Molecular Biology Exam2

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which nucleotides are purines? what does their structure look like?: adenine and guanine.. double ring of carbon
which nucleotides are pyrimidines? double or single ring?: thymine and cytosine= single ring
What are the final destinations for the proteins processed in posttranslational import?: the final destinations for the proteins are in the cytoplasm, peroxisome, mitochondria, chloroplasts, or the nucleus
how are proteins destroyed in post-translational import?: by the proteosome
What are the final destinations for the proteins processed in co-translational import?: the final destinations for the proteins are in the ER, Golgi, Lysosome, Endosome, Outside of cell
how are proteins destroyed in co-translational import?: by the lysosome
What are some key features of protein processing via co-translational import?: signal peptide, and the use of an endomembrane system
what are the organelles found in the endomembrane system?: Endoplasmic Reticulum, Golgi, secretory vesicles, Lysosome, Endosomes
what would you expect to find in the nucleus?: nucleotides, GTP, phosphate,
how is the template strand read?: 3'-5'
the_____ _______ makes up the internal structure of the nucleus; the nuclear _____ lines the inside of the nuclear envelope: nuclear matrix, nuclear lamina
how is the coding or nontemplate strand read?: 5'-3'
How is RNA made?: RNA is made 5'-3'
genes can be arranged, give an example of this...: instead of having genes which code for all possible antibodies we have a few antibody genes which are rearranged into different combinations of V, J, D, and C segments on an antibody protein
in mammals, the nucleoli and its contents are ______ after adequate amounts of hemoglobin mRNA are made.: deleted-
what is the term for all cells within an organism containing the same genome?: totipotent
how can an organism control the availability or number of genes for transcription?: amplify/delete genes
rearrange genes
methylate the DNA
deacetylate histones
what happens when the DNA gets methylated?: it inactivates some genes- ex: female somatic cells must inactivate one of their x-chromosomes by methylating it... this might be to prevent large amounts of x-chromosome protein being made.
what does the nuclear matrix have to do with transcription?: it appears to promote gene transcription by holding the TX complex in place and concentrating substrates in one area
what happens when a histone is deacetlyated? what enzyme performs this function?: gene transcription is repressed- when acetyls are present on histones, it interferes with histones binding to chromatin=== you get gene transcription
how can the transcription process of genes occur?: the presence or absence of transcription factors.
what are the two types of transcription factors?: general TFs and

Regulatory transcription factors
how do general transcription factors work?: -bind to the core promoter and RNA polymerase
how do regulatory TFs work?: they have two domains: a DNA binding domain and a transcription regulation domain. the DNA binding domains could have a helix-turn-helix motif, a zinc finger motif, a leucine zipper motif, or a helix-loop-helix motif.
what general transcription factors are essential for transcription of all genes: TFIIA,B,D,E,H,J
where do general TFs assemble? what are DNA sequences located 100-200 BP upstream of this region called?: at the core promoter; proximal control elements are DNA sequences located 100-200 BP upstream of the core promoter
what are two examples of proximal control elements?: The CAAT box and the GC box.
how do regulatory control elements work?: increase or decrease Tx by interacting with proximal control elements.
distal control elements which are also called enhancers/silencers are found where on the DNA?: far away from the core promoter... 70000-80000 bp away
activators and repressors bind to TFIID causing what to happen?: the DNA becomes looped, results in recruiting general TFs and RNA Pase to a region. activatiors and repressor binding can result in the stabilization of transcriptional machinery and can also serve as an active site for another protein (coactivator) to regulate transcription.
give an example of protein phosphorylation controlling the activity of transcription factors: the cAMP cascade can trigger the activation of Protein Kinase A which then causes phosphorylation of CREB (cAMP response Element Binding protein) the CREB can interact with the cAMP response element(CRE) located near a specific promoter to stimulate Tx
give an example of gene Tx being affected by temperature: the gene that encodes for hsp70 has a heat shock response element 62bp upstream from the Tx start site. when the temp goes up, a transcription factor changes shape and can now fit into this Response Element -activating transcription of this Chaperonin.
what are some examples of alternative splicing of pre mRNA?: production of antibody, receptors (olafaction), fibronectin
how is mRNA degredation controlled?: an example would be transferrin production... transferrin is a transmembrane channel for getting iron into the cell. if there is low iron in the cell= binding protein protects mRNA (receptor upregulation) if there is high iron, it will bind to the protective protein and expose the mRNA for transferrin to degredative enzymes (receptor downregulation)
what is a translational control mechanism?: the feedback mechanism in ferritin biosynthesis regulated by iron. ferritin is an iron binding protein in the cytoplasm

low iron=translation prevented because IRP is bound to IRE on mRNA
High Iron=iron binds to IRP and lifts it off of the IRE on the mRNA allowing translation to occur.
how do we target proteins for degredation?: we ubiquitinize them.
there are two types of DNA... what are they?: Positive (right-handed twist)
Negative (left-handed twist)
Enzymes which interconvert DNA are called: TOPOISOMERASES
Type I - nicks one strand only
Type II - nicks both strands
GYRASE is a type II topoisomerase.... what does it do?: promotes strand separation during replication
what are tandemly repeated DNA sequences also known as?: Minisatellite-used in paternity testing because these regions of repetition vary among individuals. Mutations of these can cause cancer and diabetes.

Microsatellite â€“ high mutation ratesâ€”used for anthropological tracing of ancestry.
Interspersed repeated DNA can comprise 24%-80% of the genome, what does this code for>: sometimes codes for tRNA or rRNA but most of the time, these sections of genes lack a coding function
in talking about Non repeated DNA Sequences its obvious that there is only a single copy, but what do these sequences code for?: Always are at a specific spot on a chromosome
Are actual protein-coding GENES
the nuclear envelope is contiguous with what?: the ER
transport across the nuclear membrane is achieved how?>: passively-nucleotides and similarly small molecules diffuse freely via one of up to nine channels per pore.
Actively- the movement of mRNA and polymerases... first the NLS containing protein binds to importin and is transported to the pore where the complex binds to the pore complex. the final step is dependent on GTP which allows entry and importin is sent back into the cytoplasm
what is the nucleolus: it is not membrane bound, it has a fibrillar component -DNA and RNA (rRNA), A Granular component- Nascent Ribosomal units, Nuclear Organizer Region (NOR) carrying rRNA genes.
one gene per _______. (mRNA/tRNA/rRNA) Core promoter and many regulatory elements: one gene per mRNA.
(mRNA/tRNA/rRNA) has multiple copies of the gene for it. Has Downstream control element.: tRNA
rRNA = multiple copies separated by a nontranscribed spacer Upstream control element: rRNA:
28S, 18S, 5.8S are from the same gene and pre rRNA, and processed into separate rRNAs Another 5S unit comes from a separate gene but is transcribed by RNA PolIII.
common promoter elements include....: (a) CCAAT box
(b) GC-rich regions
What are the steps in Binding/Initiation?: PROMOTER = DNA sequence ---- TATA box
in Elongation how is DNA read and how is RNA made?: â€“DNA read in 3â€™ïƒ 5â€™ direction, RNA made in 5â€™ïƒ 3â€™ direction.
v. in eukaryotes why is Termination not as important as in prokaryotes?: processing is much more relevant... eukaryotes have the means to process proteins
list the three steps in RNA PROCESSING: 1. Removal of intervening sequences on pre rRNA
2. Residues are methylated for protection
3. Uses small nucleolar RNAs (snoRNAs) to cut pre-rRNA.
list the five steps in tRNA PROCESSING: 1. Removal of 5â€™ leader sequence
2. Chemical modification of bases
3. Excision of intron
4. Replacement of 3â€™ nucleotides with CCA
5. Charging (addition of amino acid on 3â€™ end)
list the five steps in mRNA PROCESSING: 1. 5â€™ CAP
2. 3â€™ poly A tail
3. Alternative splicing - removal of some sequences
4. Probable mechanism of splicing
5. Involves 5â€™ GU and 3â€ AG along with snURP proteins (SPLICOSOME)
in translating rRNA what is made?: Ribosomes - Two subunits made up of rRNA and proteins.
Prokaryotes - 50S + 30S protein units and 23S, 5S and 16S rRNA
Eukaryotes - 60S + 40S protein units and 28S + 5.8S, 5S and 18S rRNA
what is the Wobble Hypothesis and what does it do for translation?: =third base at 3â€™ and in mRNA codon can bind to different base in 5â€™ end of anticodon allowing flexibility in translating proteins
what are the three steps of translation?: INITIATION, ELONGATION, and TERMINATION
what happens in Initiation?: required factors - eIFs in eukaryotes
1. Requires energy GTP
2. met is the first amino acid (AUG = start codon)
what happens during Elongation?: - growing polypeptide
1. Ribosome structure - A-site, P-site, and E-site
2. Factors involved:
(a) EF-Tu - binds to 2GTP molecules and escorts charged aa-tRNA into place in the A site
(b) EF-Ts â€“ regenerates/recycles EF-Tu-GTP (stripped of the amino acid) for next round
(c) Each three bases on mRNA is a codon and codes for one amino acid that is delivered by a charged tRNA by complementary base pairing of the anticodon (tRNA) to the codon (mRNA)
(d) EF-G - facilitates translocation step to free up the P site where a new codon resides.
what are the three types of exocytosis?: 1. Constitutive Secretion
2. Regulated Secretion
3. Plasma membrane receptor insertion
what is ENDOCYTOSIS, what is its purpose?: Taking materials from outside of cell inside to be processed in lysosome.
ii. Recycling plasma membrane.
iii. Downregulating receptors on plasma membrane
2. ORGANELLES IN THE ENDOMEMBRANE SYSTEM: ⬢ Endoplasmic Reticulum
⬢ Golgi
⬢ Secretory Vesicles
⬢ Lysosome
⬢ Endosomes
regarding protein processing and transport, what are the Two possibilities?: 1. Cytoplasm to organelle (or stay in cytoplasm). Ribosomes are in the cytoplasm and are not associated with the ER = POSTTRANSLATIONAL IMPORT
2. Protein delivered into the lumen of the ER and processed through membrane system = COTRANSLATIONAL IMPORT
what are the Postranslational import â€œzip codes" that direct proteins to their destination for the Nucleus, Peroxisome, Mitochondrion: i. Nucleus (NLS sequence
ii. Peroxisome (SKL sequence)
iii. Mitochondrion (Transit peptide) - have amino acids alternating from +-charged to hydrophobic = amphipathic helix
how does Cotranslational Import occur and which proteins undergo this process?: 1. A signal peptide on newly synthesized polypeptide is recognized by the SIGNAL-RECOGNITION PARTICLE (SRP) which binds to the SRP RECEPTOR on the ER membrane
2. SRP has six polypeptides and an RNA component
3. The protein components have 3 active sites:
(a) Binds signal peptide
(b) Binds to SRP receptor
(c) Prevents further translation (using GTP as energy)
4. Steps ===
(a) SRP binds to signal peptide and blocks translation
(b) SRP binds to SRP receptor - ribosome docks on membrane
(c) GTP binds to receptor and polypeptide moves to pore protein (translocon)
(d) GTP hydrolyzed and SRP released
(e) Polypeptide translocates and moves into lumen of ER (a chaperone protein might help pull protein inside lumen)
(f) Polypeptide is completed and cleaved by signal peptidase

Secreted and Transmembrane Proteins
What when centrifuged becomes microsomes: When centrifuged, the Endoplasmic Reticulum becomes microsomes
describe the Smooth Endoplasmic Reticulum and list some functions occuring within.: (a) No ribosomes attached
(b) Tubular in shape
(c) Synthesis of steroids
(d) Hydroxylation reactions and Drug detoxification
(e) Activation of carcinogens
(f) Drug sensitivities
(g) Stores calcium
(h) Glycogen metabolism in liver - glucose-6-phosphatase in membrane which dephosphorylates glucose-6-P within the cytoplasm of the hepatocyte so that free glucose can leave the cell and increase blood glucose (fasting conditions).
describe the Rough Endoplasmic Reticulum and list some functions occuring within.: has ribosomes associated with outer surface, looks like a bunch of Large flattened sheets continuous with outer membrane of nuclear envelope.
Membrane contains receptor proteins that help ribosomes attach (signal hypothesis).
Proteolytic processing of proteins occurs here as well as Chemical modifications in conjunction with the Golgi - methylation, phosphorylation, acetylation, glycosylation.
CORE GLYCOSYLATION
what is it about Integral membrane proteins that keeps them embedded in organelle membranes?: Integral membrane proteins - have a STOP TRANSFER sequence (hydrophobic) that keeps them embedded in the membrane
the inside of the ER is like the __________ of the cell.: THE INSIDE OF THE ER IS LIKE THE OUTSIDE THE CELL
which proteins are tagged by the glucosyltransferase enzyme? what happens when they are tagged?: Bad, MISFOLDED proteins are tagged by glucosyltransferase enzyme This added glucose molecule enables passage across ER membrane. The Protein is recognized by a proteosome and destroyed.
describe the GOLGI COMPLEX: A series of flattened membrane-bounded cisternae (disk-shaped sacs) Typically 4-8 sacs but can be more.

The Size and number of Golgi complexes differs with cell type

it has a Dynamic structure - budding and fusing of vesicles with the Golgi
what are the functions of the golgi complex?: i.Protein glycosylation â€“ addition of sugar groups on asparagines

Protein Sorting =secretory proteins, hydrolytic enzymes, golgi proteins, integral membrane proteins.
describe the Cisternal Maturation: Cargo stays and Golgi processing enzymes are delivered at appropriate time and order by retrograde transport so that each cisternae matures into the next.
describe Anterograde Vesicle Transport: Golgi enzymes stay within appropriate and different cisternae. Instead cargo proteins are delivered by vesicle transport.
name three types of Coats you might find around vesicles coming from or going to the golgi: COPII = ER to Golgi vesicles
COPI = Golgi back to ER vesicles(KDEL sequence)
CLATHRIN
what is the purpose in having coats around vesicles?: a. Help pinch off the membrane
b. Select and aggregate cargo proteins for export
c. Have transmembrane proteins that help dock and fuse the vesicle to its target membrane.
what are the Other Proteins Required for Vesicle Fusion: v-SNARE (vesicle SNARE)

t-SNARE (target SNARE)

NSF: forms barrel around SNARE complex. ATP hydrolysis unfolds and recycles SNARES
give a summary of EXOCYTOSIS/SECRETION: Rough ER->transition vesicles ->cis cisternae of Golgi->medial cisternae->trans cisternae ->secretory vesicles ->fusion with cell membrane and release of protein to exterior of cell.
Define Constitutive and Regulated secretion and give an example of each: Constitutive â€“ continuous secretion (absence of signal) e.g.- mucus production in intestine

Regulated â€“ controlled secretion (needs a signal) e.g. - insulin secretion, or digestive enzymes
Default secretion occurs on ________ whereas Polarized secretion only occurs on ___surface of the cell: Default â€“ all sides of cell

Polarized â€“ only from one surface of the cell e.g. - digestive enzymes
define ENDOCYTOSIS-: intake of material and progressive invagination of the plasma membrane to recycle membrane after exocytosis
what are three types of endocytosis?: Bulk-phase endocytosis=uptake of fluid in a nonspecific manner

Phagocytosis â€“ â€œfoodâ€

Receptor-mediated endocytosis
describe Receptor-mediated endocytosis tell why its important.: RECEPTORS â€“ proteins on cell surface that LIGAND binds to causing coated pit of clathrin to form.

CURL =compartment for uncoupling receptor from ligand=pH diffs break ionic bonds between ligand and receptor

Short loopïƒ receptor back out to PM from curl.

Long loopïƒ receptor has to go to Golgi for repair or modification before it goes back to PM.
why would a receptor be in the Long loop: receptor has to go to Golgi for repair or modification before it goes back to PM. Way to downregulate receptors that are not needed!
why would a receptor be in the Short loop: Receptor back out to PM from curl. Usually to get receptors back out to the surface quickly=upregulation.

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