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Cell Biology Exam 1
Organells to Initiation of translation
| Question | Answer |
|---|---|
| What is an organelle? | A membrane bound structure found subcellularly (within the cell) |
| What are common examples of organelles? | Nucleus, mitochondrion, chloroplast, endoplasmic reticulum. |
| In what ways do promote greater efficiency? What is this called? | Called compartmentation, organelles allow for specilization of tasks and greater regulation by having reactions take place in localized area - the reactions take place at a greater rate. This allows the process to be controlled in their place. |
| Which common cellular structures are not organelles? | neither ribosomes nor the cell wall are considered organelles. Also, the plasma membrane surrounding both eu/procaryotic cells is not an organelle. |
| What is cytosol? | It is a concentrated aqueous gel surrounding the organelles. |
| What is the cytoskeleton and its function? | It is a network of protein fibers that supports the eucaryotic cell shape. It is not an organelle |
| What is the strongest type of bond and on average how much energy does it take to break it? | Covalent bonds are the strongest bonds requiring an average of 90kcal/mol to break. |
| How do nonpolar covalent bonds share electrons? | These bonds share electrons equally or almost equally between the atoms. Examples of this would be C-C; C-H; or O=O |
| Why do hydrophobic (water fearing) molecules not mix well with H20? | Like solutions dissolve like substances. H2O is a polar liquid and as such will not dissolve nonpolar substances. They will not make hydrogen bonds. |
| What is the strongest type of bond and on average how much energy does it take to break it? | Covalent bonds are the strongest bonds requiring an average of 90kcal/mol to break. |
| What is an Ionic bond? | One atom loses an electron to another. |
| What is the interaction between Ions and macromolecules? | Ions can pair with macromolecules. |
| What is the "native" conformation for most macromolecules? | Noncovalent bonds give macromolecules their most stable arrangement. |
| Ionic bonds are very strong but weak in aqueous solutions, why is this? | Once in solution, the ions will separate and each will be surrounded by a shell of H2O molecules. In this formation the Oxygen of H2O would face the positively charged Ion. |
| Why do hydrophobic (water fearing) molecules not mix well with H20? | Like solutions dissolve like substances. H2O is a polar liquid and as such will not dissolve nonpolar substances. They will not make hydrogen bonds. |
| How are polar covalent bonds shared? Why are they like this? | Polar covalent bonds have an unequal sharing of electrons as the electrons are moe strongly attracted to the electronegative oxygen or nitrogen atoms. Hydrogen and Carbon are not strongly electronegative. |
| What are the 4 types of noncovalent bonds/interactions? | Ionic bond, hydrogen bonds, van der waals interactions, and hydrophobic forces. |
| What is a hydrogen bond? | Partially charged H atoms are attracted to partially negative charged atoms of another molecule. |
| Where do hydrogen bonds occur and how strong are they? | Hydrogen bonds are weak at about 1kcal/mol. they occur in molecules with polar bonds (hydrophilic molecules) and always involve a hydrogen atom with a positive charge. |
| Each H2O molecule can form up to 4 H-bonds with other H2O molecules. How does this work? What does this form? | The H2O molecules join transiently in a hydrogen-bonded lattice. The Hydrogen atoms flicker from one oxygen atom to the next. Each time it only lasts for a nanosecond before flickering off again. This short lived assembly is called a flicering cluster |
| What is the cohesive nature of H2O responsible for? | Water's high surface tension, specific heat, and heat of vaporization. |
| What are hydrophobic forces? | association of nonpolar molecules in order to avoid interfering with interactions between water molecules. |
| what are lipids? | Fatty acids. They are aphipilic molecules that possess both hydrophobic and hydrophilic regions. |
| what gives lipids their amphiphilic protperties? | The carboxylic head group releases H+ in solution and is hydrophilic. The hydrocarbon tail, which is nonpolar, is hydrophobic. |
| What is a micelle? | It is the bubble or group that fatty acids and lipids cause when placed in water. The outter hydrophilic head faces the water while the hydrophobic tails face the middle. |
| How is a micelle essential to the basis of a cell? | The micelle system is the basis for the self sealing lipid droplets in cell cytoplasm. The lipid bylayers also form the cellular membranes. |
| What are Van der waals attractions? | the weakest interactions, 0.1kcal/mol, these short lived electrical attractions occur between any two atoms due to unequal electron distribution (temporary dipole)they occur only at very short distances. In large numbers they help hold molecules together |
| What is a protein? | it is a linear polymer of amino acids. |
| How may the side chain ( R group) differ in proteins? | It may be acidic, basic, hydrophobic, or polar. |
| Which isomers are found in proteins? | Only the L-amino optical isomers are found in proteins. D-amino acids are found in bacterial cell membranes. |
| What is the primary structure of a protein? | In a protein, it is the linear sequence of amino acids linked by covalent peptide bonds. |
| What determines the overall structure of folded proteins? | It is the unique sequence of each protein as well as the properties of the 20 different amino acid side chains. |
| What largely determines the 3D structure of a protein? | 3D structure is largely determined by noncovalent bonds. |
| What are the ways in which H-bonds can occur in proteins? | Hydrogen bonds can occur in 3 ways; between atoms of 2 peptide bonds(2nd structure), between atoms of a peptide bond and a side chain, or between 2 side chains. |
| What is the function of chaperones in cells? | these proteins help newly synthesized polypeptides fold into the most stable conformation with great efficiency. Otherwise, it would have to wait for hydrophobic forces to fold the protein. |
| What determines the most stable conformation of a protein? | The combined strength of many covalent bonds. |
| What is the effect of hydrophobic forces on protein structure? | hydrophobic forces cause nonpolar R-gruoups to be concentrated in the interior of the protein. |
| What is often the most significant force determining the most stable conformation? | hydrophobic forces. |
| Where are charged polare side chains usually located and what is their interaction? | Polar side chains are usually found on the surface of the protein as it forms hydrogen bonds with water or paired in Ionic bonds. If found in the interior, these groups usually hydrogen bond to other groups or are paired in ionic bonds for stability. |
| What is a protein domain? | a region of a protein that folds independently of the rest of the protein. |
| How do side chains of amino acids interact in hydrogen bonding in the secondary structure? | Side chains are NOT involved in the hydrogen bonds of secondary structure. |
| Which groups of a peptide bond can form H-bonds with another peptide bond? | The carbon-oxygen (C=O) and the nitrogen-hydrogen (N-H) groups of a peptide bond. |
| What is the alpha helix? | the alpha helix is a rght handed helix with hydrogen bonds parallel to the axis of the helix. |
| How many amino acids make up the turn of an alpha-helix? | A turn in the helix contains 3.6 amino acids. |
| Where do hydrogen bonds in the beta sheet occur? | H-bonds in a beta sheet occur between the peptide bonds of adjacent polypeptide chains. |
| What is a potential product of amphiphilic alpha helixes? | Aphiphilic alpha helixes can form a coiled coil. |
| What is an amphiphilic alpha helix in terms of structure? | An amphiphilic alpha helix has nonpolar amino acid R-groups on one face, adn polar amino acid R-groups on the opposite face. |
| Where are amphiphilic Helices found? | Found in globular proteins with the hydrophobic side facing the interior. |
| How is an amphiphilic coil produced? | 2 or 3 aphiphilic helices can twist together to form a coiled coil in which hydrophobic forces push the nonpolar R-groups to the inside of the coil. |
| What are example of amphiphilic alpha helixes? | Fibrinogen, alpha-keratin, leucine zippers, myosin. |
| What is the tertiary structure of a protein? | tertiary structure is the complete 3D conformation. it includes the interactions of the amino acid side chains. |
| What is quaternary structure? | Only proteins that contain 2 or mroe polypeptide chains have quaternary structure. it is the interaction between these proteins. |
| How does tamiflu inhibit the influenza virus? | It inhibits the flu virus neurominidase from cleaving the sialic acid from the surface of infected cells. |
| what types of bonds/interactions are tertiary structure and Quaternary structure most dependent on? | most are dependent on the 4 types of noncovalent interactions. the exception are proteins that are secreated from cells which often contain covalent disulfide bonds which are for stability. |
| between which 2 amino acids are disulfide bonds formed? | Cysteine-Cysteine bonds. |
| What is the equation for the change in free energy? | (delta)G= G(products) - G(reactants) |
| How is the delta G of a reaction changed by enzymes? | enzymes cannot change the delta G of a reaction. |
| What is the value for delta G in energetically favorable reactions? | the delta G is negative for energentically favorable ractions. |
| Why does entropy increase? | Entropy will increase because part of the reactants chemical energy is lost as heat energy. |
| What does a negative delta G tell us? | It means the reaction may occur, but it does not tell us when or how it will occur. |
| What does delta G not tell us? | It does nto tell us the mechanism of reactions or the rate of the reaction. |
| What can enzymes catalyze? | Enzymes can only catalyze energetically favorable reactions with negative Delta G values, or coupled reactions in which the total Delta G is a negative value. |
| What does an enzyme do? | They increase the rate of energetically favorable reactons. they act as a catalyst to speed up reaction(as much as 10^14 increase in rate) They can change the mechanism of reaction thus lowering the activation energy required to start the reaction. |
| What is the active site of an enzyme? | It is a highly specific site for the substrate and the reaction catalyzed. |
| What happens to the enzyme at the end of reaction? | The enzyme is ALWAYS regenerated, ready for another round of catalysis. |
| The Delta G for a pathway is the (BLANK) ? | Sum of the Delta Gs for each step. |
| How may an enzyme drive a reaction witha positive delta G? | It may couple with/to a reaction with a negative Delta G. The Net Delta G must always be a negative reaction however. |
| What is usually involved in binding the substrate to the enzyme? | Usually it is multiple noncovalent bonding forces. |
| Where does an enzyme bind its substrate? | It binds its substrate in the active site. |
| Where do proteins such as hemoglobin or recpetors bind their ligands? | they bind their receptors in highly specific binding sites/ |
| What role does the microenvironment of the active site play? | It stabilizes the transition state of the reaction by bringing reactants together in optimum orientation. By destabilizing bonds of the substrate, or by Favoring the reaction with Charged side chain groups that alter the elctron distribution. |
| What is a protein prosthetic group? | It is any nonprotein molecule that is a permanent part of the final structure. It usually aids in catalysis or function of the protein. Metals, vitamins, sugars, or RNA molecules may be attached covalently or bound noncovalently. |
| What are some common examples of a prosthetic group? | Heme of hemoglobin; Retinal, from vitamin A; RNA bound to telomerase. |
| What is retinal? | Retinal is a pigment bound by the protein rhodopsin in the eye. Light adsorption by retinal attached to rhodopsin triggers the signal transduction in vision. |
| what is an allosteric protein? | They are enzymes or proteins that contain a binding site. Binding a ligand in this allosteric binding site triggers a change in conformation that affects activity at the catalytic site/ |
| What is the relationship between feedback inhibition and allosteric regulation? | Feeedback inhibition of an enzyme that catalyzes a reaction in a pathway by the product of the pathway usually works by allosteric regulation. |
| How does phosphorylation affect the regulation of some properties? | They are regulated by phosphorylation of an amino acid side chain which triggers a conformation change. |
| How are GPTases activated? Inactivated> | GTP binds to these proteins. when the GTP is hydrolyzed from the GTP to GDP + Phosphate, the protein switches back to its inactive form. |
| What does GTPase superfamily of proteins regulate? | They regulate many of the cellular processes, including protein synthesis, transport of molecules into and out of the nucleus, and signaling pathways. |
| What is a chromosome comprised of? | Chromosomes are comprised of DNA plus the protein bound to the DNA. |
| What are the component of a neucleotide? | Nitrogen-rich base, a sugar, and a 1-3phosphate group. |
| What is the Delta G for hydrolysis of the last phosphate linkage? What is its impact? | The Delta G for hydrolysis of the last phosphate linkage in a neuclotide is (-)7.3kcal/mol, making ATP a useful short term energy carrier. |
| What is the definition of a neucleic acid? | They are chains of neucleotides linked by phosphodiester bonds. |
| Where is the new bond formed between neucleotides in neucleic acid? | Bond is formed between the 3'-OH of the first neucleotide and the 5'-PO4 of the second neucleotide. |
| What is exhibited at the two ends fo a neucleotide? | the two ends are polar(chemically different) |
| What are the five different bases of DNA and RNA? which are different between the 2? | Adenine, guanine, cytosine are in both. Uracil is in RNA only. Thymine is in DNA only. |
| What is the difference between pyrimidines and purines? | Pyrimidines have only one ring while purines have 2. |
| How are basepairs in DNA arranged? | the basepairs are flat, and stacked perpendicular to the axis of the helix. the strands are antiparallel. |
| In addition to H-Bonding, how is the Helix stabalized? | The helix is stabalized by hydrophobic forces, also called base pair stacking interactions, and van der waals attractions. |
| How is Eucaryotic DNA packaged? | it is packaged into chromosomes that each contain one linear molecule of DNA. |
| How long can one linear molecule of DNA be? | Extremely long; 1cm to 5cm in length. |
| Why must DNA be condensed into packaging? | The average nucleus is only 5um (10^-6 meter) in diameter. |
| When are chromosomes most highly condensed? | During mitosis the chromosome may be up to 10,000 fold reduced in length. this allows it to be visible in the light microscope. |
| What is the name for the complex of DNA and bound chromosomes? | Chromatin. |
| What is the nuclear envelope? | It is the two membranes that surround the nucleous/ |
| what is the nucleolus? | Its the site of rRNA gene transcription and ribosome subunit assembly. |
| Where is the point of exit in the nucleus? | Nuclear pores/ |
| What is the nuclear lamina? | It is a part of the cytoskeleton that lines the inside of the nucleus. chromosomes may be attached to it. |
| What is a neucleosme? | they are what chromatin are packaged into. |
| how is a neucleosome complex formed? | Positively charged histone proteins bind to DNA to form the complex. |
| For what reason are histone positively charged? | They are rich in positively charged arginine and lysine residues. |
| A core nucleosome contains what? | it contains about 147bp of DNA wrapped almost twice around 2 copies each of Histones H2A,H2B, H3,H4(8 polypeptides total) |
| about how much DNA is in a portion of linker DNA? | ~50bp in linker DNA. |
| With which histone is linker DNA normally associated? | It is normally associated with the H1 which is not a core histone but that results in the more compavt 30 nm fiber. |
| How is the octametric Histone core remover from the neucleosome? | First, nuclease digests the Linker DNA. This releases the neucleosome core particle. Dissociation with a high concentration of Salt yields the octametric histone core + 147-neucleotide-pair DNA double helix. |
| How was the arrangement of nucleosomes discovered? | In 2005, Thomas Schalch and coworkers discovered that 4 nucleosomes are grouped in a tetraneuclosome in a zigzag arrangement. Using xray crystallography. this data supports a zig zag model for the 30nm chromatin fiber. |
| What is the function of Condensin protein complexes? | In mitotic chromosomes, the looped domains are further coiled around a central scaffold by these complexes. |
| What is the result of a chromatin remodeling complexes? | they use energy of ATP hydrolysis to slide a neucleosome along DNA, partially remove a neucleosome core, or replace core histones with nonstandard histones called variant histones. |
| What is the result of covalent modification to chromatin? | The covalent modification changes the chromatin stucture in the histone tail domains. |
| What is acetylation? | acetylation of histone tails is associated with expression fo genes in that region of chromatin. Acetylation removes the +charge on a lysine residue. |
| What is a histone code? | a specific pattern of covalent modification of core histones and it may signal gene expression. |
| Eucaryotic gene expression includes... ? | Transcription, RNA processing, export fromt he nucleus, and protein synthesis. |
| What are the steps transcript RNA must take to go to protein transcription? | In eucaryotes, this "pre-mRNA" must be processed into messenger (mRNA) RNA. fully processed mRNAs must be exported through nuclear pores to the cytoplasm. translation occurs only in the cytoplasm. |
| What is the function of mRNA? | it is translated into protein. |
| what is the function of rRNA? | is part of the ribosomes. |
| what is the function of tRNA? | deliverrs Amino Acids to ribosomes. |
| What is the function of small nuclear RNA? | snRNA is involved in RNA processing |
| What is the function of microRNA? | it and small interfering RNA are regulators of eucaryotic gene expression. |
| rRNA, tRNA,and snRNA fold to form what? | fold to form internal base pairing called secondary structure. |
| What is the function of RNA polymerase? | It transcribes DNA into RNA, coupled to hydrolysis of the high-energy bonds of NTPs. RNA pol unwinds the DNA helix and adds neucleotides to the 3'-OH. |
| How many subunits are there on RNA pol in procaryotes and eucarotes? | 5subunits for procaryotes. 12 subunits for eucaryotes. |
| How does synthesis proceed in RNA pol? | it proceeds 5' -> 3' on the RNA and 3' ->5' on the DNA template. |
| What is the promoter? | The promoter is the regulatory DNA sequence to which RNA Pol Holoenzyme first binds. It sets the start position (position +1) for transcription. |
| What are consensus sequences? | procaryotic promoters contain consensus sequences at (-10) and (-35) bp upstream of the start site that are recognized by the sigma 70-holoenzyme. |
| What is the sigma subunit of RNA pol required for? | Required for recognition and specific binding to the promoter sequence. |
| How is it determined which strand is terminated? | The asymmetry of the promoter sequence determines this. Only one strand of a gene can be transcribed in the 5' ->3' direction. |
| How many nuclear RNA polymerases are there in eucaryotic cells? | There are 3 nuclear RNA polymerases. they resemble eachother but have many more subunits. Mitochondria and chloroplast have their own RNA polymerases. The 3 forms of RNA Pol transcribe genes with different promoters. |
| What is the function of RNA Pol I | transcribes most of the rRNA genes in the neucleus. |
| what is the function of RNA Pol II? | transcibes all protein-coding genes, the genes encoding most of the snRNAs and a few genes encoding small regulatory RNAs. |
| What is the function of RNA Pol III? | Transcribes all the tRNA genes, the 5s rRNA gene, one snRNA gene, and a few genes encoding small RNAs |
| which nuclear RNA polymerases dont require other factors in order to bind promoters? | ALL nuclear RNA polymerases require other factors. |
| Eucaryotic RNA Pols cannot bind a promoter without What? | The assistance of proteins called general transcription factors (Tf) Bacterial RNA pol only requires the sigma subunit to initiate transcription. |
| In both pro/eucaryotes the promoter determines what? | It determines the binding site RNA Pol, the initiation (start) site for transcription, and which strand is transcribed. |
| In eucaryotes, RNA Pol joins the general TF at the promoter to form what? | it forms an initiation complex in the proper orientation to transcribe the correct strand. |
| Why do general transcription factors play a minor role in regulation of expression for most genes? | Because almost all protein-coding genes use the same set of general transcription factors. Although, they are REQUIRED for RNA Pol Binding. |
| Which RNA II promoters are assembled by general Transcription Factors? | The general transcription factors assemble ALL the RNA Pol II promoters. |
| What do many Pol II promoters contain at the -25bp upstream? | they contain some sort form of an A/T rich sequence called the TATA box. |
| What does assembly of the transcription initiation complex begin with? | It begins with binding of general factor TFIID to the TATA box, causing a distortion in the DNA. The remaining general TFs may then join the complex in an ordered sequence or may form a complex with RNA Pol II before binding. |
| What do the general facotrs do for RNA Pol II? | They position RNA Pol II correctly,aid in strand separation, and help RNA Pol leave the promoter. |
| What are the 6 steps of initiation of transcription at RNA Pol II promoters? | TFIID binds tata box. TFIID acts as a chaperone, helpin RNAPolII bind. Remaining factors bind last initiation complex. Onesubunit TFIIH acts as a helicase. TFIIH phosphorylates CTD. CTD provides binding site for RNA processing proteins. |
| What is the tata-binding protein (TBP) a subunit of? | TFIID subunit |
| Where does TBP specifically bind the Tata box? | binds in eucaryotic promoters in the minor groove of DNA. |
| How does TBP cause a distortion in the DNA and what may this serve as? | TBP fits over DNA like a saddle causing kinks in the DNA that is seperated by partially unwound DNA. Creates a bend of about 70degrees in the helix. Distortion may serve as a landmark for the initiation complex |
| Initiation of Transcription in eucaryotic cells requires what? | It requires regulatory activator proteins and mediator. |
| In relationship to the promoter, where may enhancers be located? | They may be located far from the promoter. |
| What are mediator complexes? | connectors between activators and the initiation complex. |
| What does looping allow for? | allows for cooperative binding. |
| What are the 4 characteristics of RNA Pol shared in both eu/procaryotic cells? | Composed of a single polypeptide chain. Seperates DNA strands in entire region of the gene before beginning RNA synthesis on template strand. Adds neucleotides to the 3'-OH of RNA during synthesis. Couples formation of each new phosphodiester bond in RNA |
| What are the 3 steps required to process primary transcript RNA to mRNA in the nucleus of eucaryotic cells? | Capping, removal of introns by RNA splicing, polyadenylation. |
| What is capping? | Capping is the addition of 7-methylguanosine to the 5'-end of the primary transcript. the link is an unusual 5'-5' bond. |
| What is polyadenylation? | The addition of a poly A tail to the 3' end of the RNA by cleavage at the conserved sequence, followed by addition of about 200 A residues to the new 3' end. |
| Fully processed mRNAs are bound by proteins that recognize what? | They recognize that all splicing and other processing events are complete. |
| What is the action of nuclear export receptors? | This complex of proteins guides mRNAs through pore complexes to the cytoplasm. |
| What is the level of gene expression dependent on? | it is dependent ont he efficiency of each step of transcription, processing,export from the nucleus, and translation in the cytoplasm. |
| when and how is the 7-methylguanosine cap added? | The cap is added when the RNA is only about 25 neucleotides long by 3 enzymes bound to the CTD of RNA Pol II. |
| What does capping do and what is it required for? | the cap is unusual as a triphosphate linkage which causes the cap to stick out at/in a distinctive conformation. The cap is required for export from the neucleus and binding to a ribosome in the cytosol. it protects mRNA from degredation. |
| What are introns and exons? | Eucaryotic genes contain noncoding Introns between coding regions called exons. Procaryotic genes do not contain introns. |
| Which sequences are conserved? which are not? | Intron sequences are not conserver; exon sequences are conserved between species or different copies of a gene. The number of introns can be very large. |
| Where is RNA splicing catalyzed | catalyzed by snRNA in the Sliceosome complex. |
| How are small nuclear ribonucleoprotein particles (snRNPs) formed? | 5 snRNAs (U1,U2,U4,U5,U6 snRNA) for 5 snRNPs with at least 7 subunits each. |
| What is the role of the U1 snRNP? | it forms base pairs with the 5' splice junction and the BBP (Branch-point Binding Protein) and U2AF(auxillary factor) recognize the branch-point site. |
| What is the role of the U2 RNP? | it displaces BBP and U2AF and forms base pairs with the branch-point consensus site. |
| What is the role of the U4,U5,U6 "triple" snRNP? | enters reaction. U4+U6 snRNAs are held firmly together by base-pair interactions. Subsequent rearrangements create the active site of the spliceosome and position the appropriate portions of the pre-mRNA sustrate for first phosphoryl-transfarase reaction |
| what happens when the U6/U4 base pairs break apart? | This allows the U6 snRNP to displace U1 @ the 5' splice junction to form the active site for the second phosphoryl-transfarase reaction, which completes the splice. |
| When rearrangements take place, 3'OH reacts with 5' end to form what? | The 3'OH reacts with the 5'end of the next exon in the second transesterification reaction. |
| To where is the poly A tail added? | It is added to the 3'end of the pre-mRNA. |
| What functions/processes are carried on by the CTD of RNA Pol II? | The factors for capping, splicing, and adding the poly-A tail. |
| What does CPSF do? | CPSF ( cleavage and polyadenylation specificity factor) binds the sequence AAUAAA in the RNA. |
| Where does CstF Bind? | It binds downstream the GU-rich region. |
| What does Poly-A polymerase (PAP) do? | It immediately adds ~200 A residues one at a time to the new 3'end. |
| What is the effect of the Poly A tail? | It is required for the transport out of the nucleus and then enhances the lifetime of an mRNA in the cytosol and aids in translation. |
| What can regulation of RNA produce? | It can produce more than one type of mRNA |
| What is alternative splicing?(alternative processing) | Many eucaryotic genes undergo alternative splicing to produce mRNAs, and thus different polypeptides, from the primary transcript of a single gene. |
| How can an alphabet of 4 nucleotides specify 20 AA? | 3 nucleotides per AA : 4^3=64 (more than enough) |
| How is an AA specified by codons? | a condon of 3 neucleotides specifies one AA: there are extra codons for some AA; variation occurs in the 3rd position. The genetic code is universal among procaryotes and eucaryotes(except for mitochondrial dna) |
| What does tRNA deliver? what does it fold? | It delivers the correct AA to the ribosome during protein synthesis. Internal base-pairing (secondary structure) causes tRNA to fold into helical L-shape. |
| How can tRNAs bind >1 codon? | they mismatch the third position. |
| How is the correct AA linked to each tRNA? | 20enzymes called Aminoacyl-tRNA synthetases catalyze covalent attachment of each aa to correct tRNA. Reaction is coupled to ATP->AMP, resulting in high energy bond between AA+ tRNA. Mistake by 1 of these enzyme would result in incorporation of a wrong AA. |
| Where does protein synthesis occur? | It occurs on ribosomes in the Cytosol or attached to the rough ER |
| How many molecules make up the large and small subunits? | There are 3 rRNA molecules in the large subunit, and one in the small subunit of eucaryotes. The large subunit is 60s while the small subunit is 40s. |
| what is the difference between eucaryotic and procaryotic Ribosome? | Procaryotic ribosomes have one less rRNA molecule in the large subunit, and are smaller overall, with fewer proteins. |
| How many binding sites does a ribosome have? | A ribosome has 3 binding sites for tRNA and one for mRNA. Only 2 fo the sites are normally occupied by tRNAs at the same time. |
| What does the ribosomal small subunit do? | the small subunit matches the tRNA anticodons to the codons of the mRNA. |
| What does rRNA in the large subunit do? | It catalyzes the formation fo the peptide bond. |
| What does the small subunit of the ribosome do? | It binds the mRNA and sets the reading frame. A mistake would result in a nonsense protein |
| Why is initiation important? | It controls the rate of protein synthesis. |
| How does translation always begin? | It always begins with the methionine codon AUG, and a special initiator tRNA for methionine (eucaryotes) or formylmethionine (procaryotes) |
| How is the function of the small ribosomal subunit different in eucaryotes from procaryotes? | In Procaryotes, the small subunit rRNA basepairs with the ribosome-binding sequence of mRNA a few neucleotides upstream of the AUG. In Eucaryotes, the small subunit of the ribosome binds the 5'cap + scans the 1st AUG, preferably in the sequence 5'-AUG-3' |
| What does polycistronic mean? | an mRNA may encode for more than one protein. |
| what does monocystronic mean? | mRNA contains the information for only one protein. *do not confuse: alternative processing-> multiple mRNAs; each monocystronic. |
| In step1 of elongation, what does procaryotic elongation factor EF-Tu(EF-1 in eucaryotes) do? | It hydrolyses a GTP to a GDP after it accurately delivers each amino-acyl-tRNA to the A-site. The small subunit rRNA checks codon-anticodon basepairing. |
| About how fast is elongation? | elongation is very rapid at ~2 AAs /sec in eucaryotic cells. |
| Where does the peptidyl transfarase reaction take place? | It is catalysed by the 23S rRNA of the large procaryotic subunit, not by a ribosomal protein. |
| What is a ribozyme? | a molecule that catalyses a reaction. |
| In which direction does protein synthesis proceeed? | It precedes from the Amino terminal end to the carboxy terminal end. |
| What is peptide bond formation coupled to? | coupled to the hydrolysis of the high energy bond between the carboxy group of the AA and the 3'-end of the tRNA in the P-site. |
| When does termination occur? | It occurs when a release factor binds a stop codon in the A-site. The bond between the c-terminal end of the polypeptide and the last tRNA is hydrolyzed, and the ribosome/mRNA dissociates. |
| What is a polysome. | a single mRNA can be translated by several ribosomes at once, forming a polyribosome=polysome. |
| How do polysomes differ between procaryotes and eucaryote? | in procaryotes, polysomes are linear. In eucaryotes, initiation factor 4G binds both initiation factor 4E (attached to 5' cap) and the poly-A-binding protein I, linking the 5' + 3' ends in a circle. |
| Why is a polysome so beneficial to eucaryotes? | This greatly increases the efficiency of translation by putting the ribosome subunits in position to reinitiate translation at the 5'end of the mRNA immediately after dissociating at the 3'end. |
| Why is the cost of protein sythesase so high? | In total their is the equivalent of hydrolysis of 4high energy phosphate bonds per peptide bond. There are additional costs too. |
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