ribosome reads 5' to 3'. Think about prokaryotes. In prokaryotes transcription and translation happens simultaneously (since there is no nucleus). mRNA is synthesized 5 to 3, thus the 5 end is the loose one being the only end available for the ribosome to attach and start translating.
Involved in generation of mature mRNA transcripts. Complement with proteins. Central components of the splicing apparatus. Also involved in regulation of:Transcription factors RNA pol II activity, Telomere maintenance
regulation of gene expression (eg regulate whether mRNAs get translated Silencing of gene expression (RISC)
DNA hypomethylation agents: 5-azacytidine, 5-aza-2’-deoxycytidine (Decitabine)
Cytidine analogues are DNA hypomethylation agents They have an N in the base portion (instead of a C) and thus prevent methylation, which is important for transcriptional regulation. Once incorporated into DNA and RNA they cause hypomethylationas a methyl group cannot be added to the Nitrogen at position 5. Additionally, these drugs are know to bind and inhibit DNA methyl transferase enzymes. In eukaryotes, methylationof cytosine is an important mechanism of transcriptional regulation.
Prokaryote DNA supercoiling
accomplished by the action of two enzymes -DNA gyrase and DNA topoisomerase I, and the association of the DNA with proteins -primarily HU proteins (DNA is held by them in coils).
what indroduces negative supercoils in eukar DNA?
Topo II introduces (-) supercoils using ATP. (Gyrase does this in prok)
Acetylation removes the +ve charge of Lysine. DNA has a negative charge. The removal of the positive charge on the histone Lysine reduces the affinity between histone and DNA. As a result transcription is increased.
Histone acetyltransferases (HAT) acetylate the nucleosome (access to DNA is facilitated)
Deacetylation via histone deacetylase restores +ve charge (DNA more tightly wound). Histone Deacetylases (HD or HDACs) tighten nucleosome complex.
Prokary. DNA pol I
removes RNA primer and replace with DNA
Prok DNA pol III
synthesis of leading and lagging strand.
in Eukaryotes. Main replicative enzyme.(similar to pol III in prok). Highly processive. 3'-5' exonuclease activity.
Binds the TATA box in Euk (promoter region), recruits other transcription factors.
phosphorylates RNA pol and activates it. has helicase function to unwind DNA.
Euk RNA Pol I transcribes
5.8S, 18S, and 28S r RNAgenes
Euk RNA polymerase II transcribes
all protein-coding genes (mRNA), some snRNAs and microRNA(miRNA)
Euk RNA polymerase III transcribes
tRNA genes and some snRNAs
Autoimmune disease. Individuals with this condition possess antibodies that react with the U1 RNA component of the spliceosome.
reduction or absence of beta chains in RBC. Etiology: splicing errors. Mutations in the beta-globin gene that generate additional splice sites within the mRNA.
Limb Girdle Muscular Dystrophy
mutation in the calpain-3 gene that generates a new splice site within the exon16 (coding sequence)
Small nuclear(splicing of mRNA)
Small nucleolar RNA(splicing of rRNA)
P,A, E site
The P site holds the tRNA that carries the growing polypeptide chain. A site holds the tRNAthat carries the next amino acid to be added to the chain. The E site is the exit site, where discharged tRNAsleave the ribosome
inactivation of EF-2 by ADP-ribosylation
Elongation factor (EF-2) in euk (EF-G in prok): facilitates movement of the ribosome three nucleotides along the mRNA 5’->3’ (P is now in E, A is now in P, A is empty). The toxin stops translocation.
initiation inhibitor. Prevents assembly of ribosome (binds to 30s subunit).In E.coli the small 30S subunit is involved in the initial binding to the mRNA.
antibiotic elongation inhibitor. Prevents tRNA access to the A-site
Elongation inhibitor. Binds to the 50S subunit of the complete (70S) ribosome. Blocks ribosome translocation.
Antibiotic elongation inhibitor. Inhibits peptidyl transferase activity in prokaryotes .
Inhibits eukaryotic peptidyl transferase activity
Causes premature termination of translation in both prokaryotes and eukaryotes
Proinsulin matures in the
Golgi where it is cleaved forming insulin and C-peptide
PH = pKa + log [conjugate base]/[weak acid]
carbonic anhydrase inhibitor. Causes acumilation of carbonic acid (no conversion to bicarb ion. Found in kidney. Allows reabs. of bicarbonate, sodium, and chloride. These are excreted if enzyme inhibited. BP is lowered, PH decreases.
functions as a buffer and accepts H+ formed by CO2 coming together with water and forming H2CO3 which then loses a proton
Carbonic anhydrase inhibitors cause hyponatremia. Bicarb in lumen combines with H to form H2CO3. Carbonic anhydr. Splits this into CO2 and water. The CO2 goes into the cell. There it is converted by carb anhydr. Into bicarb and a proton. The proton goes back into the lumen in exchange for Na+ (antiporter). The bicarb meanwhile it sent into the blood. When you inhibit carb anhydr. You inhibit the reabs of Na+. causes hyponatremia in blood. It also causes acidosis, because we are losing all the bicarbs in the urine which would be alkaline.
The bicarb in the lumen is lost (can’t turn it into water and CO2). Thus we decrease bicarb in the blood (lose part of our buffer system)
Metabolic alkalosis is caused by
Vomiting, pyloric stenosis
Injury to the phrenic nerve (supplies diaphragm) can result in
Hypoxia (eg high elevation) may result in
respiratory alkalosis (due to hypervent)
acid base disorder ID
If the PCO2 change is the opposite direction of the pH change, then it is a respiratory disorder. Eg: If pH-low and PCO2-high (respiratory). If the PCO2 change is in the same direction as pH change, then it is a metabolic disorder. Eg: If pH-low and PCO2-low (metabolic)
differs from other AAs. Side group forms a ring imine (secondary group as opp to prim). Leads to bends in protein chain. Collagen is rich in Pro. Proline is an alpha helix breaker. (both Pro and Ala are hydrophobic)
Non-polar aliphatic side chains
glycine, alanine, proline. They are hydrophobic. Proline is cyclic. Valine, Leucine, Isoleucine are in the same category, but they are BCAs.
AA's with aromatic side chains
Phenylalanine, Tryptophan, and Tyrosine have aromatic side chains. Trp has two rings. They are mostly non-polar, but Trp and esp Tyr are more polar (due to OH grp on Tyr ring. Tyr otherwise looks just like Phe.) Trp has a higher absorbance than Tyr.
Polar uncharged AA groups
Asparagine and glutamine. (from aspartate and glutamine respectively). Ser, Threonine contain OH groups. May be phosphorylated, glycosylated.
Sulfur containing AAs: Methionine (non-polar) Cysteine (more polar – uncharged at neutral pH). The SH groups can undergo redox rxns. Cysteine contains a sulfhydril group. 2 Cys can form a disulfide bond. This oxidation rxn results in cystine.
AAs with neg side chain
Asp and Glu
AAs with positive side chains
Arg, His, Lys
GABA is a neurotransmitter. It is formed by the decarboxylation of glutamate
mediates allergic and inflammatory responses, gastric secretion and neurotransmission: it is formed by the decarb of histidine.
turns into 5-Hydr-Trp (hydroxylation). Then a CO2 comes (decarb) off to form serotonin. Prozac is a selective ser reupt inhib. (SSRI). LSD affects serot receptors
dopamine, norepinephrine and epinephrine are formed from tyrosine. Tyrosine is hydroxylated to dihydroxy-phenylalanine (L-DOPA). L-DOPA is decarboxylated to dopamine, the first catecholamine. Dopamine can act as neurotransmitter or it can be used as an intermediate for the synthesis of norepinephrine and epinephrine
AA's affecting helix structure
Alpha helix (secondary strux) can be disrupted by proline (bend or kink), glycine (allows rotation)
TSE Transmissible Spongiform Encephalopathy
Prion (infectious protein) disease (resistant to degradation by cell). Contains no nucleic acid. The abnormal form of PrPis called PrPsc (turns int open prot conform and spreads).
Type I collagen
represents >90% of total body collagen content. thick fibrils, regular staggered, cross-linked, striated, high tensile strength, diseases: Ehlers-Danlos Syndromes (EDS) , Osteogenesis Imperfecta
Type II collagen
thinner fibrils, less cross-linked, high hydroxyproline content, cartilage-like structures
Type III collagen
thin fibrils, network in skin vascular vessels, muscle, often associated with Type I collagen. EDS.
Type IV collagen
no fibrils but a mesh network that forms the basement membrane (basal lamina) together with the glycoproteins laminin and fibronectin. Type IV contains a globular carboxy-terminal domain.
Type V collagen
leads to small fibers with a globular N-terminal domain. Type V is often associated with Type I and mutations result in the classic forms of EDS
soluble. synthesized in fibroblasts, osteoblasts, chondroblasts. Procollagen has S-S bonds, mature collagen does not.Procollagen goes from golgi to ECM
biochemical defects in Ehlers-DanlosSyndromes (EDS)
Can result from a mutation of a gene for the pro-al[ha chains of collagen (often Type I, III, or V collagen. Can also result from a hereditary defect (in enzyme itself). Type III collagen generally affected.
biochemical defect in Osteogenesis Imperfecta(OI)
Hereditary, related to collagen.Bones bend or fracture easily. Can result in less amounts of normal collagen or it can result in
abnormal collagen of Type I , often a mutation displacing a glycine by serine or cysteine. OI Type I is the mildest form, OI Type II is the most severe form.OI TypeIII is severe and OI Type IV is deforming but with normal sclerae
biochemical defect in Marfan’s syndrome
Results from an autosomal dominant hereditary defect in the gene that encodes fibrillin-1. Note: the gene for elastin is normal. long, thin limbs.
Hb vs myoglobin
The conformation of myoglobin and a single globin monomer (eg beta chain of Hb) of hemoglobin are practically superimposable.
Hemoglobin A (HbA)
is a pair of identical αβ-dimers (α2β2tetramer). subunit interactions are Hydrophobic, Ionic, Hydrogen bonds. 4 globin monomers means that 4 O2 molecules may be carried on Hb. Alpha1-beta1 dimers combine with apha 2-beta 2
conformational change in the Hb molecule following oxygen binding
Normally the Fe ion is slightly out of plane in the heme ring. Fe ion moves into the plane of the heme when oxygenated.
Proximal histidine and its associated residues are pulled along with the iron ion (tugging). Change is transmitted to other Hb molecules - cooperativity.
promotes formation of the taut state; decreases O2 affinity for Hb. 2.3 BPG has a (-) charge. 2,3-BPG allows the formation of additional salt bridges between the αβ/ αβ dimers
Think right = release (more apt to). DPG, aka 2,3 BPG will shift curve to right.
2.3 BPG is an intermediate of glycolysis. A hexokinase deficiency, which precedes the conversion to 2,3 BPG, would lead to a decrease in 2.3 BPG and thus the O2 would be more tightly bound (left shift).
Effects of Pyruvate kinase deficiency
Elevated 2,3-BPG levels, Right shift on binding curve, Decreased O2 affinity
H+ ions promote oxygen release from Hb. As pH decreases, Hb O2 affinity decreases (right shift)
Effect of low pH on Hb
Reduced pH (more H+ions) allows formation of more interactions between the salt bridges betw the alpha and beta dimers of Hb, & increased stabilization of the taut state. O2 is given up more easily (right shift).
Fetal hemoglobin binds to 2,3-BPG less tightly, so it has slightly higher O2 affinity. HbF is left shifted.
MetHb does not function as an O2 carrier. contains a Fe3+ (ferric ion)in the porphyrin ring. Methemoglobin is formed by the release of superxide (O2-) ion from the iron in regular Hb.
Normally it is enzymatically converted back to the ferrous form. But when deficient in converting factor blue people syndrome occurs. Methylene blue can be used as a therapeutic reductant.
Myoglobin v Hemo
Hemo = O2 transport, Myo = O2 storage (has higher affinity). In Myo affinity does not change with PO2. No allosteric regulation and it is a monomer, not a tetramer.
Sickle Cell Mutation (Hemoglobin S (HbS))
Position 6 on β-chains, Glu is replaced by Val. Hydrophobic interaction between Hb leads to aggregation. Deoxygenated HbS polymerizes into filaments altering cellular shape. sickle cells block blood flow. Caused by single bp mutation.
Which AA can act as a buffer?
His (pka about 6, close to physiological)
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