Biochemistry Video 7

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What type of bond is formed between amino acids?: peptide bond
What is an important element in the side chain of methionine?: Sulfur
What is the important characteristic of the side chain of a tyrosine?: it contains a phenol group
in what direction are proteins synthesized?: they are synthesized in the amino to carboxy direction
What are the two sites of a ribosome?: P site and A site
What does P site stand for?: it is the peptide site
this is where the peptide is held
What does A site stand for?: it is the accceptor site is where the incoming tRNA with it's amino acid would bind to
What initiates translation of mRNA?: the small ribosomal subunit must recognize the 5' methyl cap in the eukaryote or the shine dalgamo sequence in the prokaryote
What is the name of the small ribosomal subunit that recognizes the shine dalgamo sequence?: 16S subunit
Which ribosomal site does the initial methionine bind to?: the P site
What energy is used in the initiation of translation?: GTP, not ATP, connects the large ribosomal subunit to the small ribosomal subunit along with the mRNA
What are the three steps of elongation?: 1. aminoacyl-tRNA binds to A site
2. peptide Bond Forms
3. Translocation of ribosome to next codon
What are the needed elements for the Aminoacyl-tRNA binding to the A site?: GTP
EF's in prokaryotes
eEF's in eukaryotes
What are the needed elements for the peptide bond formation between the amino acid in the A and p site?: peptidyl transferase in large subunit
Uses the 2 ATP used when the aminoacyl-tRNA was activated by placing an amino acid at the 3' end acceptor arm of the tRNA
What are the needed elements for the translocation of ribosome along RNA?: GTP
EF's in prokaryotes
eEF's in eukaryotes
What are the stop codons?: UAG
UGA
UAA
What is the elongation factor in eucharyotes which is needed for the translocation of ribosome along the mRNA?: eEF-2
What is the form of energy used in translation?: GTP
How many high energy bonds are used for each added amino acid to the chain?: 4 high energy bonds
what is a polysome?: aka - polyribosome
this is when multiple ribosomes are reading a single strand of RNA at the same time
What types of antibiotics inhibit the 30S subunit of prokaryotic ribosomes?: aminoglycosides and tetracyclins
How do aminoglycosides work?: they inhibit the initiation of translation by binding the 30S subunit in the in the initiation complex, and NOT ALLOWING THE BINDING THE THE INITIAL tRNA to the P SITE

they also kink, or distort, the mRNA in prokaryotes to where the genetic code is unreadable
What are the side effects of aminoglycosides?: nephro and oto-toxicity
What is the mechanism of tetracyclins?: They bind in the A site of ribosomes, thus preventing elongation by preventing the binding of the next aminoacyl-tRNA
How do you recognize a tetracyclin drug by name?: they all end in -cyclin
In what types of infections are tetracyclins expecially used?: chlamydia or rickettsia
What are the side effects of tetracyclins?: fairly minimal...they cause kilation, which is the discoloring of bone and teeth, and thus tetracyclins are not given to pregnant mother or children

And if a patient takes expired tetracyclins they can cause symptoms of renal failure known as a fanconi (Sp?) like syndroe
Waht are the inhibits or the 50S subunit of ribosomes?: chloramphenical
macrolides
clindomycin
What is the mechanism of chloramphenical?: it binds to the 50S subunit and inhibits the peptidyl transferase enzyme
For what disease is chloramphinicol used for?: meningitis caused by h. Influenzae
bacause soluble through the blood brain barrier
What are the two point that chloramphenical is famous for?: The is associated with grey baby syndrome
and
aplastic anemia
What is the mechanism of action of macrolides and clindomycin?: inhibits the translocation of ribosomes
What are macrolides regularily used against?: mycobacterium
What type of diseases is clindomycin commonly used against?: bone infection
What is one main side effect of clindomycin use?: Clostridium difficil
What is the primary structure of the proteins? secondary? tertiary? quaternary?: primary = actual amino acid sequence
secondary = folding of amino acids into ALPHA HELIX or BETA PLEATED SHEATS
tertiary = this is the way that the alpha helixes and beta pleated sheets arrange themselves in 3D.
quaternary = refers to multi-subunit proteins, such as RNA polymerase of prokaryotes and hemoglobin
what type of bonds form the quaternary structure?: disulfide
What is the first characteristic of proteins that will be targeted (destined for somewhere other than the cytoplasm)?: Their N-terminus will be very hydrophobic. this is known as a SIGNAL SEQUENCE.
What is the first step in targeting of proteins?: Due to the hydrophobic signal sequence the ribosome will hooked by SIGNAL RECOGNITION PARTICEL (SRP) onto the membrane of the ER
What does this ribosomal binging to the ER by signal recognition particle (SPR) cause?: This is what forms the RER.
What happens to the protein after the ribosome is bound to the ER?: The signal sequence is removed by SIGNAL PEPTIDASE
what happens to the proteins after the signal sequence has been recomed by signal peptidase?: The proteins are glycosylated in the ER and continues in the golgi
Where do the glucose molecule bind to the protein?: Glycosylation occurs on the N (nitrogen of key amino acids) of key amino acids
What molecule of glycosylation require?: Dolichol-P
(Dolichol-Phosphate)
Where does Dolichol-Phosphate come from?: it is an intermediate of cholesterol metabolism
How are newly synthesized proteins packaged into lysosomes?: After the protein which started with the N terminus hydrophobic region has been gylcosylated in the ER and golgi, in the golgi some of the sugars will be phosphorylated.
Which sugars are phosphorylated in the golgi, thus tagging the protein to be destined to the lysosome?: mannose
What enzyme in the golgi phosphorylates the mannose sugars on the new protein?: phosphotransferase
What disease results from a lack of phosphotransferase? What is the mechanism?: I cell disease

Without the hydrolysing enzymes in the golgi apparatus, debri is not broken down, and thus inclusion (hence I cell) bodies build up. These hydrolytic enzymes are also free in the to do damage to the cell
What does gamma-carboxylation do? Which amino acid does it work on?: This is the addition of an extra carboxyl group on glutamate amino acids
What is the result of gamma-carboxylation? Why is this important?: produces Ca2+ binding sites

Calcium is an important modulating factor in systems such as clotting factors
Which clotting factors require gamma carboxylation and therefore Ca++ bonding?: 2,7,9,10
What is the mechanism of warfarin?: it inhibits the gamma-carboxylation of glutimates in factors 2,7,9, and 10
What is prenylation?: it is the addition of turpins to the protein to give it the ability to anchor inself within the membrane
What is the smallest amino acid?: glycine
What is the significance of glycine in collogen?: it is every third amino acid

it form a very tight helix for collogen
Besides glycine, what are two other main amino acids in collogen?: Proline and Lysine
Why ar eproline and lysine important in collogen?: They are hydroxylated in the ER by HYDROXYLASES
What is a co-factor for hydroxylases?: Vitamin C
What is the result of a lack of vitamin C?: No Vitamin C...No hydroxylation of proline or lysine...no hydroxylation of proline and lysine in collogen.....breakdown of collogen...THIS IS THE DISEASE KNOWN AS SCURVY
What happens to collogen after the proline and lysine has been hydrolysed?: it is glycosylated
What happens after the collogen has been glycosylated?: three pro-alpha chains will wrap together to form a triple helix
What happens to the triple helix?: it is finally secreted form the RER and the peptide ends are cleaved to form (mature)COLLAGEN, ALSO KNOWN AS TROPOCOLLAGEN
What happens after the mature collogen is formed?: it is assembled into fibrils (large fibers of collogen)
What are these fibrils (bundles of collagen) stabilized by?: Lysyl oxidase
What is the co-factor for lysyl oxidase?: Cu+
Which enzymes in the production of collogen require co-factors?: hydroxylases = require Vitamin C for hydroxylation of proline and lysine

extracellular lysyl oxidase = requires copper to stabilize the fibrils of collogen
What are two diseases in which there is a dificiency in copper?: menkes disease

wilson's disease
Which enzyme needs copper as a cofacter?: lysyl oxidase
What is the mechanism for menkes disease?: there is a deficit in an efflux protein that is found in the GI epithelial cells. This deficient protein is necessary for copper to be absorbed in our body.
Why does menkes disease present with steely hair?: tyrosinase is another enzyme that requires copper as a cofactor. tyrosinase is an enzyme that produces melanin.
What does tyrosinase deficiency itself result in?: albinism
What is osteogenesis imperfecta due to?: mutations in collagen genes that are autosomal dominant
What is pathomneumonic for osteogenesis imperfecta?: blue sclera
What is ehler-danlos syndromes due to?: mutations in collagen genes
Where is the mutation is ehlers-danlos type 9?: lysine hydroxylase
What does Ehlers Danlos type 4 have a problem making?: collagen type III - found in skin, blood vessels and GI walls because it is strong but very flexible.
What is one major cause of death in ehlers-danlos patients? what are they famous for?: they are extremely flexible but can rupture their aorta very easily
What is required placing of proteins into the lysosomes.: phosphorylation of mannose residues

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