucocorticoids are corticosteroids that bind to the glucocorticoid receptor (GR),[1] that is present in almost every vertebrate animal cell. The name glucocorticoid (glucose + cortex + steroid) is composed from its role in regulation of glucose metabolism, synthesis in the adrenal cortex, and its steroidal structure (see structure to the right). GCs affect cells by binding to the glucocorticoid receptor (GR). The activated GR complex, in turn, up-regulates the expression of anti-inflammatory proteins in the nucleus (a process known as transactivation) and represses the expression of proinflammatory proteins in the cytosol by preventing the translocation of other transcription factors from the cytosol into the nucleus (transrepression).
Pentose Phosphate Pathway
Glucose 6-phosphate can have other catabolic fates other than being oxidised to pyruvate. For example, the oxidation of glucose 6-phosphate to pentose phosphates by the pentose phosphate pathway. In this oxidative pathway, NADP⁺ is the electron acceptor yielding NADPH. Rapidly dividing cells, such as those of bone marrow, skin and intestinal mucosa, and those of tumors, use the pentose ribose 5-phosphate to make RNA, DNA and coenzymes such as ATP, NADH, FADH₂, and coenzyme A. In other tissues, the essential product of the pentose phosphate pathway is not the pentoses but the electron donor NADPH, needed for reductive biosynthesis or to counter the damaging effects of oxygen radicals(how? maybe electrons from NADPH are used to neutralise the radical by giving electrons and reducing it to a more stable compound). Tissues that carry out extensive fatty acid synthesis(liver, adipose, lactating mammary gland) or very active synthesis of cholesterol and steroid hormones(liver, adrenal glands, gonads) require NADPH provided by this pathway. Erythrocytes and the cells of the lens and cornea are directly exposed to oxygen and thus to the damaging free radicals generated by oxygen. By maintaining a reducing atmosphere (a high ratio of NADPH to NADP⁺) and a high ratio of reduced to oxidized glutathione), such cells can prevent or undo oxidative damage to proteins, lipids and other sensitive molecules. In erythrocytes, the NADPH produced by the pentose phosphate pathway is so important in preventing oxidative damage that a genetic defect in glucose 6-phosphate dehydrogenase, the first enzyme of the pathway, can have serious medical consequences.
Tell me about glycine as a co-agonist. Tell me about glycine's therapeutic uses.
Glycine is a required co-agonist along with glutamate for NMDA receptors. In contrast to the inhibitory role of glycine in the spinal cord, this behaviour is facilitated at the (NMDA) glutamatergic receptors which are excitatory. The LD50 of glycine is 7930 mg/kg in rats (oral), and it usually causes death by hyperexcitability. A 2014 review on sleep aids noted that glycine can improve sleep quality, citing a study in which 3 grams of glycine before bedtime improved sleep quality in humans. Glycine has also been positively tested as an add-on treatment for schizophrenia.
What is a graded potential? What causes a graded potential? Where do graded potentials tend to form?
Graded potentials are changes in membrane potential that vary in size, as opposed to being all-or-none. They arise from the summation of the individual actions of ligand-gated ion channel proteins, and decrease over time and space. They do not typically involve voltage-gated sodium and potassium channels. These impulses are incremental and may be excitatory or inhibitory. They occur at the postsynaptic dendrite as a result of presynaptic neuron firing and release of neurotransmitter, or may occur in skeletal, smooth, or cardiac muscle in response to nerve input. The magnitude of a graded potential is determined by the strength of the stimulus. Purpose of graded potentials : my reasoning double check: Its more useful to allow the heart to beat at multiple BPMs, allowing the most efficient BPM at the right time. You don't only want the heart to beat fast or slow, you want a gradient.
Tell me about rickettsia rickttsii
Gram negative Weil-Felix Reaction Egg Yolk Culture Giemsa Stain Treat with doxycycline
Why doesn't penicillin work against gram negative bacteria?
Gram negative bacteria have an ADDITIONAL membrane on the outside of the cell wall, which prevents penicillin from coming in. Thus penicillin doesn't work on gram negatives.
clostridium difficile
Gram positive check patients faeces for its toxins can cause diarrhoea, especially if you use a lot of antibiotics resistant to a lot of antibiotics, but can use metronidazole or vancomycin
Listeria monocytogenes
Gram positive Grows well at cold temperatures Beta hemolytic Catalase-positive causes septic shock
enterococcus
Gram positive can cause UTIs, nitrite negative in urinalysis have developed resistance by using different subunits for their cell walls. So vancomycin doesn't work on them . So you can use linezolid non-hemolytic ampicillin used to treat
Are lysozymes more effective at killing Gram positive or Gram negative bacteria? Why?
Gram positive. Although Gram-negative bacteria do have thin cell walls made of peptidoglycan, their cell walls are largely protected by the outer membrane, limiting the effects of lysozyme. Gram-positive bacteria have thick layers of peptidoglycan and lack an outer membrane, making their cell walls most vulnerable to lysozyme.
Gram Positive
Gram-positive bacteria take up the crystal violet stain used in the test, and then appear to be purple-coloured when seen through a microscope. Characterisitics: Teichoic acids and lipoids are present, forming lipoteichoic acids, which serve as chelating agents, and also for certain types of adherence. Peptidoglycan chains are cross-linked to form rigid cell walls by a bacterial enzyme DD-transpeptidase.
Tell me about Propionibacterium acnes characteristics
Gram-positive rod aerotolerant anaerobic
Granulocytes
Granulocytes are a category of white blood cells characterized by the presence of granules in their cytoplasm nucleus is normally lobed into 3 segments neutrophils are the most common granulocyte eosinophils, basophils, and mast cells are other types of granulocytes
What are granzymes
Granzymes are serine proteases that are released by cytoplasmic granules within cytotoxic T cells and natural killer (NK) cells. They induce programmed cell death in the target cell, thus eliminating cells that have become cancerous or are infected with viruses or bacteria. The granzymes also kill bacteria and inhibit viral replication
What is Gullain Barr Syndrome
Guillain-Barré syndrome (GBS) is a rapid-onset muscle weakness caused by the immune system damaging the peripheral nervous system. The initial symptoms are typically changes in sensation or pain along with muscle weakness, beginning in the feet and hands. This often spreads to the arms and upper body with both sides being involved. The symptoms develop over hours to a few weeks. During the acute phase, the disorder can be life-threatening with about 15% developing weakness of the breathing muscles requiring mechanical ventilation. Some are affected by changes in the function of the autonomic nervous system, which can lead to dangerous abnormalities in heart rate and blood pressure.
Tell me about H2A variants. How and where do H2A variants differ from each other?
H2A has the most variants, so has the widest array of diversity for nucleosome composition. H2A variants differ from each other mostly at their C-terminus which is responsible for intra-nucleosome binding and DNA binding. The acidic patch is also altered between variants, which is involved in higher order chromatin organization.
Tell me about H2B
H2B forms a (H2A-H2B)-2 tetramer. This tetramer and it's component dimers are easily exchanged in and out of the nucleosome compared to H3 and H4, meaning that modifications on H2A and H2B are less likely to be maintained in chromatin.
Tell me about H3K9
H3K9 can both: turn on genes by getting acetylated, and silence them when methylated. H3K9ac is a particularly important acetylation: it is highly correlated with active promoters. H3K9ac also has a high co-occurrence with H3K14ac and H3K4me3 which together are these three marks are the hallmark of active gene promoters
Tell me about Histone H4K5 function
H4K5 is the closest lysine residue to the N-terminal tail of histone H4. Histone H4 forms a strong tetramer with histone H3. Like histone H3, H4 has a long N-terminal tail that is subject to various acetylations and methylations that are associated with many cellular processes. H4 has much less sequence variation than the other histones across species; it seem to be structurally restrained by evolution likely due to important function H4K5 has not been shown to be methylated, there is only data on its acetylation. Like all acetylations, H4K5ac is catalyzed by several enzymes, including Tip60 and CBP/p300 proteins in mammals H4K5ac has also been implicated in epigenetic bookmarking. Epigenetic bookmarking the name given to a proposed process that allows gene expression patterns to be faithfully passed to daughter cells through mitosis. Important cell-type specific genes are marked in some way that prevents them from being compacted during mitosis and ensures their rapid transcription. H4K5ac has been implicated as one such mark (Zhao et al., 2011). Zhao et al. found that transcriptional activity during interphase causes acetylation of H4K5 and H4K12 which are passed through mitosis. These marks then recruit BRD4 which de-compacts the local chromatin environment and permits transcriptional activation. Similarly, other papers have found that H4K5ac can serve as a primer for rapid transcription in other contexts. H4K5ac appears to prime activity-dependent genes expressed during learning (Park et al., 2013). The mark may permit the rapid expression of certain genes required during the learning process.
Tell me about Histone H4K8
H4K8 is another lysine on that tail of histone H4 that doesn't get a lot of attention. Like the others in this group, it is only known to be acetylated, it has not been shown to be methylated as of yet. This group of lysines are known to act as transcriptional activators. These lysines are also an excellent example of the histone code hypothesis in action.
What is HIRA?
HIRA is a histone chaperone. In particular HIRA has been linked to to transcription activation and is known to have an evolutionarily conserved role in heterochromatin formation. The specific function of this protein has yet to be determined; however, it has been speculated to play a role in transcriptional regulation and/or chromatin and histone metabolism.
Tell me about histamine
Histamine is an organic nitrogenous compound involved in local immune responses as well as regulating physiological function in the gut and acting as a neurotransmitter for the brain, spinal cord and uterus. Histamine is involved in the inflammatory response and has a central role as a mediator of pruritus. As part of an immune response to foreign pathogens, histamine is produced by basophils and by mast cells found in nearby connective tissues. Histamine increases the permeability of the capillaries to white blood cells and some proteins, to allow them to engage pathogens in the infected tissues.
How is histamine synthesized?
Histamine is derived from the decarboxylation of the amino acid histidine, a reaction catalyzed by the enzyme L-histidine decarboxylase. It is a hydrophilic vasoactive amine.
Which 4 amino acids contain aromatic rings?
Histidine Tryptophan Tyrosine Phenylalanine
List the 4 core histones
Histones H2A, H2B, H3 and H4 are known as the core histones, and they come together to form one nucleosome.
Basics: What are Histones?
Histones are proteins that condense and structure the DNA of eukaryotic cell nuclei into units called nucleosomes. Their main functions are to compact DNA and regulate chromatin, therefore impacting gene regulation.
What are Homeobox genes?
Homeobox genes are a large family of similar genes that direct the formation of many body structures during early embryonic development.
Homology Directed Repair
Homology directed repair (HDR) is a mechanism in cells to repair double strand DNA lesions. The most common form of HDR is homologous recombination. The HDR mechanism can only be used by the cell when there is a homologue piece of DNA present in the nucleus, mostly in G2 and S phase of the cell cycle. Other examples of homology-directed repair include single-strand annealing and breakage-induced replication
Tell me about HSP90
Hsp90 (heat shock protein 90) is a chaperone protein that assists other proteins to fold properly, stabilizes proteins against heat stress, and aids in protein degradation. It also stabilizes a number of proteins required for tumor growth, which is why Hsp90 inhibitors are investigated as anti-cancer drugs.
How E6 and E7 contribute to tumorigenesis?
Human Papilloma Virus expresses 2 proteins (E6 and E7) --> inhibitors of p53 and Rb E6: triggers p53 degradation E7: triggers Rb degradation
What causes cervical cancer?
Human papilloma virus (HPV)
Tell me about the Amplification step in SOLiD sequencing
Hybridization to beads Adapter allows fragments to bind to a bead PCR occurs, so there are now millions of copies of beads on each bead. Centrifugation of the beads separate beads with and without DNA fragments attached. Beads with DNA fragments attach to a polystyrene bead. This decreases its density. So when centrifuged, these beads will remain on top.
What is the fundamental problem that causes acne?
Hyperkeratinization. Skin cells don't shed away properly. Hyperkeratinzation causes blockage of the pore, causing sebum to fill up and swell up. This causes propioni Bacterium acnes to proliferate rapidly, causing an infection and an immune response.
Give an example of an imprinted gene
IGF2 IGF2 allele is expressed when inherited from the father, but not expressed when it is inherited from the mother.
Interleukin 13
IL-13 nterleukin-13 is a central regulator in IgE synthesis, goblet cell hyperplasia, mucus hypersecretion, airway hyperresponsiveness, fibrosis and chitinase up-regulation. It is a mediator of allergic inflammation and different diseases including asthma
What do you know about the permeability of the inner mitochondrial membrane to: NADH ATP Pyruvate
IMM is impermeable to NADH IMM is impermeable to ATP IMM is permeable to Pyruvate
When does p53 go to the nucleus, and what happens when it goes to the nucleus?
If the cell is stressed or there is something wrong, then p53 is passed to the nucleus where is dimerizes and eventually tetramerizes to act as a transcription factor.
What is IgE?
Immunoglobulin E (IgE) is a type of antibody that has only been found in mammals. IgE is synthesised by plasma cells. IgE's main function is immunity to parasites such as helminths like Schistosoma mansoni, Trichinella spiralis, and Fasciola hepatica
Tell me about the Biosynthesis of Serotonin
In animals including humans, serotonin is synthesized from the amino acid L-tryptophan by a short metabolic pathway consisting of three enzymes: tryptophan hydroxylase (TPH), aromatic amino acid decarboxylase (DDC) and pyridoxal phosphate. The TPH-mediated reaction is the rate-limiting step in the pathway. TPH has been shown to exist in two forms: TPH1, found in several tissues, and TPH2, which is a neuron-specific isoform. Serotonin can be synthesized from tryptophan in the lab using Aspergillus niger and Psilocybe coprophila as catalysts. The first phase to 5-hydroxytryptophan would require letting tryptophan sit in ethanol and water for 7 days, then mixing in enough HCl (or other acid) to bring the pH to 3, and then adding NaOH to make a pH of 13 for 1 hour. Asperigillus niger would be the catalyst for this first phase. The second phase to synthesizing tryptophan itself from the 5-hydroxytryptophan intermediate would require adding ethanol and water, and letting sit for 30 days this time. The next two steps would be the same as the first phase: adding HCl to make the pH = 3, and then adding NaOH to make the pH very basic at 13 for 1 hour. This phase uses the Psilocybe coprophila as the catalyst for the reaction
What are sulfonamide antibiotics?
In bacteria, antibacterial sulfonamides act as competitive inhibitors of the enzyme dihydropteroate synthase (DHPS), an enzyme involved in folate synthesis. Sulfonamides are therefore bacteriostatic and inhibit growth and multiplication of bacteria, but do not kill them. Humans, in contrast to bacteria, acquire folate (vitamin B9) through the diet. Structural similarity between sulfonamide (left) and PABA (center) is the basis for the inhibitory activity of sulfa drugs on tetrahydrofolate(right) biosynthesis
What is beta oxidation?
In biochemistry and metabolism, beta-oxidation is the catabolic process by which fatty acid molecules are broken down in the cytosol in prokaryotes and in the mitochondria in eukaryotes to generate acetyl-CoA, which enters the citric acid cycle, and NADH and FADH2, which are co-enzymes used in the electron transport chain. It is named as such because the beta carbon of the fatty acid undergoes oxidation to a carbonyl group. Beta-oxidation is primarily facilitated by the mitochondrial trifunctional protein, an enzyme complex associated with the inner mitochondrial membrane, although some fatty acids are oxidized in peroxisomes. Beta oxidation also generates large amounts of water which is essential for animals such as camels that often have limited access to water.
What is confluency
In cell culture biology, confluence is the term commonly used as an estimate of the number of adherent cells in a culture dish or a flask, referring to the proportion of the surface which is covered by cells. For example, 50 percent confluence means roughly half of the surface is covered and there is still room for cells to grow. 100 percent confluence means the surface is completely covered by the cells, and no more room is left for the cells to grow as a monolayer.
Draw the Thioester functional group. How do you form a Thioester? And give an example of a thioester derivative in biochemistry.
In chemistry thioesters are compounds with the functional group R-S-CO-R'. They are the product of esterification between a carboxylic acid and a thiol. In biochemistry, the best-known thioesters are derivatives of coenzyme A, e.g., acetyl-CoA.
Tell me about pyrophosphate
In chemistry, a pyrophosphate is a phosphorus oxyanion. Compounds such as salts and esters are also called pyrophosphates. The group is also called diphosphate or dipolyphosphate, although this should not be confused with phosphates. As a food additive, diphosphates are known as E450. A number of hydrogen pyrophosphates also exist, such as Na2H2P2O7, as well as the normal pyrophosphates.
Tell me about de novo methylation pattern
In de novo methylation, the polycomb complex (PRC2) targets genes that, under normal conditions, have unmethylated CpG island promoters. These genes are repressed due to the methylation of H3K27. Methylation of H3K27 is mediated by the histone methylase EZH2. The methylated H3K27 then binds to the chromodomain-containing complex (PRC1), thereby giving rise to a type of heterochromatin. During normal development, targeted de novo methylation can take place at certain sites on DNA. Similarly, it can occur abnormally in cancer. The explanation offered for this phenomenon suggests that the histone methylase EZH2 recruits Dnmt3a and Dnmt3b. Some studies show that the polycomb complex PRC2 may be released from the methylated islands. This event results in a more stabilized form of methylation-mediated repression, which occurs instead of the flexible polycomb repression mechanism. Alterations to DNA methylation patterns play a major role in the onset of cancer. In fact, all tumors that have been studied exhibit changes in DNA methylation. Early studies seem to suggest that widespread demethylation is characteristic of cancer. Many believe that de novo methylation is a completely random process. This theory helps to explain the presence of methylated tumor suppressor genes in some cancer types. However, more recent research reveal DNA methylation in cancer to involve hundreds of CpG islands that are methylated in a more pre-determined way. Under the older theory, it is believed that DNA methylation causes genes to become inactivated. In contrast, the newer theory revealed that the genes targeted for methylation have already been inactive. Many of these targeted genes have a polycomb complex nearby, which may explain how the methylases are recruited to carry out the gene modification. Thus, the newer theory based on programmed methylation suggests that de novo methylation in cancer occurs on gene sites that were targeted regardless of whether the genes are active or inactive. The target sites are also independent of whether the genes affect tumorigenesis. Nonetheless, studies on human colon cancer reveal the possibility that DNA methylation can cause a more permanent repression mechanism than that of the normally flexible polycomb repression mechanism; this observation links DNA methylation to tumorigenesis.
Sometimes, methylation is not EXCLUSIVE to CpG sites in Human DNA? Under what conditions can you observe a large amount of 5-methyl cytosine that isn't part of a CpG site?
In embryonic stem cells. There is a substantial amount of 5-methylcytosine outside the CpG context. Differential DNA methylation of pluripotence-associated genes such as Nanog and Oct4/Pou5f1 has been observed between pluripotent and differentiated cells.
How many classes are there of RNA polymerase in eukaryotic cells? What is the difference in fucntion between these polymerases?
In eukaryotic cells there are three distinct classes of RNA polymerase, RNA polymerase (pol) I, II and III. Each polymerase is responsible for the synthesis of a different class of RNA.
Negatives of Telomerase expression?
In mice with higher levels of telomerase, it was discovered they also had a higher rate of cancer which therefore led to a shorter lifespan. In addition, telomerase favours tumorigenesis. Telomerase fosters cancer development by allowing uncontrolled cell growth which eventually proliferates into tumors. In fact, Telomerase activity has been observed in approximately 90% of all human tumors which suggests that the uncontrolled growth of a cell as conveyed by Telomerase has a key role in cancer.
Where does fatty acid breakdown occur?
In mitochondria.
Tell me about association cortex
In the brain, the site of higher mental activities; 95% of the cerebral cortex of humans is association cortex
Tell me how GABA causes hyperpolarization
In vertebrates, GABA acts at inhibitory synapses in the brain by binding to specific transmembrane receptors in the plasma membrane of both pre- and postsynaptic neuronal processes. This binding causes the opening of ion channels to allow the flow of either negatively charged chloride ions into the cell or positively charged potassium ions out of the cell. This action results in a negative change in the transmembrane potential, usually causing hyperpolarization.
During senescence what happens to chromatin?
Increase in methylation (silences genes) & Histones are modified by deacetylation which creates unique regions in chromatin called Senescence-associated heterochromatin foci (SAHF)
Give examples of drugs that have known to extend the lifespan of mice
Indeed, several drugs, including rapamycin, acarbose, 17α-estradiol and nordihydroguaiaretic acid (NDGA) have been shown to extend the lifespan of mice by the National Institute on Aging Interventions Testing Program8, 9 and metformin will be tested in a clinical trial for its ability to delay onset of multiple age-related diseasesff
Tell me some pro-survival pathways in cells
Indeed, using a bioinformatics approach, we recently identified several pro-survival pathways, including the Bcl-2/Bcl-XL, p53/p21, PI3K/AKT, and serpine anti-apoptotic pathways that, when inhibited, result in death of senescent murine and human cells.
What does IL-6 do?
Inflammatory: attract immune cells. together with the increased expression of immune cell-interacting molecules on senescent cells, can lead to immune surveillance and subsequent elimination of senescent cells, leading to tumor regression. IL-6 is an important mediator of fever and of the acute phase response. It is capable of crossing the blood-brain barrier and initiating synthesis of PGE2 in the hypothalamus, thereby changing the body's temperature setpoint. acts in an autocrine feedback loop to reinforce senescence growth arrest
Tell me about Pyruvate Dehydrogenase E1 complex
Initially, pyruvate and thiamine pyrophosphate (TPP or vitamin B1) are bound by pyruvate dehydrogenase subunits. The thiazolium ring of TPP is in a zwitterionic form, and the anionic C2 carbon performs a nucleophilic attack on the C2 (ketone) carbonyl of pyruvate. The resulting hemithioacetal undergoes decarboxylation to produce an acyl anion equivalent (see cyanohydrin or aldehyde-dithiane umpolung chemistry, as well as benzoin condensation). This anion attacks S1 of an oxidized lipoate species that is attached to a lysine residue. In a ring-opening SN2-like mechanism, S2 is displaced as a sulfide or sulfhydryl moiety. Subsequent collapse of the tetrahedral hemithioacetal ejects thiazole, releasing the TPP cofactor and generating a thioacetate on S1 of lipoate. The E1-catalyzed process is the rate-limiting step of the whole pyruvate dehydrogenase complex.
How do you initiate bacterial replication?
Initiating bacterial DNA replication involves 4 key proteins: DnaA (the initiator), DnaB (the helicase), DnaC (the loader) and DnaG (the primase). DnaA forms a complex with ATP and binds the 9bp high affinity binding sites (R1-R5) in the OriC (Fig 5 and 6). This partially unwinds the DNA in the region of the DUE (grey oval Fig 5). A DnaB hexamer is then loaded onto each strand of unwound DNA by a hexamer of DnaC proteins (Fig 6). DnaG is recruited to, and binds, DnaB forming a complex sometimes referred to as the 'primosome', and marking the end of the initiation phase of DNA replication.
What hormonally activates and inhibits Acetyl-CoA carboxylase?
Insulin activates ACC Glucagon inhibits ACC
Tell me about fisetin and piperlongumine
Interestingly, the natural compounds fisetin, a quercetin-related flavonoid, and piperlongumine also have senolytic activity in certain cell types in culture
How are hemiacetals and hemiketals formed?
Intramolecular alcohols spontaneously react with intramolecular aldehydes and ketones
Give examples of DNA sequences that are difficult to clone
Inverted repeats, origins of replication, centimeters and telomeres
What does Arsenate do in glycolysis?
It acts as an uncoupler of the oxidation and phosphorylation stages when converting triose phosphate to 1,3diphosphoglycerate and converting 1,3diphosphoglycerate to 3-phosphoglycerate. It can replace a phosphate which it closely resembles, to form a very unstable intermediate incapable of phosphorylating ADP. Arsenate can replace inorganic phosphate in the step of glycolysis that produces 1,3-bisphosphoglycerate from glyceraldehyde 3-phosphate. This yields 1-arseno-3-phosphoglycerate instead, which is unstable and quickly hydrolyzes, forming the next intermediate in the pathway, 3-phosphoglycerate. Therefore, glycolysis proceeds, but the ATP molecule that would be generated from 1,3-bisphosphoglycerate is lost - arsenate is an uncoupler of glycolysis, explaining its toxicity. As with other arsenic compounds, arsenate can also inhibit the conversion of pyruvate into acetyl-CoA, blocking the Krebs cycle and therefore resulting in further loss of ATP.
How does Antimycin A work?
It blocks the transfer of electrons between cytochromes Antimycin A binds to the Qi site of cytochrome c reductase, inhibiting the oxidation of ubiquinone in the Qi site of ubiquinol thereby disrupting the Q-cycle of enzyme turn over. The inhibition of this reaction disrupts the formation of the proton gradient across the inner membrane of the mitochondria. The production of ATP is subsequently inhibited, as protons are unable to flow through the ATP synthase complex in the absence of a proton gradient.
Tell me what you know about mitochondrial DNA
It carries the genes for the synthesis of many but not all mitchondrial proteins. The DNA is loosely coiled and is very prone to mutation by oxidation, leading to decrease in mitochondrial efficiency and may be a contributory factor in cell ageing.
What reaction does acetyl-CoA carboxylase catalyse?
It catalyses the conversion of acetyl-Coa to Malonyl-CoA
What reaction does malonyl transacylase catalyse?
It catalyses the transfer of a malonate group from malonyl CoA onto the ACP domain. ACP domain is highly specific for malonyl CoA and helps prepare for elongation of the fatty acid chain.
What does Aldolase do?
It cleaves fructose 1,6 bisphosphate into 3-phosphoglyceraldehyde and dihydroxy-acetone phosphate.
Why is sucrose not a reducing sugar?
It does not have an OH bond bonded to a carbon that is bonded to an O. So the ring structure cannot open and you can't get an aldehyde when the molecule tautomerizes.
Tell me about Heterochromatin Protein 1
It doesn't take a PhD is biochemistry to guess what heterochromatin protein 1 (HP1) does. HP1 is a family of three proteins that are vital for the formation of transcriptionally inactive heterochromatin.
Tigecycline
It exhibits bacteriostatic activity by binding to the 30S ribosomal subunit of bacteria and thereby blocking the interaction of aminoacyl-tRNA with the A site of the ribosome
Prostaglandin E2
It has important effects in labour (softening the cervix and causing uterine contraction) and also stimulates osteoblasts to release factors that stimulate bone resorption by osteoclasts. PGE2 is also the prostaglandin that ultimately induces fever. It is also implicated in duct-dependent congenital heart diseases and is used in infusion in order to open the duct although PGE1 is more commonly used. It is a direct vasodilator, relaxing smooth muscles, and it inhibits the release of noradrenaline from sympathetic nerve terminals. It does not inhibit platelet aggregation, where PGI2 does. PGE2 also suppresses T cell receptor signaling and may play a role in resolution of inflammation. Up-regulation of PGE2 has been implicated as a possible cause of nail clubbing. Furthermore, its postpartal synthesis in newborns is considered as one cause of patent ductus arteriosus Mechanism of Action: PGE2 is a potent activator of the Wnt signaling pathway. It has been implicated in regulating the developmental specification and regeneration of hematopoietic stem cells through cAMP/PKA activity.
How does the protein modification change the p53 protein?
It increases half life of p53 protein, from 20 minutes to hours, increasing concentration of p53. also the ability of the p53 protein to bind to specific DNA sequences and promote the transcription of genes regulated by those DNA sequences is enhanced
What does p14ARF do?
It inhibits hdm2.
What does Mg 2+ do in PCR?
It is a Co-factor (helper) for Taq polymerase
Homocysteine?
It is a homologue of the amino acid cysteine, differing by an additional methylene bridge (-CH2-). It is biosynthesized from methionine by the removal of its terminal Cε methyl group. Homocysteine can be recycled into methionine or converted into cysteine with the aid of certain B-vitamins.
What does NF-kB do in senescence?
It is a master regulator of the SASP, and influences more genes than pRB and p53 combined.
what does MDM-2 do?
It is a negative regulator of p53 tumour suppressor. It is an inhibitor of p53 transcriptional activation.
Alpha-synuclein
It is abundant in the brain while smaller amounts are found in the heart, muscles, and other tissues. In the brain, alpha-synuclein is found mainly at the tips of nerve cells (neurons) in specialized structures called presynaptic terminals. Within these structures, alpha-synuclein interacts with phospholipids and proteins Although the function of alpha-synuclein is not well understood, studies suggest that it plays a role in maintaining a supply of synaptic vesicles in presynaptic terminals by clustering synaptic vesicles.
What does DNA glycosylase do? 2 Main classes of DNA glycosylase
It is involved in base excision repair. Breaks the n-glycosidic bond creating an apurinic or apyrimidinic site. There are two main classes of glycosylases: monofunctional and bifunctional. Monofunctional glycosylases have only glycosylase activity, whereas bifunctional glycosylases also possess AP lyase activity that permits them to cut the phosphodiester bond of DNA, creating a single-strand break without the need for an AP endonuclease.
What is acylthioesterase a part of? What are the different types of acylthioesterase and what do they do?
It is part of the Fatty acid synthetase complex. The long chain acylthioesterase is part of the fatty acid synthetase complex and cleaves off FA chain lengths longer that C16. The medium chain acylthioesterase cleaves off the growing FA chain at or before it reaches C16.
Why is a primer needed?
It is required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA.
What is PEG used for?
It is used to fuse two different cell types. Most often B-Cells and Myelomas to create hybridomas.
How does a water molecule binding to the zinc change the pka of water?
It makes the pka smaller because, positively charged zinc is more stabilised by a negatively charged hydroxyl, rather than neutral water. (The strong positive charge is dampened).
Give some characteristics of NF-kB.
It regulates inflammation. It is tumor suppressive.
What does succinate dehydrogenase do?
It transfers electrons from succinate to coenzyme Q
Why is propionibacterium acnes called that way?
It was named after its ability to generate propionic acid (propanoic acid)
What was the first application of PCR?
It was used to diagnose sickle cell anemia.
Why is L-DOPA used to increase dopamine concentrations in the treatment of Parkinson's disease and dopamine-responsive dystonia?
L-DOPA crosses the protective blood-brain barrier, whereas dopamine itself cannot.
Tell me about L-DOPA
L-DOPA is an amino acid that is made and used as part of the normal biology of humans, some animals and plants. Some animals and humans make it via biosynthesis from the amino acid L-tyrosine and tyrosine hydroxylase. L-DOPA is the precursor to the neurotransmitters dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline) collectively known as catecholamines. Furthermore, L-DOPA itself mediates neurotrophic factor release by the brain and CNS. L-DOPA can be manufactured and in its pure form is sold as a psychoactive drug As a drug, it is used in the clinical treatment of Parkinson's disease and dopamine-responsive dystonia. Dopamine is formed by the decarboxylation of L-DOPA by aromatic L-amino acid decarboxylase (AADC).
What are the naturally occurring α-amino acids often referred to as?
L-amino acids
Mechanism for the SERCA P-type Pump?
Large conformational changes Phosphorylation and Dephosphorylation of the critical Asp residue in the P domain, that occurs during a catalytic cycle. For the SERCA pump, each catalytic cycle moves two Ca²⁺ ions across the membrane and converts an ATP to ADP and Pi. ATP has 2 roles in this mechanism, one catalytic and one modulatory (ATP is a catalyst??? So its regenerated? No, I don't think so. I think it just causes the reaction to happen). The role of ATP binding and phosphoryl transfer to the enzyme is to bring about the inter-conversion of two conformations (E1 and E2) of the transporter. In the E1 conformation, the Ca²⁺-binding sites are exposed on the cytosolic side of the ER or the sarcoplasmic reticulum and bind Ca²⁺ with high affinity(sucks up Ca²⁺ from cytosolic easily). ATP binding and Asp phosphorylation drive a conformational change from E1 to E2 in which the Ca²⁺ binding sites are now exposed on the lumenal side of the membrane and their affinity for Ca²⁺ is greatly reduced. (Maybe the two binding sites were always there, but you can just "open" and "close" them on the luminal/cytoplasmic side, depending on the E1 and E2 conformation) By this mechanism, the energy released by ATP hydrolysis during one phosphorylation-dephosphorylation cycle drives Ca²⁺ across the membrane against a large electrochemical gradient.
What are the characteristic features of senescent cells?
Large, flat morphology, increase in senescence-associated ß galactosidase (enzyme) activity change in chromatin organisation (senescence-associated heterochromatin foci (SAHF))
Tell me about leukocyte esterase
Leukocyte esterase (LE) is an esterase (a type of enzyme) produced by leukocytes (white blood cells). A leukocyte esterase test (LE test) is a urine test for the presence of white blood cells and other abnormalities associated with infection. White blood cells in the urine usually indicate a urinary tract infection (UTI). Positive test results are clinically significant. The LE test is also used to screen for gonorrhea and for amniotic fluid infections. The combination of the LE test with the urinary nitrite test provides an excellent screen for establishing the presence of a UTI. Urine test strips (dipsticks) can screen for both. A urine sample that tests positive for both nitrite and leukocyte esterase should be cultured for pathogenic bacteria.
What are Lewy bodies
Lewy bodies are abnormal aggregates of protein that develop inside nerve cells, contributing to Parkinson's disease (PD), the Lewy body dementias (Parkinson's disease dementia and dementia with Lewy bodies), and some other disorders. A classical Lewy body is an eosinophilic cytoplasmic inclusion consisting of a dense core surrounded by a halo of 10-nm-wide radiating fibrils, the primary structural component of which is alpha-synuclein. A Lewy body is composed of the protein alpha-synuclein associated with other proteins, such as ubiquitin, neurofilament protein, and alpha B crystallin. Tau proteins may also be present, and Lewy bodies may occasionally be surrounded by neurofibrillary tangles. Lewy bodies and neurofibrillary tangles can occasionally exist in the same neuron, particularly in the amygdala
What are ionotropic receptors
Ligand-gated ion channels, also commonly referred as ionotropic receptors, are a group of transmembrane ion channel proteins which open to allow ions such as Na+, K+, Ca2+, and/or Cl− to pass through the membrane in response to the binding of a chemical messenger (i.e. a ligand), such as a neurotransmitter.
Androgens and inflammation
Low grade inflammation is connected with the hormonal changes occuring with ageing Testosterone has been found capable of reducing systemic inflammatory cytokines such as tumor necrosis factor-α, interleukin-6, and interleukin-1β and stimulating the antiinflammatory cytokine interleukin-10 However, in premenopausal and older women, high testosterone and estradiol and low sex hormone-binding globulin levels are associated with insulin resistance and diabetes, conditions characterized by low-grade inflammation Thus, age-related changes in sex hormones contribute to the development of a proinflammatory state. Hormonal changes and their potential effects on inflammation may, in part, affect conditions, such as atherosclerosis, cardiovascular diseases, metabolic syndrome, and type 2 diabetes. Although the role of sex hormones on aging and age-related diseases is still unclear, there are clear age associations, which are likely reducing healthy aging and negatively impacting longevity
lymphadenopathy
Lymphadenopathy or adenopathy is disease of the lymph nodes, in which they are abnormal in size, number, or consistency. Lymphadenopathy of an inflammatory type (the most common type) is lymphadenitis, producing swollen or enlarged lymph nodes This symptom is present in syphillis
In H3K4, what does the K stand for?
Lysine
What are maturation-promoting factors?
MPFs activate other proteins through phosphorylation. These phosphorylated proteins, in turn, are responsible for specific events during cycle division such as microtubule formation and chromatin remodeling. MPFs are cyclin-cdk complexes. It stimulates the mitotic and meiotic phases of the cell cycle. MPF promotes the entrance into mitosis (the M phase) from the G2 phase by phosphorylating multiple proteins needed during mitosis. MPF is composed of: 1) Cyclin-dependent kinase 1 2) Cyclin, a regulatory subunit. The mitotic cyclins can be grouped as cyclins A & B. These cyclins have a nine residue sequence in the N-terminal region called the "destruction box", which can be recognized by the ubiquitin ligase enzyme which destroys the cyclins when appropriate.
What is MHC?
Major Histocompatability complex is a group of genes that code for proteins found on the surfaces of cells that help the immune system recognize foreign substances. MHC proteins are found in all higher vertebrates. In human beings the complex is also called the human leukocyte antigen (HLA) system. MHC encodes a protein that can basically present an antigen fragment to other cells (such as T cells), which will then take an appropriate action depending on what fragment is being presented.
Describe how Maxam-Gilbert sequencing works.
Maxam-Gilbert sequencing requires radioactive labeling at one 5′ end of the DNA fragment to be sequenced (typically by a kinase reaction using gamma-32P ATP) and purification of the DNA. Chemical treatment generates breaks at a small proportion of one or two of the four nucleotide bases in each of four reactions (G, A+G, C, C+T). For example, the purines (A+G) are depurinated using formic acid, the guanines (and to some extent the adenines) are methylated by dimethyl sulfate, and the pyrimidines (C+T) are hydrolysed using hydrazine. The addition of salt (sodium chloride) to the hydrazine reaction inhibits the reaction of thymine for the C-only reaction. The modified DNAs may then be cleaved by hot piperidine; (CH2)5NH at the position of the modified base. The concentration of the modifying chemicals is controlled to introduce on average one modification per DNA molecule. Thus a series of labeled fragments is generated, from the radiolabeled end to the first "cut" site in each molecule. Visualise the fragments with fluorescence or autoradiography
Why do 1/3 of all catalytic enzymes contain bound metal ions?
Metal ions are reactive due to their strong positive charge Metal ions can form relatively strong bonds, but these bonds are also kinetically labile. Some metal ions are stable in more than 1 oxidation state.
Tell me about methemoglobin
Methemoglobin (English: methaemoglobin) (pronounced "met-hemoglobin") is a form of the oxygen-carrying metalloprotein hemoglobin, in which the iron in the heme group is in the Fe3+ (ferric) state, not the Fe2+ (ferrous) of normal hemoglobin. Methemoglobin cannot bind oxygen, unlike oxyhemoglobin.[2] It is bluish chocolate-brown in color. In human blood a trace amount of methemoglobin is normally produced spontaneously, but when present in excess the blood becomes abnormally dark bluish brown. The NADH-dependent enzyme methemoglobin reductase (diaphorase I) is responsible for converting methemoglobin back to hemoglobin. Normally one to two percent of a person's hemoglobin is methemoglobin; a higher percentage than this can be genetic or caused by exposure to various chemicals and depending on the level can cause health problems known as methemoglobinemia. A higher level of methemoglobin will tend to cause a pulse oximeter to read closer to 85% regardless of the true level of oxygen saturation.
Tell me about methylphenidate
Methylphenidate (MPH) is a stimulant that is used to treat attention-deficit hyperactivity disorder (ADHD). MPH is known to be highly abused by the general population, especially college students. In an online poll conducted by Nature magazine, 12.4% of 1400 corresponding readers admitted use of MPH for non-medical reasons. Their reasoning behind its use was for increasing concentration, sleep deficit, and jetlag. Studies involving this drug oppose each other, some saying it improves performance, others say it actually impairs performance. Further studies need to be conducted, looking at different doses of MPH
Tell me about Modafinil
Modafinil is a wakefulness-promoting drug that decreases fatigue, increases vigilance, reduces daytime sleepiness, and improves mood.Modafinil is currently licensed for treating patients with disorders such as narcolepsy, sleep apnea, and shift work sleep disorder. This drug also seems promising in the treatment of depression and bipolar disorder. Modafinil is currently being used by United States Air Force personnel for missions of great duration in an attempt to decrease fatigue amongst aircrew.
Tell me about screening for clones with desired DNA inserts and biological properties in molecular cloning
Modern bacterial cloning vectors (e.g. pUC19 and later derivatives including the pGEM vectors) use the blue-white screening system to distinguish colonies (clones) of transgenic cells from those that contain the parental vector (i.e. vector DNA with no recombinant sequence inserted). In these vectors, foreign DNA is inserted into a sequence that encodes an essential part of beta-galactosidase, an enzyme whose activity results in formation of a blue-colored colony on the culture medium that is used for this work. Insertion of the foreign DNA into the beta-galactosidase coding sequence disables the function of the enzyme, so that colonies containing transformed DNA remain colorless (white). Therefore, experimentalists are easily able to identify and conduct further studies on transgenic bacterial clones, while ignoring those that do not contain recombinant DNA. The total population of individual clones obtained in a molecular cloning experiment is often termed a DNA library. Libraries may be highly complex (as when cloning complete genomic DNA from an organism) or relatively simple (as when moving a previously cloned DNA fragment into a different plasmid), but it is almost always necessary to examine a number of different clones to be sure that the desired DNA construct is obtained. This may be accomplished through a very wide range of experimental methods, including the use of nucleic acid hybridizations, antibody probes, polymerase chain reaction, restriction fragment analysis and/or DNA sequencing.
Tell me about Origin of replication in prokaryotes
Most bacteria have a single circular molecule of DNA, and typically only a single origin of replication per circular chromosome. DUE(DNA unwinding Element) contains 3AT rich sequences, 5 9bp regions (R1-R5) that act as recognition sites, and several GATC nucleotide sequences. GATC repeats are targets for Dam methylase mediated methylation, which serves as the regulator for DNA replication Most archaea have a single circular molecule of DNA, and several origins of replication along this circular chromosome
How is histamine stored and when is it released?
Most histamine in the body is generated in granules in mast cells and in white blood cells (leukocytes) called basophils. Mast cells are especially numerous at sites of potential injury — the nose, mouth, and feet, internal body surfaces, and blood vessels. Non-mast cell histamine is found in several tissues, including the brain, where it functions as a neurotransmitter. Another important site of histamine storage and release is the enterochromaffin-like (ECL) cell of the stomach. The most important pathophysiologic mechanism of mast cell and basophil histamine release is immunologic. These cells, if sensitized by IgE antibodies attached to their membranes, degranulate when exposed to the appropriate antigen. Certain amines and alkaloids, including such drugs as morphine, and curare alkaloids, can displace histamine in granules and cause its release. Antibiotics like polymyxin are also found to stimulate histamine release. Histamine release occurs when allergens bind to mast-cell-bound IgE antibodies. Reduction of IgE overproduction may lower the likelihood of allergens finding sufficient free IgE to trigger a mast-cell-release of histamine.
Tell me about Non-homologous end joining
NHEJ is a pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homology directed repair, which requires a homologous sequence to guide repair.
How has Cas9 been simplified by researchers
Native Cas9 requires a guide RNA composed of two disparate RNAs that associate to make the guide - the CRISPR RNA and the trans-activating RNA. Cas9 targeting has been simplified through the engineering of a chimeric single guide RNA.
Why is DNA negatively charged?
Negative charges repel each other, meaning DNA is straight when denaturalised, allows transcription to work
What is negative control?
Negative controls are groups where no phenomenon is expected. They ensure that there is no effect when there should be no effect.
Neisseria
Neisseria is a large genus of bacteria that colonize the mucosal surfaces of many animals. Of the 11 species that colonize humans, only two are pathogens, N. meningitidis and N. gonorrhoeae. Neisseria species are Gram-negative bacteria included among the proteobacteria, a large group of Gram-negative forms.
What are Neurotrophic Factors
Neurotrophic factors (NTFs) are a family of biomolecules - nearly all of which are peptides or small proteins - that support the growth, survival, and differentiation of both developing and mature neurons. Most NTFs exert their trophic effects on neurons by signaling through tyrosine kinases, usually a receptor tyrosine kinase. In the mature nervous system, they promote neuronal survival, induce synaptic plasticity, and modulate the formation of long-term memories. Neurotrophic factors also promote the initial growth and development of neurons in the central nervous system and peripheral nervous system and that they are capable of regrowing damaged neurons in test tubes and animal models. Some neurotrophic factors are also released by the target tissue in order to guide the growth of developing axons. Most neurotrophic factors belong to one of three families: (1) neurotrophins, (2) glial cell-line derived neurotrophic factor family ligands (GFLs), and (3) neuropoietic cytokines. Each family has its own distinct cell signaling mechanisms, although the cellular responses elicited often do overlap. Currently, neurotrophic factors are being intensely studied for use in bioartificial nerve conduits because they are necessary in vivo for directing axon growth and regeneration.Currently, neurotrophic factors are being intensely studied for use in bioartificial nerve conduits because they are necessary in vivo for directing axon growth and regeneration.
What is the effect of lysozymes against viruses?
No effect, as they do not contain peptidoglycan.
Give the approximate equilibrium potentials of K⁺ Na⁺ and Cl⁻. What do you notice about the equilibrium potential for Cl⁻ and why is this the case
Notice that the equilibrium potential for Cl- is near the resting membrane potential of the cell. This is because no ATP energy is being expended to keep it out of equilibrium. For this reason, the resting membrane potential of a cell will cause the concentration of Cl- inside the cell to remain at a much lower level so that the concentration gradient (inward) and electrical potential difference (outward) have equal and opposite effects. Thus, if the membrane potential is at the equilibrium potential for a specific ion, there is no net tendency for that ion to move in or out of the cell. But what if the membrane potential is not at the equilibrium potential for a specific ion, and there are open ion channels that will allow the ion to cross? In that case, the ion will tend to move across the membrane.
Which four "common" ingredients are in a PCR bead?
Nucleotides (dNTPs) Taq polymerase Buffer Mg 2+
What is the most abundant monounsaturated fatty acid in the body?
Oleic acid
What enzyme converts L-DOPA to dopamine once it has entered the central nervous system?
Once L-DOPA has entered the central nervous system, it is converted into dopamine by the enzyme aromatic L-amino acid decarboxylase, also known as DOPA decarboxylase.
Once eaten, what is α-linolenic acid converted into?
Once eaten, the body converts ALA to EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid), the two types of omega-3 fatty acids more readily used by the body
What are endorphins?
One of a group of small neuropeptides produced by the vertebrate brian, like morphine, endorphins modulate pain perception
Tell me about the hippocampus
One of the major components of the limbic system, along with the amygdala and hypothalamus. Humans and other mammals have two hippocampuses, one in each side of the brain. The hippocampus plays important roles in the consolidation of information from short-term memory to long-term memory, and in spatial memory that enables navigation. The hippocampus is located under the cerebral cortex.
Tell me about the amygdala
One of the major components of the limbic system. Along with the hippocampus and hypothalamus
Daptomycin
One of the most powerful antibiotics against resistant gram positives, but not effective for pneumonia
Tell me about the pons
One of the subdivisions of the hindbrain
Tell me about the medulla oblongata
One of the three components of the brain stem in humans, coordinates the autonomic nervous system.
What is the hindbrain?
One of the three main parts of the vertebrate brain, the hindbrain (rhombencephalon) in humans is the cerebellum, which plays an important role in coordination of movement and body position
What is the midbrain
One of the three main parts of the vertebrate brain; the midbrain (mesencephalon) is part of the brain stem in humans
What would have to happen to the EGFR for uncontrolled cell division to occur?
Overexpression of tyrosine kinase receptors can also lead to cancer of epithelial cells (ie, breast, ovarian, rectal) if a cell expresses too many receptors, the excess receptors may stimulate growth at inappropriatea times. Drugs and antibodies have been developed that can bind to these overexpressed receptors, thereby deavtivating their activity. Herceptin is one such drug that targets tyrosine kinase receptors called Her2 that are overexpressed in many breast cancer patients.
Which toxin does Pseudomonas Aeruginosa release?
P. aeruginosa uses the virulence factor exotoxin A to inactivate eukaryotic elongation factor 2 via ADP-ribosylation in the host cell, much as the diphtheria toxin does. Without elongation factor 2, eukaryotic cells cannot synthesize proteins and necrotise. The release of intracellular contents induces an immunologic response in immunocompetent patients. In addition P. aeruginosa uses an exoenzyme, ExoU, which degrades the plasma membrane of eukaryotic cells, leading to lysis. Increasingly, it is becoming recognized that the iron-acquiring siderophore, pyoverdine, also functions as a toxin by removing iron from mitochondria, inflicting damage on this organelle.
What is the purpose of the p53 pathway?
P53 allows the cell to temporarily stop cell division. so any damage to DNA can be repaired. If damage is irreversible by cell's standards, p53 is left permanently active and may lead to senescence or apoptosis. The negative effects from intrinsic or extrinsic stresses that lead to inaccurate DNA replication or genome instability. are mitigated. They ensure that the cell cannot divide to pass on these genetic defects. So this reduces occurrence of cancer in cell cycle populations.
How does p53 change microenvironment?
P53 pathway leads to secretion of proteins that change microenvironment. They can change extra-cellular matrix and encourage angiogenesis. mutant p53 proteins are able to (i) alter the secretion of enzymes involved in the modulation of extracellular matrix components; (ii) alter the secretion of inflammatory cytokines; (iii) increase the extracellular acidification; and (iv) regulate the crosstalk between cancer and stromal cells.
What are penicillin binding proteins?
PBPs are DD-transpeptidases. Penicillin-binding proteins (PBPs) are a group of proteins that are characterized by their affinity for and binding of penicillin. They are a normal constituent of many bacteria; the name just reflects the way by which the protein was discovered. All β-lactam antibiotics (except for tabtoxinine-β-lactam, which inhibits glutamine synthetase) bind to PBPs, which are essential for bacterial cell wall synthesis. PBPs are members of a subgroup of enzymes called transpeptidases.
Give examples of viruses with DNA genomes
Papilloma and adenovirus
Pepstatin
Pepstatin is a potent inhibitor of aspartyl proteases. It is a hexa-peptide containing the unusual amino acid statine (Sta, (3S,4S)-4-amino-3-hydroxy-6-methylheptanoic acid), having the sequence Isovaleryl-Val-Val-Sta-Ala-Sta (Iva-Val-Val-Sta-Ala-Sta). It was originally isolated from cultures of various species of Actinomyces due to its ability to inhibit pepsin at picomolar concentrations. Pepstatin A is well known to be an inhibitor of aspartic proteinases such as pepsin, cathepsins D and E. Except for its role as a proteinase inhibitor, however, the pharmacological action of pepstatin A upon cells remain unclear. Pepstatin A suppresses receptor activator of NF-κB ligand (RANKL)-induced osteoclast differentiation. Pepstatin A suppresses the formation of multinuclear osteoclasts dose-dependently. This inhibition of the formation only affected osteoclast cells, i.e., not osteoblast-like cells. Furthermore, pepstatin A also suppresses differentiation from pre-osteoclast cells to mononuclear osteoclast cells dose-dependently. This inhibition seems to be independent of the activities of proteinases such as cathepsin D, because the formation of osteoclasts was not suppressed with the concentration that inhibited the activity of cathepsin D. Cell signaling analysis indicated that the phosphorylation of ERK was inhibited in pepstatin A-treated cells, while the phosphorylation of IκB and Akt showed almost no change. Furthermore, pepstatin A decreased the expression of nuclear factor of activated T cells c1 (NFATc1). These results suggest that pepstatin A suppresses the differentiation of osteoclasts through the blockade of ERK signaling and the inhibition of NFATc1 expression.
Which part of the bacteria do lysoymes degrade?
Peptidoglycan
What is phosphatidylcholine?
Phosphatidylcholines (PC) are a class of phospholipids that incorporate choline as a headgroup. (picture is 1-Oleoyl-2-palmitoyl-phosphatidylcholine)
What is Phosphopantetheine?
Phosphopantetheine is an essential prosthetic group of acyl carrier protein (ACP) and peptidyl carrier proteins (PCP) and aryl carrier proteins (ArCP) derived from Coenzyme A Phosphopantetheine fulfills two demands. 1) First, the intermediates remain covalently linked to the synthases (or synthetases) in an energy-rich thiol ester linkage. 2) Second, the flexibility and length of phosphopantetheine chain (approximately 2 nm) allows the covalently tethered intermediates to have access to spatially distinct enzyme active sites. Phosphopantetheine is found is Fatty acid synthase
Tell me about polyadenylation
Polyadenylation is the addition of a poly(A) tail to a messenger RNA. The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In eukaryotes, polyadenylation is part of the process that produces mature messenger RNA (mRNA) for translation. It, therefore, forms part of the larger process of gene expression. The process of polyadenylation begins as the transcription of a gene terminates. The 3'-most segment of the newly made pre-mRNA is first cleaved off by a set of proteins; these proteins then synthesize the poly(A) tail at the RNA's 3' end. In some genes these proteins add a poly(A) tail at one of several possible sites. Therefore, polyadenylation can produce more than one transcript from a single gene (alternative polyadenylation), similar to alternative splicing. Polyadenylation is important for nuclear export.
What are polyketides?
Polyketides are a class of secondary metabolites produced by certain living organisms in order to impart to them some survival advantage. Many mycotoxins produced by fungi are polyketides Polyketides are usually biosynthesized through the decarboxylative condensation of malonyl-CoA derived extender units in a similar process to fatty acid synthesis (a Claisen condensation). The polyketide chains produced by a minimal polyketide synthase are often further derivatized and modified into bioactive natural products. Polyketides are structurally a very diverse family of natural products with diverse biological activities and pharmacological properties. They are broadly divided into three classes: type I polyketides (often macrolides produced by multimodular megasynthases), type II polyketides (often aromatic molecules produced by the iterative action of dissociated enzymes), and type III polyketides (often small aromatic molecules produced by fungal species). Polyketide antibiotics, antifungals, cytostatics, anticholesteremic, antiparasitics, coccidiostats, animal growth promoters and natural insecticides are in commercial use Erythromycin is a polyketide
What does PCR stand for?
Polymerase Chain Reaction
Tell me about pooled lentiviral CRISPR libraries
Pooled lentiviral CRISPR libraries (heretofore referred to as CRISPR libraries) are a heterogenous population of lentiviral transfer vectors, each containing an individual gRNA targeting a single gene in a given genome. Guide RNAs are designed in silico and synthesized (see A in figure to the right), then cloned in a pooled format into lentiviral transfer vectors B. CRISPR libraries have been designed for most of the common CRISPR applications including genetic knock-out and activation or repression for both human and mouse genes. Although each library is different, there are several features that are common across most CRISPR libraries. Each library typically contains ∼3-6 gRNAs per gene to ensure modification of every target gene. Libraries can target anywhere from a single class of genes up to every gene in the genome. Thus, CRISPR libraries contain thousands of unique gRNAs targeting a wide variety of genes. Guide RNA design for CRISPR libraries follows the same general principles as designing a gRNA for a specific target. Target sequences must be unique compared to the rest of the genome and be located just upstream of a PAM sequence. Obviously, the exact region of the gene to be targeted may vary depending on the specific application (5′ constitutively expressed exons for knock-out libraries, or the promoter region for activation and repression libraries). For some libraries, Cas9 (or Cas9 derivative) is included on the gRNA-containing plasmid; for others, they must be delivered to the cells separately. NGS is next generation sequencing. NGS is used because previous generations are too slow at sequencing, not practical to be used in the experiment.
What is a positive control
Positive controls are groups where a phenomenon is expected. They ensure that there is an effect when there should be an effect, by using an experimental treatment that is already known to produce that effect
Tell me about the selectivity filter of potassium ion channels
Potassium ion channels remove the hydration shell from the ion when it enters the selectivity filter. The selectivity filter is formed by a five residue sequence, TVGYG, termed the signature sequence, within each of the four subunits. This signature sequence is within a loop between the pore helix and TM2/6, historically termed the P-loop. This signature sequence is highly conserved, with the exception that a valine residue in prokaryotic potassium channels is often substituted with an isoleucine residue in eukaryotic channels. This sequence adopts a unique main chain structure, structurally analogous to a nest protein structural motif. The four sets of electronegative carbonyl oxygen atoms are aligned toward the center of the filter pore and form a square anti-prism similar to a water-solvating shell around each potassium binding site. The distance between the carbonyl oxygens and potassium ions in the binding sites of the selectivity filter is the same as between water oxygens in the first hydration shell and a potassium ion in water solution, providing an energetically-favorable route for de-solvation of the ions. The selectivity filter opens towards the extracellular solution, exposing four carbonyl oxygens in a glycine residue (Gly79 in KcsA). The next residue toward the extracellular side of the protein is the negatively charged Asp80 (KcsA). This residue together with the five filter residues form the pore that connects the water-filled cavity in the center of the protein with the extracellular solution.
What is Prader-Willi syndrome?
Prader-Willi syndrome (PWS) is a genetic disorder due to loss of function of specific genes. In newborns symptoms include weak muscles, poor feeding, and slow development. In childhood the person becomes constantly hungry which often leads to obesity and type 2 diabetes. There is also typically mild to moderate intellectual impairment and behavioral problems. Often the forehead is narrow, hands and feet small, height short, skin light in color, and those affected are unable to have children. About 70% of cases occur when part of the father's chromosome 15 is deleted. In another 25% of cases the person has two copies of chromosome 15 from their mother and none from their father. As parts of the chromosome from the mother are turned off they end up with no working copies of certain genes. PWS is not generally inherited but instead the genetic changes happen during the formation of the egg, sperm, or in early development. There are no known risk factors. Those who have one child with PWS have less than a 1% chance of the next child being affected.
Which parts of the brain are responsible for the ability of executive function?
Prefrontal cortex plays a major role, however, it is still under debate, which parts of the brain are essential for executive function. Probably the frontal lobes need to participate in basically all of the executive functions, but it is not the only brain structure involved.
Propiospinal
Propriospinal tracts are collections of nerve fibers, ascending, descending, crossed and uncrossed, that interconnect various levels of the spinal cord. They are located in the white columns of the spinal cord where the columns meet the spinal central gray. Shorter fibers are located closer and longer fibers farther from the gray.
Tell me about the 3 types of vaccines
Purified antigen vaccines, sometimes called subunit vaccines,composed small fragments of molecules purified directly from the pathogen that generates a "protective" immune response. These molecules can be proteins, polysaccharides or exotoxins (i.e. bacterial proteins either chemically inactivated or attenuated (derived from mutated organisms) to prevent toxicity in the host.) Example: Vaccines against causative agents of meningitis in children Recombinant antigen vaccines are immunogenic proteins produced by genetic engineering. DNA encoding for an immunogenic protein of a pathogen can be inserted into either bacteria, yeast, viruses which infect mammalian cells, or by transfection of mammalian cells. The cells will then produce the protein endogenously and the protein can be harvested. Example: surface protein of Hepatitis B virus (HBsAg) Synthetic Antigen Vaccines are peptide antigens synthesized by automated machines. Synthetic polynucleotide technology also exists while synthetic polysaccharide technology is still under development. Which sequences to choose requires knowledge of the conformational structures for B cell epitopes (sequential v. assembled) and of the anchor residues of MHC for T cell epitopes. Computer algorithms are available to assist in selection, but trial-and-error approach is still required. Other aids include the generation of "protective" monoclonal Abs (B cell epitopes & phage-display libraries) and the peptide-dependent restimulation of T cells from convalescent subjects (T cell epitopes).
Tell me about Quiescence in regards to organismal cloning
Quiescence: "The state in which all but the most basic functions of a cell or group of cells has stopped. This is usually a response to an unfavourable environment, such as one in which the food supply is low or absent. The cell becomes dormant until its surroundings are more favourable. In this state the genes that define the specialist function of a cell "switch off" making the cell suitable for nuclear transfer."
RPR
Rapid plasma reagin. a type of rapid diagnostic test that looks for non-specific antibodies in the blood of the patient that may indicate a syphilis infection.
Name a way that the EGF signal transduction pathway malfunctions involving Ras
Ras gene that codes for Ras protein is mutated. Ras gene codes for Ras protein in EGF pathway is most commonly mutated gene that leads to tumor growth of epithelial epidermal cells. The mutation is the Ras gene produces a Ras protein that is incapable of ATPase activity, which means it cannot turn itself off. Therefore it will continue cell division. (GTP is on position. No ATPase means cannot convert GTP to GDP, which is the "off" position.
Where is carbonic anhydrase II found in relatively high concentrations?
Red Blood Cells
What does entero mean?
Relating to the intestine
What is renin?
Renin (etymology and pronunciation), also known as an angiotensinogenase, is a protein and enzyme secreted by the kidneys that participates in the body's renin-angiotensin aldosterone system (RAAS)—also known as the renin-angiotensin-aldosterone axis—that mediates extracellular volume (i.e., that of the blood plasma, lymph and interstitial fluid), and arterial vasoconstriction. Thus, it regulates the body's mean arterial blood pressure. Renin can be referred to as a hormone even though it has no peripheral receptors and rather has an enzymatic activity with which it hydrolyzes angiotensinogen to angiotensin I. Renin activates the renin-angiotensin system by cleaving angiotensinogen, produced by the liver, to yield angiotensin I, which is further converted into angiotensin II by ACE, the angiotensin-converting enzyme primarily within the capillaries of the lungs. Angiotensin II then constricts blood vessels, increases the secretion of ADH and aldosterone, and stimulates the hypothalamus to activate the thirst reflex, each leading to an increase in blood pressure. Renin's primary function is therefore to eventually cause an increase in blood pressure, leading to restoration of perfusion pressure in the kidneys.
Tell me the basics of ribonuclease
Ribonuclease (commonly abbreviated RNase) is a type of nuclease that catalyzes the degradation of RNA into smaller components. Ribonucleases can be divided into endoribonucleases and exoribonucleases, and comprise several sub-classes within the EC 2.7 (for the phosphorolytic enzymes) and 3.1 (for the hydrolytic enzymes) classes of enzymes.
Tell me about RPMI medium
Roswell Park Memorial Institute medium, commonly referred to as RPMI medium, is a form of medium used in cell culture and tissue culture. It has traditionally been used for growth of human lymphocytes. This medium contains a great deal of phosphate and is formulated for use in a 5% carbon dioxide atmosphere. RPMI 1640 has traditionally been used for the serum-free expansion of human lymphoid cells. RPMI 1640 uses a bicarbonate buffering system and differs from most mammalian cell culture media in its typical pH 8 formulation. Properly supplemented with serum or an adequate serum replacement, RPMI 1640 allows the cultivation of many cell types, especially human T/B-lymphocytes, bone marrow cells, and hybridoma cells. There are a variety of similar media in the RPMI series, such as RPMI 1640.
Identify the six hallmarks of cancer cells.
Self-sufficiency in growth signals (Ras, Her1/2, c-Fos, c-Mys) Insensitivity to antigrowth signals (Rb, p53, BRCA1/2) Evading apoptosis Limitless replicative potential Sustained angiogenesis Metastasis/Tissue invasion
What factors induce senescence?
Senescence also can be induced by cellular stress, including oxidative and genotoxic stresses, or by activation of certain oncogenes
What happens if NF-kB suppression and p53 inactivation occurs?
Senescence can be bypassed.
Tell me about serotonin
Serotonin or 5-hydroxytryptamine (5-HT) is a monoamine neurotransmitter. Biochemically derived from tryptophan, serotonin is primarily found in the gastrointestinal tract (GI tract), blood platelets, and the central nervous system (CNS) of animals, including humans. It is popularly thought to be a contributor to feelings of well-being and happiness. Approximately 90% of the human body's total serotonin is located in the enterochromaffin cells in the GI tract, where it is used to regulate intestinal movements. The serotonin is secreted luminally and basolaterally which leads to increased serotonin uptake by circulating platelets and activation after stimulation, which gives increased stimulation of myenteric neurons and gastrointestinal motility.[13] The remainder is synthesized in serotonergic neurons of the CNS, where it has various functions. These include the regulation of mood, appetite, and sleep. Serotonin also has some cognitive functions, including memory and learning. Modulation of serotonin at synapses is thought to be a major action of several classes of pharmacological antidepressants.
Tell me about taking serotonin orally.
Serotonin taken orally does not pass into the serotonergic pathways of the central nervous system, because it does not cross the blood-brain barrier.[124] However, tryptophan and its metabolite 5-hydroxytryptophan (5-HTP), from which serotonin is synthesized, does cross the blood-brain barrier. These agents are available as dietary supplements, and may be effective serotonergic agents. One product of serotonin breakdown is 5-hydroxyindoleacetic acid (5-HIAA), which is excreted in the urine.
Tell me the four categories of Artificial media
Serum containing media Fetal bovine serum is the most common supplement in animal cell culture media. It is used as a low-cost supplement to provide an optimal culture medium. Serum provides carriers or chelators for labile or water-insoluble nutrients, hormones and growth factors, protease inhibitors, and binds and neutralizes toxic moieties. Serum-free media Presence of serum in the media has many drawbacks and can lead to serious misinterpretations in immunological studies . A number of serum-free media have been developed . These media are generally specifically formulated to support the culture of a single cell type and incorporate defined quantities of purified growth factors, lipoproteins, and other proteins, which are otherwise usually provided by the serum . These media are also referred to as 'defined culture media' since the components in these media are known Chemically defined media These media contain contamination-free ultra pure inorganic and organic ingredients, and may also contain pure protein additives, like growth factors. Their constituents are produced in bacteria or yeast by genetic engineering with the addition of vitamins, cholesterol, specific amino acids, and fatty acids. Protein-free media Protein-free media do not contain any protein and only contain non-protein constituents. Compared to serum-supplemented media, use of protein-free media promotes superior cell growth and protein expression and facilitates downstream purification of any expressed product. Formulations like MEM, RPMI-1640 are protein-free and protein supplement is provided when required.
Bordetella Pertussis
Short rod Gram negative Bordet Gengou media Causes Pertussis or Whooping Cough
What is signal transduction?
Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalysed by protein kinases, which ultimately results in a cellular response.
What is Sir2?
Silent information regulator 2 has been found to aid in the process of silencing rRNA genes and telomeres. As yeast age (Sir2 are found in yeast), this ability is weakened.
What is SV40?
Simian vacuolating virus 40
Tell me about sgRNA of CRISPR
Single guide RNAs are a combined RNA consisting of a tracrRNA and at least one crRNA
Tell me about rapamycin
Sirolimus, also known as rapamycin, is a macrolide compound that is used to coat coronary stents, prevent organ transplant rejection and to treat a rare lung disease called lymphangioleiomyomatosis. It has immunosuppressant functions in humans and is especially useful in preventing the rejection of kidney transplants. It inhibits activation of T cells and B cells by reducing the production of interleukin-2 (IL-2). It is produced by the bacterium Streptomyces hygroscopicus and was isolated for the first time in 1972 by Surendra Nath Sehgal and colleagues from samples of Streptomyces hygroscopicus found on Easter Island. The compound was originally named rapamycin after the native name of the island, Rapa Nui. Sirolimus was initially developed as an antifungal agent. However, this use was abandoned when it was discovered to have potent immunosuppressive and antiproliferative properties due to its ability to inhibit mTOR.[medical citation needed] It was approved by the US Food and Drug Administration in September 1999 and is marketed under the trade name Rapamune by Pfizer (formerly by Wyeth).
what is snRNA?
Small nuclear ribonucleic acid (snRNA), also commonly referred to as U-RNA, is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcribed by either RNA polymerase II or RNA polymerase III,. Their primary function is in the processing of pre-messenger RNA (hnRNA) in the nucleus. They make up the spliceosome.
Tell me about spinal nerves
Spinal nerves connect the spinal cord to sense organs, muscles and glands in the body. Pairs of spinal nerves leave the spinal cord and emerge between each pair of adjacent vertebrae (see diagram 14.9). The sciatic nerve is the largest spinal nerve in the body (see diagram 14.5). It leaves the spinal cord as several nerves that join to form a flat band of nervous tissue. It passes down the thigh towards the hind leg where it gives off branches to the various muscles of this limb.
What are "lesion studies"?
Studies that look at the effects of a damaged part of the brain on overall brain functioning.
Tetracycline
Tetracycline inhibits protein synthesis by blocking the attachment of charged aminoacyl-tRNA to the A site on the ribosome. Tetracycline binds to the 30S subunit of microbial ribosomes. Thus, it prevents introduction of new amino acids to the nascent peptide chain.[20] The action is usually inhibitory and reversible upon withdrawal of the drug. Mammalian cells are less vulnerable to the effect of tetracyclines, despite the fact that tetracycline binds to the small ribosomal subunit of both prokaryotes and eukaryotes (30S and 40S, respectively). This is because bacteria actively pump tetracycline into their cytoplasm, even against a concentration gradient, whereas mammalian cells do not. This accounts for the relatively small off-site effect of tetracycline on human cells
Tell me the 3 central steps of HDR
The 5'-ended DNA strand is resected at the break to create a 3' overhang. This will serve as both a substrate for proteins required for strand invasion and a primer for DNA repair synthesis. The invasive strand can then displace one strand of the homologous DNA duplex and pair with the other; this results in the formation of the hybrid DNA referred to as the displacement loop (D loop). The recombination intermediates can then be resolved to complete the DNA repair process.
What are the two ways by which foreign proteins can be processed and recognized as being "nonself"?
The MHC proteins act as "signposts" that show fragmented pieces of an antigen on the host cell's surface. These antigens can be either self or nonself. If they are nonself, there are two ways by which the foreign protein can be processed and recognized as being "nonself." The first method is when the phagocytic cells, such as macrophages, neutrophils, and monocytes, degrade foreign particles that are engulfed during a process known as phagocytosis. Degraded particles are then presented on MHC class II molecules. The other method involves the host cell first being infected by a bacterium or virus, or being diagnosed as cancerous, then it may be able to display the antigens on its surface with a Class I MHC molecule. Cancerous cells and cells infected by a virus usually display unusual, nonself antigens on their surface. These nonself antigens, despite which type of MHC molecule they are displayed on, will initiate the specific immunity of the host's body. It is important to remember that cells constantly process endogenous proteins and display them within the context of MHC I. Immune effector cells are then built up to be non-reactive to self peptides within MHC, and are then able to recognize when foreign peptides are being presented during infection or cancer.
What is Km?
The Michaelis constant. It describes the amount of substrate needed for the enzyme to obtain half of its maximum rate of reaction. (or the amount of substrate needed to obtain Vmax/2)
Tell me about the sodium potassium pump
The Na+ - K+ Pump Cycle A. Three Na+ ions on the inside of the cell membrane bind to the pump protein (carrier molecule). B. The pump protein is phosphorylated by ATP. C. The 3 Na+ ions are released to the outside of the cell membrane, and the outside K+ binds to the pump protein. D. K+ is released to the inside of the cell and the pump protein releases the phosphate and returns to its original conformation.
What is a scintillator?
The ability of a scintillator to absorb high-energy (kiloelectronvolt-scale) X-ray photons and convert the absorbed energy into low-energy visible photons is critical for applications in radiation exposure monitoring, security inspection, X-ray astronomy and medical radiography
Acid Fast Stain
The acid-fast stain is a differential stain used to identify acid-fast organisms such as members of the genus Mycobacterium . Mycobacterium tuberculosis is the most important of this group because it is responsible for tuberculosis (TB). Acid-fast organisms like Mycobacterium contain large amounts of lipid substances within their cell walls called mycolic acids. These acids resist staining by ordinary methods such as a Gram stain.[1] It can also be used to stain a few other bacteria, such as Nocardia. The reagents used are Ziehl-Neelsen carbol fuchsin, acid alcohol, and methylene blue. Acid-fast bacilli will be bright red after staining.
What is acyl carrier protein?
The acyl carrier protein (ACP) is an important component in both fatty acid and polyketide biosynthesis with the growing chain bound during synthesis as a thiol ester at the distal thiol of a 4'-phosphopantetheine moiety.
Tell me about the adrenal medulla
The adrenal medulla is part of the adrenal gland. It is located at the center of the gland, being surrounded by the adrenal cortex. It is the innermost part of the adrenal gland, consisting of cells that secrete epinephrine (adrenaline), norepinephrine (noradrenaline), and a small amount of dopamine in response to stimulation by sympathetic preganglionic neurons. Rather than releasing a neurotransmitter, the cells of the adrenal medulla secrete hormones. The adrenal medulla is the principal site of the conversion of the amino acid tyrosine into the catecholamines; epinephrine, norepinephrine, and dopamine.
Tell me about the Catalase test
The catalase test is used to differentiate staphylococci (catalase-positive) from streptococci (catalase-negative). The enzyme, catalase, is produced by bacteria that respire using oxygen, and protects them from the toxic by-products of oxygen metabolism. Catalase-positive bacteria include strict aerobes as well as facultative anaerobes, although they all have the ability to respire using oxygen as a terminal electron acceptor. Catalase-negative bacteria may be anaerobes, or they may be facultative anaerobes that only ferment and do not respire using oxygen as a terminal electron acceptor (ie. Streptococci).
What are cephalosporins?
The cephalosporins are a class of β-lactam antibiotics Together with cephamycins, they constitute a subgroup of β-lactam antibiotics called cephems. Cephalosporins are bactericidal and have the same mode of action as other β-lactam antibiotics (such as penicillins), but are less susceptible to β-lactamases. Cephalosporins disrupt the synthesis of the peptidoglycan layer forming the bacterial cell wall. The peptidoglycan layer is important for cell wall structural integrity. The final transpeptidation step in the synthesis of the peptidoglycan is facilitated by penicillin-binding proteins (PBPs). PBPs bind to the D-Ala-D-Ala at the end of muropeptides (peptidoglycan precursors) to crosslink the peptidoglycan. Beta-lactam antibiotics mimic the D-Ala-D-Ala site, thereby irreversibly inhibiting PBP crosslinking of peptidoglycan.
Tell me about preparation of vector DNA in molecular cloning
The cloning vector is treated with a restriction endonuclease to cleave the DNA at the site where foreign DNA will be inserted. The restriction enzyme is chosen to generate a configuration at the cleavage site that is compatible with the ends of the foreign DNA. Typically, this is done by cleaving the vector DNA and foreign DNA with the same restriction enzyme, for example EcoRI. Most modern vectors contain a variety of convenient cleavage sites that are unique within the vector molecule (so that the vector can only be cleaved at a single site) and are located within a gene (frequently beta-galactosidase) whose inactivation can be used to distinguish recombinant from non-recombinant organisms at a later step in the process. To improve the ratio of recombinant to non-recombinant organisms, the cleaved vector may be treated with an enzyme (alkaline phosphatase) that dephosphorylates the vector ends. Vector molecules with dephosphorylated ends are unable to replicate, and replication can only be restored if foreign DNA is integrated into the cleavage site
What is the condensation step in the malonyl-CoA pathway?
The covalent linking of acetyl-CoA and Malonyl CoA(with the release of CoA and carbon dioxide)
Tell me about Creation of recombinant DNA with DNA ligase in molecular cloning
The creation of recombinant DNA is in many ways the simplest step of the molecular cloning process. DNA prepared from the vector and foreign source are simply mixed together at appropriate concentrations and exposed to an enzyme (DNA ligase) that covalently links the ends together. This joining reaction is often termed ligation. The resulting DNA mixture containing randomly joined ends is then ready for introduction into the host organism. DNA ligase only recognizes and acts on the ends of linear DNA molecules, usually resulting in a complex mixture of DNA molecules with randomly joined ends. The desired products (vector DNA covalently linked to foreign DNA) will be present, but other sequences (e.g. foreign DNA linked to itself, vector DNA linked to itself and higher-order combinations of vector and foreign DNA) are also usually present. This complex mixture is sorted out in subsequent steps of the cloning process, after the DNA mixture is introduced into cells.
What is the Donnan Potential?
The electric potential arising between two sides of the semi-permeable membrane. Donnan potential appears as a result of Donnan equilibrium, named after Frederick G. Donnan, which refers to the distribution of ion species between two ionic solutions separated by a semipermeable membrane or boundary. The boundary layer maintains an unequal distribution of ionic solute concentration by acting as a selective barrier to ionic diffusion. Some species of ions may pass through the barrier while others may not. The solutions may be gels or colloids as well as ionic liquids, and as such the phase boundary between gels or a gel and a liquid can also act as a selective barrier. Electric potential arises between two solutions is called Donnan potential. Donnan equilibrium is prominent in the triphasic model for articular cartilage proposed by Mow and Ratcliffe, as well as in electrochemical fuel cells and dialysis. The Donnan effect is extra osmotic pressure attributable to cations (Na and K) attached to dissolved plasma proteins.
What is an equilibrium potential?
The electrical potential difference that exactly counterbalances any diffusion due to the concentration difference and the electrochemical gradient due to a specific ion. https://courses.washington.edu/conj/membpot/equilpot.htm
Given that the membrane potential is -70 mV, in what direction will the electrical potential difference make K+ move through open K+ channels? Given that the membrane potential is -70 mV, in what direction will the concentration gradient make K+ move through open K+ channels?
The electrical potential difference will tend to make K⁺ move into the cell, but the concentration gradient will tend to make K⁺ move out of the cell
What is the major disadvantage of using natural media as a cell culture media?
The major disadvantage is poor reproducibility due to lack of knowledge of the exact composition of these natural media.
Tell me about glutamate Can you draw glutamate?
The major excitatory neurotransmitter in the vertebrate central nervous system. Glutamate receptors are implicated in Huntington disease
Which conformation do the majority of unsaturated fatty acids exist in? The cis or the trans conformation?
The majority of naturally occurring fatty acids exist in the cis conformation.
What is MecA?
The mecA gene is a gene found in bacterial cells which allows a bacterium to be resistant to antibiotics such as methicillin, penicillin and other penicillin-like antibiotics. The most commonly known carrier of the mecA gene is the bacterium known as Methicillin-resistant Staphylococcus aureus
Tell me about the Telencephalon
The most anterior portion of the brain, including the cerebrum and associated structures
What is casein?
The most common protein found in milk. As a food source, casein supplies amino acids, carbohydrates, and the two inorganic elements calcium and phosphorus. Casein is the name for a family of related phosphoproteins
What is the most likely explanation for the low rate of success in organism cloning/somatic cell nuclear transfer
The most likely explanation for the low rate of success may be failures in epigenetic reprogramming and imprinting - mechanisms to ensure that a zygote ends up with a clean slate from two different parents. "Imprinting is normally accomplished during spermatogenesis and oogenesis, processes that in humans take months and years, respectively. During SCNT, reprogramming of the somatic donor nucleus must occur within minutes or, at most, hours between the time that nuclear transfer is completed and the onset of cleavage of the activated egg begins. It is known that the cytoplasm of an oocyte can reprogram the genome of a somatic cell to an embryonic state, but the exact mechanisms are not clear.
What is the somatic nervous system?
The neurons of the peripheral nervous system that control skeletal muscle.
Tell me about the thalamus
The part of the vertebrate forebrain just posterior to the cerebrum, governs the flow of information from all other parts of the nervous system to the cerebellum
Tell me about long term potentiation
The phenomenon by which synapses that are used intensively for a short period of time display more effective synaptic transmission upon subsequent use
Tell me about the reticular activating system
The portion of the reticular formation of the brain that is involved in consciousness and alertness and controls both sleep and the waking state.
Tell me about the cerebrum
The portion of the vertebrate brain(forebrain) that occupies the skull, consisting of two cerebral hemispheres united by the corpus callosum. It is the primary association center of the brain. It coordinates and processes sensory input and coordinates motor responses
An analysis technique allows you to determine global methylation content, what applications are there using this information?
The quantification of 5-mC content or global methylation in diseased or environmentally impacted cells could provide useful information for detection and analysis of disease. (Cancer and other diseases involved with gene repression activation)
What is the rate limiting step of fatty acid synthesis?
The rate limiting step of fatty acid synthesis is the conversion of acetyl-CoA to malonyl-CoA
How is the rate of fatty acid synthesis controlled?
The rate of fatty acid synthesis is controlled by the equilibrium between monomeric ACC and polymeric ACC. The activity of ACC requires this polymerization process. This conformational change is enhanced by citrate and inhibited by long-chain fatty acids. ACC is also controlled through hormone mediated phosphorylation
Cytochrome c oxidase biochemical process in mitochondrial membrane
The reaction requires four molecules of reduced cytochrome c binding the enzyme consecutively. 1. Electrons from two molecules of reduced cytochrome c flow down an electron-transfer pathway within the cytochrome c oxidase protein. One stops at CuB and the other at heme a3. 2. An oxygen molecule binds to these reduced ions and removes an electron from each to form a peroxide bridge. 3. Two more electrons flow from reduced cytochromes to the oxygen atoms and along with two protons they reduce the ion-oxygen groups to ion-OH groups. 4. Two more protons allow the release of two H2O molecules.
Tell me about the primary motor cortex
The region of the cerebral cortex that is involved in movement of the body It is the primary region of the motor system and works in association with other motor areas including premotor cortex, the supplementary motor area, posterior parietal cortex, and several subcortical brain regions, to plan and execute movements. Primary motor cortex is defined anatomically as the region of cortex that contains large neurons known as Betz cells. Betz cells, along with other cortical neurons, send long axons down the spinal cord to synapse onto the interneuron circuitry of the spinal cord and also directly onto the alpha motor neurons in the spinal cord which connect to the muscles.
Tell me about the primary somatosensory cortex
The region of the cerebral cortex that receives input from sensory neurones in skin and muscles
Tell me about the classes of MHC
There are two major types of MHC protein molecules—class I and class II. Class I MHC molecules span the membrane of almost every cell in an organism, while class II molecules are restricted to cells of the immune system called macrophages and lymphocytes. MHC class I can be found in all nucleated cells. the MHC class I proteins contain an α chain and β2-micro-globulin. They present antigen fragments to cytotoxic T-cells that will bind to the CD8 on cytotoxic T-cells. MHC class II proteins contain α and β chains and they present antigen fragments to T-helper cells by binding to the CD4 receptor on the T-helper cells. In humans these molecules are encoded by several genes all clustered in the same region on chromosome 6. Each gene has an unusually large number of alleles (alternate forms of a gene that produce alternate forms of the protein). As a result, it is very rare for two individuals to have the same set of MHC molecules, which are collectively called a tissue type. The MHC also contains a variety of genes that code for other proteins—such as complement proteins, cytokines (chemical messengers), and enzymes—that are called class III MHC molecules.
Tell me about the olfactory nerves, the optic nerves, the auditory (acoustic) nerves, and the vagus nerve.
These are all cranial nerves. The olfactory nerves - (smell) carry impulses from the olfactory organ of the nose to the brain. The optic nerves - (sight) carry impulses from the retina of the eye to the brain. The auditory (acoustic) nerves - (hearing) carry impulses from the cochlear of the inner ear to the brain. The vagus nerve - controls the muscles that bring about swallowing. It also controls the muscles of the heart, airways, lungs, stomach and intestines
What are okazaki fragments?
These are short fragments formed complementary to the lagging template strand during semi conservative replication of DNA.
Histone acetyltransferases (HATs)
These enzymes have a huge role epigenetic regulation of gene expression. They catalyze the transfer of an acetyl group from acetyl-CoA to ε-amino group of a histone lysine residue. These acetylations then allow transcriptional access to DNA by either neutralizing the positive histone change, or serving as a binding site for chromatin remolding complexes.
what name is designated to the polyunsaturated fatty acids: linoleic and α-linolenic acid?
These two essential fatty acids are referred to as omega fatty acids. Linoleic acid is an omega-6 PUFA and α-linolenic is an omega-3 PUFA
What is piperacillin-tazobactam?
They are a combination of penicillin derivative (piperacillin) and a beta-lactamase inhibitor (tazobactam)
Hemithioacetal
They are also called thiohemiacetal. With four substituents on carbon, hemithioacetals are chiral. A related functional group are dithiohemiacetal, with the formula RCH(SH)SR.[1] Although they can be important intermediates, hemithioacetals are usually not isolated since they exist in equilibrium with the thiol and aldehyde:
What happens to excess protein in diet?
They are catabolised to provide energy. Some amino acids are converted into glucose. Other amino acids can be converted into acetyl CoA The acetyl CoA can be converted into fat to be used later or fed into TCA cycle. Other amino acids can feed directly into Krebs Cycle
How are intracellular RNA protected from ribonuclease activity?
They are protected by a number of strategies: 5' end capping 3' end polyadenylation folding within an RNA protein complex ribonuclease inhibitor
What do cyclins complex with? What does the complex cause? Give 3 examples of compounds cyclins bind to
They form a complex with Cdk, which begins to activate the Cdk, but complete activation requires phosphorylation. Complex formation results in the activation of Cdk active site. Cyclins, when bound with the dependent kinases, such as the p34/cdc2/cdk1 protein, form the maturation-promoting factor.
What are the uses of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)?
They serve as important precursors for lipid-derived modulators of cell signaling, gene expression and inflammatory processes.
What do single strand binding proteins do?
They stabilise the single stranded state of DNA, stopping the two strands from reannealing.
Thiazole
Thiazole, or 1,3-thiazole, is a heterocyclic compound that contains both sulfur and nitrogen; Thiazole itself is a pale yellow liquid with a pyridine-like odor and the molecular formula C₃H₃NS. The thiazole ring is notable as a component of the vitamin thiamine (B1).
Thioacetic Acid
Thioacetic acid is an organosulfur compound with the molecular formula CH3COSH. It is a yellow coloured liquid with a strong thiol-like odor. It is used in organic synthesis for the introduction of thiol groups in molecules
What drug therapy is currently available for cancer caused by mutations in BRCA1 and BRCA2?
Third-generation PARP inhibitors are being developed PARP is a protein involved in single-strand DNA break repairs inhibition of PARP can destroy BRCA1/2-deficient breast cancer cells b/c they cannot survive substantial DNA damage normal cells are resistant to PARP inhibitors b/c they have intact BRCA1/2
Why does methylation occur almost exclusively on CpG sites?
This causes symmetrical methylation due to the antiparallel nature of DNA. CG is a palindromic sequence.
Oxidative phase of the pentose phosphate pathway
This phase produces pentose phosphates and NADPH. The first reaction of the pentose phosphate pathway is the oxidation of glucose-6-phosphate by glucose 6-phosphate dehydrogenase to form 6-phosphoglucono-δ-lactone, an intramolecular ester. NADP⁺ is the electron acceptor, and the overall equilibrium lies far in the direction of NADPH formation(what does this mean?). The lactone is hydrolysed to the free acid 6-phosphogluconate by a specific lactonase, then 6-phosphogluconate undergoes oxidation and decarboxylation vy 6-phosphogluconate dehydrogenase to form the ketopentose ribulose 5-phosphate; the reaction generates a second molecule of NADPH. (This ribulose 5-phosphate is important in the regulation of glycolysis and gluconeogenesis). Phosphopentose isomerase converts ribulose 5-phosphate to its aldose isomer, ribose 5-phosphate. In some tissues, the pentose phosphate pathway ends at this point, and its overall equation is Glucose 6-phosphate + 2 NADP⁺ + H₂O → ribose 5-phosphate + CO₂ + 2NADPH + 2H⁺ The net result is the production of NADPH, a reductant for biosynthetic reactions and ribose 5-phosphate a precursor for nucleotide synthesis.
What is the mechanism of action of Phenobarbital?
Through its action on GABA receptors, phenobarbital increases flux of chloride ions into the neuron which decreases excitability. Direct blockade of excitatory glutamate signaling is also believed to contribute to the hypnotic/anticonvulsant effect that is observed with the barbiturates.
Why must water be excluded from the active site of hexokinase?
To prevent undesirable hydrolysis of ATP instead of the desirable reaction of promoting phosphoryl transfer to glucose.
What can we use telomerase inhibitors for?
To treat some forms of cancer
What does upstream mean?
Toward 5' end
Why did trans fatty acids exist in human food products?
Trans fatty acids occur in some foods and as byproducts of the process of hydrogenating unsaturated fatty acids to make them solids at room temperature, such as in partially hydrogenated vegetable oils.
What do you mean by transformation in molecular cloning? What is transfection?
Transformation is when cells are able to directly take up DNA from their local environment. In mammalian cell culture, the analogous process of introducing DNA into cells is commonly termed transfection. Both transformation and transfection usually require preparation of the cells through a special growth regime and chemical treatment process that will vary with the specific species and cell types that are used. "transformation" is typically used to describe non-viral DNA transfer in bacteria and non-animal eukaryotic cells, including plant cells. Transfection is the process of deliberately introducing naked or purified nucleic acids into eukaryotic cells.
How does the strecker synthesis make amino acids?
Treatment of an aldehyde with KCN and aqueous ammonia to yield an intermediate α-amino nitrile. Hydrolysis of the nitrile gives an α-amino acid. in the diagram, 2 water molecules are used as well with addition of acid React an aldehyde with aqueous ammonia. You form an alcohol and amine. This structure shuffles atoms around and you get an imine. The imine reacts with cyanide ion to form a nitrile. Hydrolysis of nitrile with water and acid occurs and you get amino acid. Look at diagram.
What is the bacteria that causes syphilis
Treponema pallidum
Type VII Collagen Function?
Type VII Collagen is restricted to the basement zone beneath stratified squamous epithelia. It functions as an anchoring fibril between the external epithelia and the underlying stroma. Mutations in this gene are associated with all forms of dystrophic epidermolysis bullosa.
Tell me about ubiquitin How does ubiquitination affect proteins What are the 3 main steps of ubiquitination
Ubiquitin is a small (8.5 kDa) regulatory protein found in most tissues of eukaryotic organisms i.e. it occurs ubiquitously. Four genes in the human genome code for ubiquitin: UBB, UBC, UBA52 and RPS27A. Ubiquitination affects proteins in many ways: it can mark them for degradation via the proteasome, alter their cellular location, affect their activity, and promote or prevent protein interactions. Ubiquitination involves three main steps: activation, conjugation, and ligation, performed by ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s), respectively. The result of this sequential cascade is to bind ubiquitin to lysine residues on the protein substrate via an isopeptide bond, cysteine residues through a thioester bond, serine and threonine residues through an ester bond, or the amino group of the protein's N-terminus via a peptide bond. A diagram of ubiquitin. The seven lysine sidechains are shown in yellow/orange.
How do uncoupling agents prevent formation of proton gradient?
Uncoupling agents can dissolve in membrane lipids and ferry H⁺ across the inner mitochondrial membrane, allowing the proton gradient to dissipate.
What are universal bases? Give 3 examples
Universal bases can bind to any of the four canonical base. Examples: Deoxy Inosine, 3-nitropyrrole, Nitroindole
How does unsaturation affect the melting point of fatty acids?
Unsaturation decreases the melting point of fatty acids
Examples of hydrogen bond disruptors?
Urea
What would you find in a urinalysis in someone with UTI?
Urine leukocyte esterase would be high, so lots of white blood cells in urine Nitrites would be there if pathogen is gram negative
How do you break disulfide bonds?
Use ammonium thioglycolate. (this chemical is used in hair perms)
How do you calculate the equilibrium potential if you know the concentration gradient for a given ion?
Use the nernst equation
Which enzymes is Molybdenum used in?
Used in enzymes that break N₂ in the process of nitrogen fixation
Tell me about dCas9
Using "dead" versions of Cas9 (dCas9) eliminates CRISPR's DNA-cutting ability, while preserving its ability to target desirable sequences. Multiple groups added various regulatory factors to dCas9s, enabling them to turn almost any gene on or off or adjust its level of activity. Like RNAi, CRISPR interference (CRISPRi) turns off genes in a reversible fashion by targeting, but not cutting a site. The targeted site is methylated, epigenetically modifying the gene. This modification inhibits transcription. Cas9 is an effective way of targeting and silencing specific genes at the DNA level. In bacteria, the presence of Cas9 alone is enough to block transcription. For mammalian applications, a section of protein is added. Its guide RNA targets regulatory DNA sequences called promoters that immediately precede the target gene. Cas9 was used to carry synthetic transcription factors that activated specific human genes. The technique achieved a strong effect by targeting multiple CRISPR constructs to slightly different locations on the gene's promoter.
Tell me about imaging genomic regions using Fluorophore-tagged dCas9
Using a dCas9 fused to a fluorescent marker (such as GFP), researchers have turned dCas9 into a customizable DNA label that can be detected in live cells. By creating unique gRNAs that bind in close proximity along a stretch of genomic DNA, a technique referred to as "tiling", researchers have imaged specific regions of the genome. The tiling technique does require multiple gRNAs to bind near one another in order to produce a detectable signal.
Tell me about the parasympathetic division
Utilizes ACh as a neurotransmitter in postganglionic neurones. Its actions are antagonistic to those of the sympathetic division.
V-Type ATPases
V-Type ATPases are a class of proton transporting ATPases, responsible for acidifying intracellular compartments (V for vacuolar). Proton pumps of this type maintain the vacuoles of fungi and higher plants at a pH between 3 and 6, well below that of the surrounding cytosol (7.5). V-type ATPases are responsible for the acidification of lysosomes, endosomes, the golgi complex, and secretory vesicles in animal cells. All V-type ATPases have a similar complex structure, with an integral (transmembrane) domain (V₀) that serves as a proton channel and a peripheral domain (V₁) that contains the ATP-binding site and the ATPase activity. The structure is similar to that of the well characterized F-Type ATPases.
Angiogenesis
VEGF is a major contributor to angiogenesis formation of new blood vessels from existing vessels allows tumors to grow and uptake nutrients and oxygen helps tumors transition from benign to malignant state
Stability of ribonuclease? Implications?
Very Stable Everything has RNA nuclease, everything you touch It is very stable due to strategically placed disulfide bonds
Stability of creutzfeld jakob protein?
Very stable Prions can be deactivated in a steam autoclave using a temperature of 270 F (132 C) at 21 psi for 90 minutes. If the prion infected material is in a solution of sodium hydroxide, steam autoclave at 250 F ( 121 C) at 21 psi for one hour. Denatured prions can be renatured thats why needs very harsh conditions but they themselves are also very stable
Tell me about virulence factors
Virulence factors are molecules produced by bacteria, viruses, fungi, and protozoa that add to their effectiveness and enable them to achieve the following:[citation needed] colonization of a niche in the host (this includes attachment to cells) immunoevasion, evasion of the host's immune response immunosuppression, inhibition of the host's immune response entry into and exit out of cells (if the pathogen is an intracellular one) obtain nutrition from the host Specific pathogens possess a wide array of virulence factors. Some are chromosomally encoded and intrinsic to the bacteria (e.g. capsules and endotoxin), whereas others are obtained from mobile genetic elements like plasmids and bacteriophages (e.g. some exotoxins). Virulence factors encoded on mobile genetic elements spread through horizontal gene transfer, and can convert harmless bacteria into dangerous pathogens. Bacteria like Escherichia coli O157:H7 gain the majority of their virulence from mobile genetic elements. Gram-negative bacteria secrete a variety of virulence factors at host-pathogen interface, via membrane vesicle trafficking as bacterial outer membrane vesicles for invasion, nutrition and other cell-cell communications. It has been found that many pathogens have converged on similar virulence factors to battle against eukaryotic host defenses. These obtained bacterial virulence factors have two different routes used to help them survive and grow: 1) The factors are used to assist and promote colonization of the host. These factors include adhesins, invasins, and antiphagocytic factors. 2) The factors, including toxins, hemolysins, and proteases, bring damage to the host.
Why are the effects of Isotretinoin permanent?
Vitamin A and similar compounds are stored in the liver for years which are gradually released. (SPECULATION)
Equation that links the following variables? [E (total)] kcat Vmax
Vmax = kcat x [E (total)] Vmax when all active sites are filled with substrate.
How do you measure respiration?
Warburg apparatus or Respirometer
MutS structure MutS homologs
When bound, the MutS2 dimer bends the DNA helix and shields approximately 20 base pairs. It has weak ATPase activity, and binding of ATP leads to the formation of tertiary structures on the surface of the molecule. The crystal structure of MutS reveals that it is exceptionally asymmetric, and, while its active conformation is a dimer, only one of the two halves interacts with the mismatch site. In eukaryotes, MutS homologs form two major heterodimers: Msh2/Msh6 (MutSα) and Msh2/Msh3 (MutSβ). The MutSα pathway is involved primarily in base substitution and small-loop mismatch repair. The MutSβ pathway is also involved in small-loop repair, in addition to large-loop (~10 nucleotide loops) repair. However, MutSβ does not repair base substitutions.
Tell me about the selection of organisms containing vector sequences in molecular cloning
Whichever method is used, the introduction of recombinant DNA into the chosen host organism is usually a low efficiency process; that is, only a small fraction of the cells will actually take up DNA. Experimental scientists deal with this issue through a step of artificial genetic selection, in which cells that have not taken up DNA are selectively killed, and only those cells that can actively replicate DNA containing the selectable marker gene encoded by the vector are able to survive.[3][10] When bacterial cells are used as host organisms, the selectable marker is usually a gene that confers resistance to an antibiotic that would otherwise kill the cells, typically ampicillin. Cells harboring the plasmid will survive when exposed to the antibiotic, while those that have failed to take up plasmid sequences will die. When mammalian cells (e.g. human or mouse cells) are used, a similar strategy is used, except that the marker gene (in this case typically encoded as part of the kanMX cassette) confers resistance to the antibiotic Geneticin.
How would you make precise modifications using Homology directed repair?
While NHEJ-mediated DSB repair is imperfect and often results in disruption of the open reading frame of the gene, Homology Directed Repair (HDR) can be used to generate specific nucleotide changes ranging from a single nucleotide change to large insertions In order to utilize HDR for gene editing, a DNA "repair template" containing the desired sequence must be delivered into the cell type of interest with the gRNA(s) and Cas9 or Cas9 nickase. The repair template must contain the desired edit as well as additional homologous sequence immediately upstream and downstream of the target (termed left & right homology arms). The length and binding position of each homology arm is dependent on the size of the change being introduced. The repair template can be a single stranded oligonucleotide, double-stranded oligonucleotide, or double-stranded DNA plasmid depending on the specific application. It is worth noting that the repair template must lack the PAM sequence that is present in the genomic DNA, otherwise the repair template becomes a suitable target for Cas9 cleavage. The efficiency of HDR is generally low (<10% of modified alleles) even in cells that express Cas9, gRNA and an exogenous repair template. For this reason, many laboratories are attempting to artificially enhance HDR by synchronizing the cells within the cell cycle stage when HDR is most active, or by chemically or genetically inhibiting genes involved in NHEJ. The low efficiency of HDR has several important practical implications. First, since the efficiency of Cas9 cleavage is relatively high and the efficiency of HDR is relatively low, a portion of the Cas9-induced DSBs will be repaired via NHEJ. In other words, the resulting population of cells will contain some combination of wild-type alleles, NHEJ-repaired alleles, and/or the desired HDR-edited allele. Therefore, it is important to confirm the presence of the desired edit experimentally, and if necessary, isolate clones containing the desired edit.
Tell me about the effects of serial cloning Tell me a possible explanation
With each iteration of serial cloning, there is a decrease in efficiency. Less and less animals are able to be successfully cloned with each generation. One possible explanation (not proven) is an accumulation of genetic or epigenetic abnormalities over successive generations. It is well known that cloned animals frequently show several abnormal phenotypes caused by genomic reprogramming errors at the time of somatic cell nuclear transfer. Thus, if a donor nucleus from a cloned animal is already epigenetically abnormal, the additional abnormalities introduced during a subsequent round of reprogramming might lead to embryo failure.
How do you stop trypsinization
You add culture media because it has trypsin inhibitors.
What does MacConkey Agar do?
You can use it to identify lactose-fermenting bacteria. MacConkey agar is a selective and differential culture medium for bacteria designed to selectively isolate Gram-negative and enteric (normally found in the intestinal tract) bacilli and differentiate them based on lactose fermentation. The crystal violet and bile salts inhibit the growth of gram-positive organisms which allows for the selection and isolation of gram-negative bacteria. Enteric bacteria that have the ability to ferment lactose can be detected using the carbohydrate lactose, and the pH indicator neutral red Neutral red is a pH indicator that turns red at a pH below 6.8 and is colorless at any pH greater than 6.8. Organisms that ferment lactose and thereby produce an acidic environment will appear pink because of the neutral red turning red. Bile salts may also precipitate out of the media surrounding the growth of fermenters because of the change in pH. Non-fermenters will produce normally-colored or colorless colonies.
Which metal is vital for catalytic activity by carbonic anhydrases?
Zinc
What are zoonoses
Zoonoses are infectious diseases that can be naturally transmitted between non-human animals (usually vertebrates) and humans
What do you form if amino acids undergo intramolecular acid-base reaction?
Zwitterion
What is p16?
a CDK inhibitor
Rhinorrhea?
a condition where the nasal cavity is filled with a significant amount of mucus fluid. The condition, commonly known as a runny nose, occurs relatively frequently.
Tell me about basal ganglia
a group of subcortical nuclei, of varied origin, in the brains of vertebrates including humans, which are situated at the base of the forebrain. There are some differences in the basal ganglia of primates. Basal ganglia are strongly interconnected with the cerebral cortex, thalamus, and brainstem, as well as several other brain areas. The basal ganglia are associated with a variety of functions including: control of voluntary motor movements, procedural learning, habit learning, eye movements, cognition, and emotion
mycoplasma pneumoniae
a milder pneumonia in younger patients chest x-ray might show interstitial consolidation, but symptoms will be mild
methicilin
a narrow-spectrum β-lactam antibiotic of the penicillin class. Like other beta-lactam antibiotics, methicillin acts by inhibiting the synthesis of bacterial cell walls. It inhibits cross-linkage between the linear peptidoglycan polymer chains that make up a major component of the cell wall of gram-positive bacteria. It does this by binding to and competitively inhibiting the transpeptidase enzyme (also known as penicillin-binding proteins (PBPs)). These PBPs crosslink glycopeptides (D-alanyl-alanine), forming the peptidoglycan cell wall. Methicillin and other β-lactam antibiotics are structural analogs of D-alanyl-alanine, and the transpeptidase enzymes that bind to them are sometimes called penicillin-binding proteins (PBPs). Methicillin is actually a penicillinase-resistant B-lactam antibiotic. Penicillinase is a bacterial enzyme produced by bacteria resistant to other B-lactam antibiotics which hydrolyses the antibiotic, rendering it nonfunctional. Methicillin is not bound and hydrolysed by penicillinase, meaning it can kill the bacteria, even if this enzyme is present.
What is an aliquot
a portion of a larger whole, especially a sample taken for chemical analysis or other treatment.
Voriconazole
a triazole antifungal medication that is generally used to treat serious, invasive fungal infections. These are generally seen in patients who are immunocompromised, and include invasive candidiasis, invasive aspergillosis
What are Mitogen-activated protein kinases?
a type of protein kinase that is specific to the amino acids serine, threonine, and tyrosine (i.e., a serine/threonine-specific protein kinase). MAPKs are involved in directing cellular responses to a diverse array of stimuli, such as mitogens, osmotic stress, heat shock and proinflammatory cytokines. They regulate cell functions including proliferation, gene expression, differentiation, mitosis, cell survival, and apoptosis. The ERK1/2 pathway of mammals is probably the best characterized MAPK system
Tell me about α-Amanitin
alpha-Amanitin or α-amanitin is a cyclic peptide of eight amino acids. It is possibly the most deadly of all the amatoxins, toxins found in several species of the Amanita genus of mushrooms, one being the death cap . α-Amanitin is an selective inhibitor of RNA polymerase II and III. This mechanism makes it a deadly toxin.
Anaphase promoting complex
an E3 ubiquitin ligase that marks target cell cycle proteins for degradation by the 26S proteasome. The APC/C's main function is to trigger the transition from metaphase to anaphase by tagging specific proteins for degradation. The three major targets for degradation by the APC/C are securin and S and M cyclins. Securin releases separase (a protease) after being degraded. The separase triggers the cleavage of cohesin, the protein complex that binds sister chromatids together. During metaphase, sister chromatids are linked by intact cohesin complexes. When securin undergoes ubiquitination by the APC/C and releases separase, which degrades cohesin, sister chromatids become free to move to opposite poles for anaphase. The APC/C also targets the mitotic cyclins for degradation, resulting in the inactivation of M-CDK (mitotic cyclin-dependent kinase) complexes, promoting exit from mitosis and cytokinesis. Unlike the SCF, activator subunits control the APC/C. Cdc20 and Cdh1 are the two activators of particular importance to the cell cycle. These proteins target the APC/C to specific sets of substrates at different times in the cell cycle, thus driving it forward. The APC/C also plays an integral role in maintenance of chromatin metabolism, particularly in G1 and G0, and plays a key role in phosphorylation of H3 through destruction of the aurora A kinase. The critical substrates of the APC/C appear to be securin and the B type cyclins. This is conserved between mammals and yeast. In fact, yeast are viable in the absence of the APC/C if the requirement for targeting these two substrates is eliminated
Pelvic Inflammatory Disease
an infection of the upper part of the female reproductive system namely the uterus, fallopian tubes, and ovaries, and inside of the pelvis
Teichoic acids
are bacterial copolymers of glycerol phosphate or ribitol phosphate and carbohydrates linked via phosphodiester bonds. Teichoic acids are found within the cell wall of most Gram-positive bacteria such as species in the genera Staphylococcus, Streptococcus, Bacillus, Clostridium, Corynebacterium, and Listeria, and appear to extend to the surface of the peptidoglycan layer.They can be covalently linked to N-acetylmuramic acid or a terminal D-alanine in the tetrapeptide crosslinkage between N-acetylmuramic acid units of the peptidoglycan layer, or they can be anchored in the cytoplasmic membrane with a lipid anchor. The main function of teichoic acids is to provide rigidity to the cell-wall by attracting cations such as magnesium and sodium. Teichoic acids can be substituted with D-alanine ester residues,[4] or D-glucosamine, giving the molecule zwitterionic properties.These zwitterionic teichoic acids are suspected ligands for toll-like receptors 2 and 4. Teichoic acids also assist in regulation of cell growth by limiting the ability of autolysins to break the β(1-4) bond between the N-acetyl glucosamine and the N-acetylmuramic acid.
Give examples of Oncogenes
c-Myc Ras
Intronic polyadenylation
can cause truncated mRNAs Polyadenylation in introns can lead to conversion of an internal exon to a 3′ terminal exon, which is termed composite terminal exon, or usage of a 3′ terminal exon that is otherwise skipped, which is termed skipped terminal exon.
What is the formula of Oleic acid?
carboxylic acid with 18 carbons and 1 double bond
Staphylococcus aureus
catalase positive coagulase positive Beta-Hemolytic gram positive occurs in clusters live on skin cells normally staph aureus have developed enzymes that target and destroy penicillins, called beta-lactamases can kill with nafcillin or vancomycin
What's the other name for cdk1
cell division cycle protein 2 homolog or cdc2
staphycoccus aureus
common in hospitalized patients and people with a recent flu
What is beta hemolysis
complete hemolysis the area appears lightened (yellow) and transparent
What are Hemiacetals and hemiketals?
compounds that are derived from aldehydes and ketones respectively Hemiacetals and hemiketals are generally unstable compounds. Hemiacetals are compounds formed by formal addition of an alcohol to the carbonyl group.
What are the basic environmental requirements for cells to grow optimally?
controlled temperature, substrate for cell attachment, and appropriate growth medium and incubator that maintains correct pH and osmolality. The most important and crucial step in cell culture is selecting appropriate growth medium for the in vitro cultivation. A growth medium or culture medium is a liquid or gel designed to support the growth of microorganisms, cells, or small plants. Cell culture media generally comprise an appropriate source of energy and compounds which regulate the cell cycle. A typical culture medium is composed of a complement of amino acids, vitamins, inorganic salts, glucose, and serum as a source of growth factors, hormones, and attachment factors. In addition to nutrients, the medium also helps maintain pH and osmolality.
What is the gram stain?
crystal violet dye. Gram positive bacteria are dyed violet. Then counter stain is added which is pink (commonly safranin or fuchsine). The gram negative bacteria and gram positive bacteria are both stained pink, but this pink colour is only noticed in gram negative bacteria, because the violet colour dominates over the light pink colour in gram positive bacteria.
Which genes are commonly mutated in Hereditary nonpolyposis colorectal cancer (HNPCC) and which DNA repair pathway is impacted?
defects in pathway of DNA mismatch repair involves MSH2 or MLH1 ("two hit model") MSH2: identifies DNA containing mismatch errors MLH1: part of a complex that repairs these errors
Evading Apoptosis
disrupted balance of pro-apoptotic and anti-poptotic proteins (BLC-2 family of proteins is dysregulated: BAX, PUMA, BID) reduced caspase function (proteins involved in initiation and execution of apoptosis) impaired death receptor signaling
What are c-Fos and c-Myc?
early response genes transcription factors that stimulate cell proliferation Normally, mRNA and protein levels of c-FOS and c-Myc are unstable and decline within hours of stimulation In cancer, c-myc is often constitutively expressed. This leads to the increased expression of many genes, some of which are involved in cell proliferation, contributing to the formation of cancer. In the human genome, C-myc is located on chromosome 8 and is believed to regulate expression of 15% of all genes through binding on enhancer box sequences (E-boxes). c-Fos encodes a 62 kDa protein, which forms heterodimer with c-jun (part of Jun family of transcription factors), resulting in the formation of AP-1 (Activator Protein-1) complex which binds DNA at AP-1 specific sites at the promoter and enhancer regions of target genes and converts extracellular signals into changes of gene expression.
Landscaper Genes
encode products that, when mutated, contribute to the neoplastic growth of cells by fostering a stromal environment conducive to unregulated cell proliferation
What substitutions can be added to phosphatidic acid?
ethanolamine (phosphatidylethanolamines, PE), choline (phosphatidylcholines, PC: also called lecithins), serine (phosphatidylserines, PS), glycerol (phosphatidylglycerols, PG), myo-inositol (phosphatidylinositols, PI: these compounds can have a variety in the numbers of inositol alcohols that are phosphorylated generating polyphosphatidylinositols), and phosphatidylglycerol (diphosphatidylglycerols, DPG; more commonly known as cardiolipins).
How many ligands is zinc often bound to?
four or more
Brucella melitensis
gram negative Obligate aerobe Castaneda media Urease-positive Causes Brucellosis
vibrio cholerae
gram negative does not ferment lactose cause very watery diarrhoea grow well on bile salt plates like other vibrios Oxidase positive can go away if you leave alone, but you should rehydrate the patient
capylobacter jejuni
gram negative microaerophilic spiral shaped grow well at warm temperatures cause diarrhoea but can also cause Gullain-Barr syndrome. Ciprofloxacin and Azithromycin work well against it
Pseudomonas aeruginosa Characteristics? Which Antibiotics is it susceptible to? Where is it found? Which diseases is it involved in?
gram negative rod shaped It is citrate, catalase, and oxidase positive. grow well under aerobic conditions produces a green pigment Cefepime and Zosyn(Pip-Taz) used to kill it It is found in soil, water, skin flora, and most man-made environments throughout the world. It thrives not only in normal atmospheres, but also in low-oxygen atmospheres, thus has colonized many natural and artificial environments. common in cystic fibrosis and hospitalized patients has a lot of antibiotic resistance can cause UTIs in catheterized patients
Streptococcus Pneumoniae
gram positive Chains Quellung reaction occurs in pairs Sensitive to optochin Most commonly causes pneumonia producing a rusty brown sputum but also meningitis and otitis media Catalase negative but alpha hemolytic young children and the elderly are more susceptible Can use penicillin to kill
staphylococcus saprophyticus Tell me its characteristics, antibiotic treatment, diseases its involved in
gram positive catalase positive coagulase negative nitrite NEGATIVE in urinalysis Beta hemolytic second most common cause of UTIs in young women, lives in vagina. Causes UTI in sexually active women. Nafcillin or Vancomycin can be used to kill
Helicobacter pylori
gram-negative, microaerophilic bacterium found usually in the stomach.
How do you locate an anomeric carbon?
http://www.chem.ucla.edu/~harding/ec_tutorials/tutorial08.pdf
What is alpha hemolysis? Which genus of bacteria is alpha hemolytic?
incomplete hemolysis and partial hemolysis When alpha hemolysis (α-hemolysis) is present, the agar under the colony is dark and greenish. Streptococcus pneumoniae and a group of oral streptococci (Streptococcus viridans or viridans streptococci) display alpha hemolysis. This is sometimes called green hemolysis because of the color change in the agar. Alpha hemolysis is caused by hydrogen peroxide produced by the bacterium, reducing hemoglobin producing the green oxidized derivative methemoglobin.
FAP
inherited predisposition to develop adenomatous polyps in colon --> may develop into carcinomas
What is the Gibbs-Donnan Effect generally?
is a name for the behaviour of charged particles near a semi-permeable membrane that sometimes fail to distribute evenly across the two sides of the membrane. The usual cause is the presence of a different charged substance that is unable to pass through the membrane and thus creates an uneven electrical charge
Thiamine
is a vitamin found in food
Tell me about GABA
is the chief inhibitory neurotransmitter in the mammalian central nervous system. Its principal role is reducing neuronal excitability throughout the nervous system. In humans, GABA is also directly responsible for the regulation of muscle tone
What is the Michaelis Menten Equation?
kM=(k-1+kcat)/k1
conversion of pyruvate to phosphoenol pyruvate
lehninger 570
Pyruvate dehydrogenase complex requires 5 coenzymes
lehninger 634
Substrate channeling intermediates never leave the enzyme surface. Give the mechanism for PDH
lehninger 636
Hormones trigger mobilizatin of stored triacylglyercols
lehninger 669
Fatty acids are activated and transported into mitochondria
lehninger 670
beta oxidation of saturated fatty acids has four basic steps
lehninger 673
complete oxidation of odd number fatty acids requires three extra reactions
lehninger 677
oxidation of unsaturated fatty acids requires two additional reactions
lehninger 677
peroxisomes also carry out beta oxidation
lehninger 682
How is the flux of glucose 6 phosphate into glycolysis or into the pentose phosphate pathway decided?
lehninher 580
streptococcus agalactiae or group b strep
live in vagina beta hemolytic can kill with penicillin
At low concentrations of α-amanitin, which RNA class's synthesis is affected?
mRNA
What does conducive mean?
making a certain situation or outcome likely or possible.
What do secreted factors do?
may act in a paracrine manner to trigger senescence or, conversely, stimulate proliferation and/or transformation of adjacent immortalized cells
A ____ mutation in a single TP53 allele can produce a tetramer with at least one non-functional subunit.
missense this can impact p53 function
Define Chaperones
molecular chaperones are proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures One major function of chaperones is to prevent both newly synthesised polypeptide chains and assembled subunits from aggregating into nonfunctional structures
Identify the target of the drug trastuzumab (Herceptin) used in the treatment of some breast cancers.
monoclonal antibody binds extracellular domain of Her2 inhibition of receptor dimerization and activation
What is the role of Rb in retinoblastoma?
mutation in Rb no longer prevents cell division in the absence of a growth signal impacts Rb in immature cells of the retina
Describe some methods to activate p53 by deactivating other genes?
mutational inactivation of some tumor suppressor genes including retinoblastoma (Rb), and adenomatous polyposis coli (APC) or the mutational activation of some oncogenes such as ras and myc.
Mutations in some carbonic anhydrases are associated with what?
mutations in some carbonic anhydrases have been found to cause osteopetrosis (excessive formation of dense bones accompanied by anemia) and mental retardation.
NORAD long non-coding RNA?
non-coding RNA activated by DNA damage (NORAD)—has recently been shown to be required for maintaining genomic stability NORAD interacts with proteins involved in DNA replication and repair in steady-state cells and localizes to the nucleus upon stimulation with replication stress or DNA damage. In particular, NORAD interacts with RBMX, a component of the DNA-damage response, and contains the strongest RBMX-binding site in the transcriptome.
Give 4 factors that can cause double stranded breaks
nucleases reactive oxygen species ionizing radiation ultraviolet light
Acyclovir
nucleoside analogue that is especially good against herpes family virus
Tell me what the antigens in the ABO blood system are made of?
oligosaccharide (O) antigen. N-acetylgalactose (A) or galactose (B) monosaccharide. AB blood group has both A and B antigens.Additional antigens are bound to define the positive or negative state of the ABO blood groups.
What is meant by the "two hit" model?
one allele of the gene has an inherited mutation the second allele must be hit by an independent mutation (same cell) leads to tumorigenesis example: retinoblastoma
Give an example of a commonly used cloning plasmid
pBR322 picture shows: Diagram of a commonly used cloning plasmid; pBR322. It's a circular piece of DNA 4361 bases long. Two antibiotic resistance genes are present, conferring resistance to ampicillin and tetracycline, and an origin of replication that the host uses to replicate the DNA.
What is the isoelectric point?
pH at which lack of movement during electrophoresis, as amino acid has no net charge in the statistical mean.
Name 2 essential fatty acids
polyunsaturated fatty acids such as linoleic acid and α-linolenic acid
What is ∆G of acetyl CoA → Fatty acid chain?
positive. Need ATP to make it negative by coupling
Tell me about primer design
primer should be 18-24 nucleotides in length If it is too short, it would lack specificity. If it is too long, annealing efficiency would be reduced. The GC content of the primer should be between 50-60% dont want long runs of GC GC affects melting temperature of primer. melting temperature of primer should be between 5 degrees of each other, otherwise, you cant use those primers simultaneously in PCR melting temperature should be between 55 to 65 degrees at 3' end there should be a G/C pair, this is called a G/C clamp, tighter fit primer self complementarity, hair pin loops form if primer is complementary to itself, primer dimers form if the primer is complementary to the other primer
Gonadotropin-releasing hormone
produced and released by the hypothalamus stimulates the production and pulsatile release of luteinizing hormone and follicle-stimulating hormone in the anterior pituitary
Enterotoxigenic E coli or ETEC
produces heat stable and heat labile enterotoxins which make intestines secrete electrolytes and water normally causes diarrhoea in travellers kill it with cipro
What are the general names for the group of molecules that regulate and mediate p53 activation?
protein kinases histone acetyl-transferases methylases ubiquitin sumo ligases.
Caretaker genes
responsible for the integrity of the genome. Caretaker genes encode products that stabilize the genome. inactivation of caretaker genes --> rapid accumulation of DNA damage in a normal cell --> cancer ex: BRCA1/2 Caretaker genes contribute to genome stabilization for example, proper cell-cycle checkpoints, DNA repair pathways, and other actions that ensure cell survival following DNA damage. Specific DNA maintenance operations encoded by caretaker genes include nucleotide excision repair, base excision repair, non-homologous end joining recombination pathways, mismatch repair pathways, and telomere metabolism.
tbc
tbc
What is the first reduction step in the malonyl-CoA pathway?
the first reduction step is the conversion of acetoacetyl-ACP to ß-hydroxybutryl-ACP (using up one NADPH2),
difference between α and β glucose in terms of hydroxyl group?
the orientation of the hydroxyl group about the anomeric carbon of α-D-glucose is axial and equatorial in β-D-glucose.
How does the Trp Operon Work? Contrast the Trp operon with the Lac operon briefly
the tryptophan (Trp) operon is inhibited by a chemical (tryptophan). This operon contains five structural genes: trp E, trp D, trp C, trp B, and trp A, which encode tryptophan synthetase. It also contains a repressive regulator gene called trp R. trp R has a promoter where RNA polymerase binds and synthesizes mRNA for a regulatory protein. The protein that is synthesized by trp R then binds to the operator which then causes the transcription to be blocked. In the lac operon, allolactose binds to the repressor protein, allowing gene transcription, while in the trp operon, tryptophan binds to the repressor protein effectively blocking gene transcription (trpytophan activates the repressor that binds to the operon, physically obstructing RNA polymerase. If in a low tryptophan environment, then trp does not bind to the repressor, so transcription CAN occur). In both situations, repression is that of RNA polymerase transcribing the genes in the operon. Also unlike the lac operon, the trp operon contains a leader peptide and an attenuator sequence which allows for graded regulation. It is an example of repressible negative regulation of gene expression. Within the operon's regulatory sequence, the operator is blocked by the repressor protein in the presence of tryptophan (thereby preventing transcription) and is liberated in tryptophan's absence (thereby allowing transcription). Tryp Operon can be found in E-coli genome
Tell me about primary Ercc1−/− murine embryonic fibroblasts
they have reduced DNA repair capacity, which senesce rapidly if grown at atmospheric oxygen.
In bacteria, what do you call chains?
they have strepto in their name like streptococcus
What does downstream mean?
toward 3' end
transketolase
transfers two carbon fragment from a ketose donor to an aldose acceptor.
Intravasation
tumor cell must enter circulation via degradation of vascular basement membrane
Neurofibromin and NF1
tumor suppressor that converts active Ras into inactive Ras. NF1(gene) codes for neurofibromin, a GTPase-activating protein that negatively regulates RAS/MAPK pathway activity by accelerating the hydrolysis of Ras-bound GTP NF1 has a high mutation rate and mutations in NF1 can alter cellular growth control, and neural development, resulting in neurofibromatosis type 1
How do Hif-1α and Hif-β contribute to tumor growth?
under hypoxic conditions --> HIF1alpha is not hydroxylated --> escapes degradation HIF1alpha pairs with HIF1beta --> activates transcription of genes that promote angiogenesis
viviparous
viviparity is development of the embryo inside the body of the parent, eventually leading to live birth, as opposed to reproduction by laying eggs that complete their incubation outside the parental body.
Can inflammation lead to p53 activation?
ye
Tell me about hemocytometer
you can use it to count cells. hemocytometer was originally used to count blood cells
What is the other name for 2-oxoglutarate?
α-ketoglutarate
What are the 3 major types of omega 3 fatty acids
α-linolenic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA).
