MCB 150 Week 4 - Week 8

RNA viruses have 3 different "flavors"

1. (+) sense strand RNA viruses: RNA can be translated directly, just as if it were mRNA 2. (-) sense strand RNA viruses: RNA is complementary to mRNA 3. retroviruses: Make RNA via a ds-DNA intermediate using reverse transcriptase plus and minus don't indicate charge they're just arbitrary designations negative and positive are compliments of one another

5 stages of M phase

1. Prophase 2. Prometaphase 3. Metaphase 4. Anaphase 5. Telophase

List at least 3 differences between transcription and DNA replication

1. Replication used DNA polymerases while transcription uses RNA polymerases. 2. Replication makes DNA from DNA whereas transcription makes RNA from DNA. 3. Oris are start sites for replication, and promoters are start sites for transcription. 4. Replication ends when the last base is added and the genome is fully replicated and transcription has specific stop sites (for example in bacteria there are Rho-dependent or Rho-independent termination sites). 5. During replication, all of the DNA is replicated. Only certain regions are transcribed at any given time. 6. During replication the DNA is separated and forms a hybrid between parental DNA and daughter DNA, and the parental strands do not come back together. In transcription the DNA strands are only separated where the RNA polymerase is located, and then the DNA strands come back together. 7. DNA ends up double stranded during replication, but we make a single strand of RNA. This RNA strand is peeled away from the DNA strand when transcription is finished

describe the 2 most important parts of a tRNA (acceptor and anticodon end

1. acceptor end: amino acid covalently linked to adaptor molecule. 3' end. CCA from 5' - 3' 2. anticodon end: a series of three bases that is going to be complementary and antiparallel to a codon in an mRNA molecule. So the anticodon will sit down on an mRNA codon and allow for the amino acid attached on the other end of it to be added to a growing protein chain.

How does an amino acid get covalently linked onto tRNA?

1. amino acid binds to ammoacyl tRNA synthase and molecule of ATP 2. once binded to the ATP, ATP is hydrolyzed, breaking off its phosphate group an leaving AMP 3. AMP covalently links to amino acid 4. release the phosphate group from AMP 5. a random uncharged tRNA molecule will bump into tRNA synthetase and tRNA syntheses will attempt to recognize anticodon of that tRNA 6. if it recognizes anticodon, amino acid will covalently link to the 3' end and AMP molecule is released 7. charged tRNA molecule is released That energy is going to come indirectly from ATP, but come directly from breaking the bond that we have just formed during this charging process. In other words, that tRNA-amino acid-covalent interaction is storing potential energy for us right now that we will use during the process of translation later.

7 basic steps of the "life" cycle of viruses: does every virus go through every step?

1. attachment 2. penetration 3. early gene expression 4. replication 5. late gene expression 6. assembly 7. release some viruses don't need to go through every single step but must do the same thing every time

3 repeated steps of elongation repeated until stop codon is reached?

1. binding of next charged tRNA in A site: comes in accompanied by accessory molecule and molecule of GTP 2. peptide bond formation between amino acids in P site and amino acids in A site 3. translocation: movement of ribosome 3 bases closer to 3' end of mRNA molecule + another Ef-Tu and GTP

The life cycle of most cells consists of four major processes:

1. cell growth 2. DNA replication 3. distribution of replicated chromosomes 4. cell division this gives each daughter cell a complete genome

energy dependence of translation

1. cost a molecule of ATP to bind amino acid to tRNA molecule 2. in the first step in the elongation phase, which was binding a charged tRNA molecule into the open A site, that also took a nucleoside triphosphate. It was GTP, but it's still a triphosphate group 3. translocation costs a molecule of GTP 3 ATP/amino acid x 1,000 = another 3,000 ATP equivalents (using lacZ example)

What are some of the processes the cell can use a combo of myosin and actin filament for? 3 things

1. cytokinesis 2.cell crawling 3. move transport vesicles from point A to B inside a cell

4 stages of cell crawling

1. extension: cell pushes lamelipod forward. driven by rapid polymerization of actin filaments at leading edge of cell membrane 2. adhesion: lamelipod adheres to the substratum using adhesion sites 3. translocation of the cell body: contraction of actin and myosin bundles in lamilepod cell body border 4. de adhesion: back of cell body releases and moves forward

"life" cycles of viruses consist of 3 tasks...

1. get into the host 2. replicate their genetic material 3. get out of the host

The Pulse-Chase experiment (1960): how its done, pulse levels, how is S35 incorporated in?

1. give a culture of actively growing cells a large amount (a pulse) of a radio-labeled amino acid a pulse is a level of radioactivity that's detectible but doesn't interfere with cell activity: radioactive sulfur is good to use (S35): found in methionine and cystine during translation some of the radioactive S35 is incorporated into the growing protein chain where there is a methionine 2. now we must chase away the radioactivity to STOP incorporating the S35. Now we're going to flood our culture of growing cells with an excess of cold, which means not labeled version of that amino acid.

2 ways transcription is different than DNA replication

1. in transcription, you unwind as you go and rewind as you go 2. in DNA replication the newly synthesized strand stays base paired to the template molecule, in transcription, the newly synthesized strand is displaced from the template so DNA can be in tact

3 steps of any cellular process dependent on a signal and relate it to pore complexes

1. present a signal (NLS) 2. recognize signal (importins) 3. take appropriate action

2 ways to make translocon close

1. presentation of stop-transfer sequence 2. lifting off the free ribosomal unit

4 steps of transcription

1. promoter recognition: find a place to start 2. initiation: begin process 3. elongation: add RNA bases 4. termination: stop

2 things needed to terminate transcription

1. pull RNA transcript away from DNA template 2. knock RNA polymerase off

2 types of secretion: size of vesicles where it goes from and to

1. regulated secretion: cell needs to be told now its appropriate to dump contents of this vesicle. So it pre prepares a lot of the molecules and doesn't send vesicle until proper signal is received (insulin). so sent out in relatively large vesicles. 2. Constitutive secretion: always needing to send it outside the cell. don't need to wait for a signal saying it should be sent outside the cell. as soon as its created its sent out (digestive enzyme). sent out in relatviely small vesicles because go as soon as they're ready secretion goes from the Golgi to the plasma membrane and fuses

Where COULD regulation occur? Where does regulation most frequently occur?

1. regulation of transcription 2. RNA degradation by nucleases 3. translation 4. degrade the polypeptide with protease 5. post translational modification basically could happen at any step But... the best place to regulate is at the step that saves the most energy from being wasted So... regulation most frequently occurs at the level of TRANSCRIPTION INITIATION: if you never make the RNA to begin with, you save yourself all of the energy in the long run

How to bacteria terminate transcription? (2 ways)

1. rho-dependent: uses accessory molecule to pull RNA transcript away from DNA template 2. intrinsic: don't need accessory protein because info on how to terminate is built into a gene

Nucleolus is the site for what...? (3 different processes)

1. ribosomal RNA (rRNA) synthesis 2. RNA processing (not splicing) 3. assembly of ribosomal subunits. NOT assembly of full ribosome. we don't want active ribosomes in the nucleus.

Order the following events, from earliest in the process to latest in the process, of a protein with an amino-terminal signal peptide being translated and folded in the ER lumen. The signal peptide gets removed by signal peptidase SRP docks on the SRP receptor and the ribosome is lined up over the translocon The protein is bound by BiP and is correctly folded The translocon opens and the ribosome resumes translation The SRP and ribosome are moved to the RER Signal peptide emerges from ribosome SRP binds to signal peptide and translation is halted

1. signal peptide emerges form a ribosome 2. SRP binds to signal peptide and translation is halted 3. The SRP and ribosome are moved to the RER 4. SRP docks on the SRP receptor and the ribosome is lined up over the translocon 5. The translocon opens and the ribosome resumes translation 6. The signal peptide gets removed by signal peptidase 7. the protein is bound by BiP and correctly folded

3 primary responsibilities of RER

1. synthesis of secreted proteins 2. synthesis of transmembrane proteins 3. modification of proteins that make their way through the secretory pathway

3 activities of reverse trasncriptase

1. takes single-stranded RNA and turns it into double-stranded DNA 2. nuclease activity: specific for RNA so its an RNAase. it will only degrade RNA component of RNA-DNA hybrid molecule: RNAh 3. DNA dependent, DNA synthesizing enzyme: makes a DNA copy of the DNA molecule we have left over after RNAse activity in this 3 step process, you go from single stranded RNA to double stranded DNA this all happens in the cytoplasm

the cell theory: 3 tennants

1. the cell is the fundamental unit of life 2. all living organisms are made of 1 or more cells 3. all cells come from prexisting cells: this is what well be studying in this lesson

Beginning with a cell in late G2, order the following cellular events from earliest (1) to latest (7). Mitotic chromosomes are lined up along an imaginary center line Spindle poles are moved toward opposite poles of the cell as sister chromatids are moved away from the middle of the cell Cytoplasmic division The nuclear envelope breaks down and two separate spindle poles are formed Mitotic MTs grow towards the midline of the cell Chromosomes decondense, the nuclear envelope reforms and the spindle pole array is depolymerized The centrioles are replicated and the interphase MTs are depolymerized

1. the centrioles are replicated and interphase Mts are depolymerized 2. the nuclear envelope breaks down and two separate spindle poles are formed 3. Mitotic Mts grow towards the midline of the cell 4. Mitotic chromosomes are lined up along an imaginary center line 5. spindle poles are moved toward opposite poles of the cell as sister chromatids are moved away from the middle of the cell 6. chromosomes decondense, the nuclear envelope reforms and the spindle pole array is depolymerized 7. cytoplasmic division

what are the 3 jobs/functions of the nucleolus?

1. transcription 2. processing 3. ribosomal subunit assembly

How many protein coding genes does a human mitochondria have?

13. represented by roman numerals that express which complex in the ETC or ATP synthase does that particular polypeptide participates in

Which one of the following is not produced within a human mitochondrion? Some ETC proteins 12S rRNA Some ATP synthase proteins Mitochondrial tRNAs 18S rRNA

18S rRNA

What does proofreading and what direction does it go in?

3' ---> 5' exonuclease activity of DNA polymerase synthesis adds bases in 5' --> 3' direction last base added is checked if incorrect, last base is removed from 3' end

Which one of the following sequences on a template strand of DNA would most likely encode an intrinsic terminator? 3'-TTTTGGGGTTTTAAAAGC-5' 3'-CACATATACACA-5' 3'-ATGTTGACAATTAG-5' 3'-TAATTGAACAACTTCAATTA-5' 3'-TAATTGGGGGGGAATTA-5'

3'-TAATTGAACAACTTCAATTA-5'

how many nucleotides per amino acids is the minimum to account for the 20 amino acids we already know about? What does this tell us about the genetic code?

3. genetic code is a triplet code 61 of the 64 codons specify an amino acid other 3 are stop codons

ribosomes read their template (mRNA) in which direction?

5' --> 3'

How much of a eukaryotic cell does actin make up?

5-10% this is a lot for just one protein

initiation produces: (2 things)

A completed Initiation Complex (70S in bacteria, 80S in eukaryotes) An occupied P (peptidyl) site and an open A (aminoacyl) site (E site also open) *Initiator tRNA occupies the P site *All other tRNAs enter into the A site

Which one of the following statements about mRNA transcription and processing in eukaryotes is incorrect? All transcription occurs in the nucleus. A single primary transcript can be turned into one of several possible mature mRNAs. A methylguanosine cap is added to the 5' end of each transcript. All splicing occurs in the nucleus. A string of adenosines is added to the 3' end of the primary transcript by the same RNA polymerase that transcribed the rest of the transcript.

A string of adenosines is added to the 3' end of the primary transcript by the same RNA polymerase that transcribed the rest of the transcript.

Why do we have transcription step?

AMPLIFICATION. We need thousands of copies of a single protein and lots at the same time from just a small amount of DNA so go to RNA first to make it more efficient. We make multiple RNAs from each DNA (act as messengers translated by ribosomes)

How do we create an environment with acidic pH within lysosome?

ATP dependent proton pump. Uses hydrolysis of ATP as energy source to move protons across a concentration gradient. Once they reach pH of 5, pumps become less active and simply maintain the pH.

what is the initiator codon?

AUG: codes for Met: thats why first charged tRNA is always Met Codes for special modified Met (N-formyl-methionine, or fMet) in bacteria, unmodified Met in eukaryotes AUG can be found in other codons, but regular Met is added in bacteria (fMet only starts chain) Archae have Met, not fMet, as first amino acid

How is a cell protected from degradation by acid hydrolases? Acid hydrolases are sequestered away from the cytoplasm by a lipid bilayer membrane. Acid hydrolases only degrade molecules containing a mannose-6-phosphate, which allows them to break down only what is targeted for degradation. Acid hydrolases only degrade foreign proteins and DNA. Each cell contains only one lysosome, which limits potential damage from acid hydrolases. None of the above is a reason that a cell is protected from degradation by acid hydrolases.

Acid hydrolases are sequestered away from the cytoplasm by a lipid bilayer membrane.

Where does lipid biosynthesis occur?

All of those precursor molecules are going to be assembled and integrated into a phospholipid by an enzyme that's bound to the cytosolic leaflet of the smooth ER membrane. In other words, this membrane-lipid synthesis happens at the smooth ER but not inside the smooth ER. It actually happens on the cytosolic side of that smooth ER membrane.

Which one of the following statements about microtubules (MTs) is incorrect? GTP in a beta-tubulin's nucleotide binding site is hydrolyzed to GDP shortly following addition of a tubulin dimer to the microtubule. Alpha and beta tubulin can each bind GTP and be incorporated independently into an MT. GTP-bound tubulin dimers are more frequently added to the plus end of a microtubule. The head to tail assembly of an MT allows for directionality of the MT itself. A microtubule is composed of 13 protofilaments.

Alpha and beta tubulin can each bind GTP and be incorporated independently into an MT.

Which one of the following statements about microtubules (MTs) is incorrect? GTP in a beta-tubulin's nucleotide binding site is hydrolyzed to GDP shortly following addition of a tubulin dimer to the microtubule. Alpha and beta tubulin can each bind GTP and be incorporated independently into an MT. GTP-bound tubulin dimers are more frequently added to the plus end of a microtubule. The head to tail assembly of an MT allows for directionality of the MT itself. A microtubule is composed of 13 protofilaments.

Alpha and beta tubulin can each bind GTP and be incorporated independently into an MT. Only beta tubulin can bind GTP

Why are you more likely to do depolymerization at pointed end and polymerization at barbed end?

At pointed end, the G actin is bound to ADP and no longer has high affinity for ATP bound G actin so it wants to leave but at barbed end, the ATP is trapped before it can get away

How often do errors occur in DNA replication?

Average in all organisms is 1 mistake in 1 billion nucleotides added

How does glucose prevent expression of β-galactosidase? (catabolite repression)

B-galactosidase is used for lactose processing. Glucose is the preferred food source even though lactose is also present so when glucose is there, the cell isn't using the lactose and therefore there is a lower expression of B-galactidose

most of the proteins that are ER resident (live and work in the ER) are responsible for protein processing and folding. what are some examples? (2)

BIP: chaperone assisted folding Signal peptidase

regulation of mRNA stability: in which direction is mRNA degraded?

Bacterial mRNAs have rapid turnover; half-life is ~2 min. Allows quick response to changes in environment Lac mRNA degraded from 3' --> 5' : lacA -->lacY --> lacZ (partly explains ratio) nuclease starts at 3' end so lacA is degraded first so less transacetylase each one has own Shine-Delgarno sequence and its own stop codon and is translated separately

Polycistronic mRNAs

Bacterial mRNAs that carry information for multiple protein products different than alternative splicing because a single piece of messenger RNA in a eukaryote that has been prepared differently is alternative splicing. So if you alternatively splice Gene X in a eukaryote you might make Version 1, Version 2, and Version 3 of that protein. Each of those mRNAs are going to make a slightly different protein product, but it is still a single unique piece of mRNA that a ribosome starts and stops on. cannot happen in eukaryotes

Which one of the following steps in elongation is directly dependent on ATP or GTP hydrolysis? Peptide bond formation Translation termination Loss of the sigma subunit Binding of a charged tRNA to the A site None of the above require an input of energy.

Binding of a charged tRNA to the A site

When is the transmembrane protein's N terminus in the lumen and C terminus in the cytoplasm? AMINO TERMINAL SIGNAL PEPTIDE

C-terminus in the cytoplasm because the ribosome finished translation while the protein had already been ejected from that translocon. N-terminus is in the lumen because the signal is ON the amino terminus signal sequence is amino terminal folded in with N terminus facing cytoplasm and C terminus facing lumen. we ARE cutting off internal signal sequence

what does it mean that viruses are obligate intracellular parasites?

Can persist (not live because viruses are not cells, they're particles) on their own under the right conditions, but... Can reproduce only within a host cell, using tools from host (parasite) Genomes may code for a few enzymes or proteins, but they must use ATP, AAs, tRNA, nucleotides, ribosomes, etc. from host to replicate (obligate intracellular) most parasites can do some of their own things but viruses are obligated to use host cell machinery

How do cells meet the demand of 5-10 million ribosomes that must be synthesized each time the cell divides?

Cells have multiple copies of their RNA genes Human cells have ~280 copies of 5.8, 18, and 28S, and ~2000 copies of the rRNA genes

Why does G1 have such a high peak?

Cells in G1 have 2n amount of DNA

Labels referring to "Summary of functional nuclear domains." photo

Chromosomes occupy distinct territories within the nucleus, and extend regions of euchromatin out into the interchromosomal territories for transcription because that is where the transcriptional machinery is located. The red regions within the chromatin loop in the inset indicate transcriptionally active genes. Not only does the chromosome occupy its own space, but the arms of the chromosome occupy their own territories and do not overlap each other. The green and red indicate chromosome arms, while the gold indicates the centromeric region of that chromosome. The darker the color, the more compact the chromatin. So the lightest yellow indicates euchromatin, found predominantly at the periphery of the chromosomal territory where transcription and/or replication are occurring, while the deepest orange/red indicates heterochromatin, buried in the interior of the territory. Foci of replication. Green color represents regions replicating early during S-phase, when the chromatin is already more unwound (and represents regions of high gene density). Red regions represent areas of low gene density, tightly bound into heterochromatin, which will not be replicated until late in S-phase. Regions of chromatin with transcriptionally active genes (white dots) will be on the periphery of a chromosomal territory, while transcriptionally inactive (or silent) genes (black circles) will be in the interior of a territory. Gold circles represent "Speckles" or clusters of transcription, replication, or repair machinery. Speckles are recruited to regions of activity from much larger collections of machinery. The Nucleolus.

Post-Transcriptional Regulation in the lac operon. How do we know this happens (ratio)?

Controls production of individual lac protein products once lac mRNA has already been transcribed 10 : 5 : 2 ration of β- gal to permease to transacetylase in a given E. coli cell: but these all come from the same operon so how are there different numbers? because they're regulated after transcription

Elongation step 1 (binding of next charged tRNA)

Correct pairing of codon and anticodon stimulates GTP hydrolysis and release of EF-Tu

Which one of the following statements regarding microtubules and centrioles is correct? Centrioles are arranged perpendicular to each other in vivo. All microtubules are anchored in the centrosome. Centrioles are a component of plant cell MOC. There are 29 microtubules in each centriole. All of the statements regarding centrioles and microtubules are correct.

Correct:Centrioles are arranged perpendicular to each other in vivo There are 9 Mts in each centriole.

Cystic Fibrosis

Cystic Fibrosis is characterized by faulty protein (CFTR) 70 percent of CF cases are due to an in-frame deletion of a Phe codon at AA 508 of a 1,400 AA protein Mutant CFTR protein doesn't fold properly, never becomes an active channel Causes Cl- to accumulate in cells, causing water to be taken into cells This causes mucus glands to produce thick, sticky mucus, which interferes with breathing and digestion natural selection hasnt eliminated it because in certain population under certain circumstances it made selective advantage: carriers can resist cholera and survive because retaining more water in their cells

how does E. coli (or any other organism) reduce the frequency of the errors it makes by 104? (2 ways)

DNA polymerases can proofread their work (check as they go) Mismatch repair (spell-checker): happens right after Both occur during or quickly after DNA replication

Is DNA replication organized? How do we know?

DNA replication IS organized. We know because in fluorescent experiments there are localized foci of color meaning localized spots of DNA.

rDNA

DNA that codes for RNA. makes up the fibular centers. located in the nucleolus

____ dependent, ______ synthesizing Primase DNA polymerase I DNA polymerase III RNA polymerase

DNA-dependent, RNA-synthesizing DNA-dependent, DNA-synthesizing DNA-dependent, DNA-synthesizing DNA-dependent, RNA-synthesizing

How does the liver use the smooth ER for detox?

Dfetoxifying enzymes that are found in the lumen of the smooth ER can take what would potentially be harmful lipid-soluble molecules; traditionally the molecule that's used as the classic example would be barbiturates like phenobarbital. These molecules are lipid-soluble and interfere with metabolism, so those drugs get moved to the liver where enzymes in the lumen of the smooth ER convert those lipid-soluble molecules into water-soluble molecules that can be then removed from the body in the urine.

Match the genetic disorder to the type of mutation. [Note: each type of mutation may be used once, more than once, or not at all] A Insertion B Loss of an amino acid C Nonsense D Missense E Deletion Duchenne's muscular dystrophy Cystic fibrosis Fragile X syndrome Huntington's disease Sickle cell anemia

Duchenne's muscular dystrophy: E Cystic fibrosis: B Fragile X syndrome: A Huntington's disease: A Sickle cell anemia: D

Which one of the following most accurately describes how the spindle poles are separated during anaphase B? Myosin on actin tracks pulling the spindle poles into position Dyneins pulling microtubules and spindle poles towards the periphery of the cell Kinesins pulling microtubules and spindle poles towards the periphery of the cell Dyneins pushing spindle poles further apart from each other Microtubules directly pushing and pulling on the spindle poles

Dyneins pulling microtubules and spindle poles towards the periphery of the cell

Origin of the mitochondria? Why do we have this theory?

Endosymbionic theory: a current day mitochondria is descendent from prokaryotic cell. at some point a larger cell engulfed a smaller cell and for some reason didn't kill it. conferred a selective advantage for the larger cell. thought to happen before evolution of nucleus so we know its a prokaryote and not a eukaryote so whats true of prokaryotes should be true of mitochondria. mitochondria have their own DNA and make a few of their own proteins

polyprotein: protease?

Eukaryotes don't do polycistronic mRNAs. They don't make multiple independent proteins from one piece of RNA. So HIV, when its full-length RNA genome gets translated, it gets translated into a polyprotein one of the proteins at the end of the polyprotein acts as a protease and cuts the polyprotein into individual pieces and can cut itself out of the polyprotein continue to make cuts even when budding off

Identify each of the following concepts or structures as being Bacterial or Eukaryotic. Unmodified methionine as the first amino acid in a polypeptide chain 5' methylguanosine cap structures 70S ribosomes Shine-Dalgarno sequences

Eukaryotic Eukaryotic Bacterial Bacterial

Why is it important that every tRNA have the same shape at the amino acid attachment site but different shapes (sequences) at the anticodon?

Every tRNA needs to be charged with an amino acid at the amino acid attachment site. Attaching an amino acid to a tRNA is a specific reaction that involves covalently linking the carboxyl group of the amino acid to the Adenine nucleotide at the 3' end of the tRNA. This reaction requires the use of an enzyme, aminoacyl tRNA synthetase. This enzyme facilitates charging and requires the amino acid attachment site to be the same shape. The shape of the anticodon needs to be different because the specific aminoacyl tRNA synthesases must be able to recognize a specific shape of an anticodon and correctly charge the tRNA. The correctly charged tRNA then uses the anticodon to complementary base pair with the mRNA codon to add the next amino acid onto the growing peptide chain.

Why is it actually an advantage that lysosomes are not indistructable?

Evolutionarilly, it would give other cells, like bacteria and viruses, the chance to copy its indestructible nature and thus become very threatening to the human body.

Anaphase A and B happen at different times during Anaphase True or false?

FALSE. they occur concurrently, just describe two different things happening simultaneously

Identify if each of the following statements is True or False. Spacer DNA sequences, also known as exons, do not code for proteins. Eukaryotic mRNAs are usually longer in length than the DNA sequence they are transcribed from. DNA must be decondensed (unwound) before it can be transcribed or replicated. Bacteria use a complex of four snRNPs to remove introns from their primary transcripts.

False False True False

Identify if each of the following statements is True or False. A mitochondrial presequence is typically found at the N-terminus of the protein being targeted to a mitochondrion. Mitochondria have their own DNA and make all their own proteins. Hsp70 and MPP are examples of chaperones found in the mitochondria. The electrochemical gradient facilitates the transport of protein from TOM to TIM and eventually to the mitochondrial matrix.

False False True True

Identify if each of the following statements is True or False. Chromosomal domains generally contain splicing factors. DNA transcription occurs in S-phase only. DNA replication occurs in S-phase only. Gene density refers to how tightly packed the chromosome is.

False False True False

Identify if each of the following statements is True or False. Glycerol-based phospholipids are synthesized in the Golgi. Sphingomyelin is a phospholipid made in the Golgi. Sphingomyelin and glycolipids are precursors of ceramide. Ceramide is synthesized in the RER.

False True False: other way around False: ceramide is synthesized in the SER

True or False... nuclear pore complexes completely close when not in use.

False. 18e complexes are never completely closed so very small molecules can still get in even when its "closed"

Identify if each of the following statements about microtubules (MTs) is True or False. A basal body has a "9 + 2" arrangement. A basal body is structurally similar to a centriole. The B tubule in an axoneme doublet is an incomplete microtuble with only 10-11 protofilaments. A cilium is not surrounded by a plasma membrane.

False. A basal body has 9 triplet arrangements of microtubules True. A basal body is structurally similar to a centriole True. The B tubule in an axoneme doublet is an incomplete microtubule with only 10-11 protofilaments False. A cilium is surrounded by a plasma membrane

Identify if each of the following statements about microtubules (MTs) is True or False. A basal body has a "9 + 2" arrangement. A basal body is structurally similar to a centriole. The B tubule in an axoneme doublet is an incomplete microtuble with only 10-11 protofilaments. A cilium is not surrounded by a plasma membrane.

False. A basal body has 9 triplet arrangements of microtubules similar to a centriole True True False. a cilium is surrounded by a plasma membrane.

Identify if each of the following statements about tubulin and/or microtubules (MTs) is True or False. In vitro, the plus end of an MT is anchored in the centrosome. In a tubulin dimer, the beta subunit has a nucleotide bind site that ATP binds to, and that ATP can be hydrolyzed to ADP. The local concentration of available GTP-bound tubulin can vary in different parts of the cell. An MT is made of 13 linear protofilaments that surround a hollow core.

False. In vitro, the minus end of an MT is anchored in the centrosome False. GTP --> GDP True. The local concentration of available GTP-bound tubulin can vary in different parts of the cell. True. An MT is made of 13 linear protofilaments that surround a hollow core

True or False... adding radioactive S35 degrades all other parts of the protein chain that does not include methionine

False. S35 is weak enough to not interfere with the protein but strong enough to be detected. Therefore, the S35 simply marks the methionines while the rest of the protein chain remains the same

True or False... Formation of the peptide bond during the process of translation indirectly uses energy from a molecule of GTP?

False. it indirectly uses ATP.

dentify if each of the following statements about tubulin and/or microtubules (MTs) is True or False. In vitro, the plus end of an MT is anchored in the centrosome. In a tubulin dimer, the beta subunit has a nucleotide bind site that ATP binds to, and that ATP can be hydrolyzed to ADP. The local concentration of available GTP-bound tubulin can vary in different parts of the cell. An MT is made of 13 linear protofilaments that surround a hollow core.

False. the minus end of an MT is anchored in the centrosome False. In a tubulin dimer, the beta subunit has a nucleotide bind site that GTP binds to, and that GTP can by hydrolyzed to GDP True True

Which one of the following statements about microtubules is incorrect? The tubulin subunits of microtubules have ATP binding sites. In animal cells, microtubules do not enter the nucleus. A sustained GTP cap causes rapid polymerization of microtubules. In vivo, the minus end of a microtubule is anchored most of the time, and therefore does not typically polymerize or depolymerize. Microtubules are very sensitive to a local concentration of GTP-bound tubulin.

False: The tubulin subunits of microtubules have ATP binding sites. The myosin subunits of microtubules have ATP binding sites

Identify if each one of the following statements about nucleo-cytoplasmic exchange is True or False. For nuclear export, the hydrolysis of ATP occurs in the cytoplasm. A protein of 10 kDa needs an energy source in the form of GTP hydrolysis to enter into the nucleus. If Protein A possesses an NLS, and Protein B does not possess an NLS, the complex of Protein A and Protein B will be localized to the nucleus. An NLS contains basic amino acids.

False: it occurs in the nucleus False True True

Which one of the following processes occurs during cell crawling? Filaments of actin are polymerizing at the leading edge of the cell, pushing the membrane forward. Microvilli function like hundreds of feet on the ventral side of the cell, allowing it to crawl forward. The sarcomere contracts, which contracts the center of the cell, allowing it to move forward. Actin cross-linking proteins depolymerize actin at the back of the cell. Intermediate filaments crosslink actin, which contracts the actin filaments and moves the leading edge of the cell forward.

Filaments of actin are polymerizing at the leading edge of the cell, pushing the membrane forward.

How are ribosomal genes organized?

Found in tandem arrays 5.8S, 18S, and 28S rRNA arrays are found on 5 different human chromosomes (13, 14, 15, 21, 22) 5S rRNA genes found in huge array on chromosome 1

During which one of the following phases of a human cell's cycle would it have a 4n amount of DNA? G0 G2 G1 S-phase Some point between the beginning of S-phase and the end of S-phase

G2

The Pulse- Chase experiment (1960): background and why we do it

George Palade developed way to trace the fate of protein using technique he called Pulse-Chase experiment Got him Nobel Prize in 1974 why we do it: protein synthesis is going on all the time in the cell so if experimenter wants to focus in on one specific protein it's hard. SO you mark set of proteins and watch only those

actin networks

Give structural stability, but are dynamic each fiber is actin indirectly linked to every other actin molecule by actin binding molecules actin bundle stays the same size but actin networks are highly dynamic. cell can rearrange to make the cell reach out or move the entire cell

HIV example of RNA virus: enveloped or naked, how many copies of viral RNA does it have in its capsid? What do the host cells need to have as a receptor for it to come in? which cells in the body have this?

HIV is an enveloped virus has 2 copies of viral RNA in its capsid gets into host cell by fusion by interaction with proteins in its envelope and receptor molecules on surface of host cells: has very specific host cells can only go to host cells that have CD4 on its receptor: immune system cells are one also need coreceptors

Retroviruses

HIV is an example Actually makes ds-DNA as intermediate from ss-RNA with a special enzyme called Reverse Transcriptase reverse transcription goes against the central dogma: make DNA from RNA

Missense mutation affect on proteins...

IF... the AA that has been altered is not critical for the folding or function of that protein... OR... if the AA that replaces it assumes those duties in roughly the same way... (both acidic/negatively charged or basic/positively charged) THEN... the protein is likely to retain at least some function, may even be fully functional. BUT... if the altered AA is critical, and the duties aren't taken up by the AA that replaces it... THEN... the protein will be inactive.

Which one of the following statements is correct about a hypothetical F-actin filament with a critical concentration (Cc) of 40 and 80 units at the plus and minus end, respectively? If the amount of available G-actin monomers in the surrounding area is 80 units, then polymerization is favored at the minus end. If the amount of available G-actin monomers in the surrounding area is 40 units, then polymerization is favored at the minus end. If the amount of available G-actin monomers in the surrounding area is 100 units, then depolymerization is favored at both ends. If the amount of available G-actin monomers in the surrounding area is 50 units, then depolymerization is favored at both ends. If the amount of available G-actin monomers in the surrounding area is 50 units, then depolymerization is favored at the minus end.

If the amount of available G-actin monomers in the surrounding area is 50 units, then depolymerization is favored at the minus end.

what would be the effect of adding a drug that blocked a phase of the cell cycle from completing?

If we administer that drug at time 0, and watch the peaks in our previous figure, what would happen to them over time, what would happen to those peaks over time with the administration of this drug? Are you going to keep a cell in m-phase, from leaving m-phase and dividing and becoming two cells? Yes you are, but what about the cells that, when you administered the drug, had just gone into G1? They're going to go through G1 just like normal, go through S just like normal, go through G2 just like normal. It isn't going to be until they get to m-phase that they feel the effect of that drug, so to speak. That means it could be 24 hours before we see the full effect of that drug. In the meantime, well before that 24 hours is up, cells that were in G2 when you administered the drug are going to back up in m-phase. Cells that are in s-phase when you administered the drug are going to backup in m-phase, and eventually even the cells that were in G1 when the drug was given are going to back up in m-phase, and since, in m-phase, you have a 4n amount of DNA, the effect on the data is going to be a noticeable, gradual decrease in the 2n peak and a complimentary rise in the 4n peak, until, 24 hours later, all of the cells would have a 4n amount of DNA. You wouldn't have any area under the curve, you wouldn't have any 2n peak, all of the cells would be lined up on the 4n peak.

Difference between bacterial and eukaryotic genes?

In bacteria most DNA codes for something so length of gene in DNA = length of RNA in eukaryotes most DNA does NOT code for proteins or RNA: called noncoding DNA. length of DNA usually longer than mRNA that participates in protein synthesis

Bacterial versus eukaryotic cycles: (DNA replication difference)

In bacteria, growth and DNA replication happen throughout the cell's life In eukaryotes, growth is mostly continuous, but DNA replication occurs in only one phase of the cycle, and distribution is a complex series of steps

How do you go from having 9 triplets to 9 pairs in the axoneme?

In every one of these triplets, and there are nine of them around the circle, one of those microtubules is going to grow up into what is to become the axoneme and will become what we call the A tubule. Another one of the three is going to grow out into the axoneme, but along the way it will lose a couple of its protofilaments and become grafted, essentially, to the one next to it. That's going to become the B tubule in every one of these doublets. And then in each of the nine triplets, one of those microtubules simply does not grow up out into the axoneme. So that's how you go from having nine triplets to having nine pairs in the cross-section of the axoneme.

Why are the 11-mers modified within the Golgi?

In order to signal to the Trans-Golgi on where to send the protein next. require different signals with different modifications of the 11-mer

Which one of the following statements about base substitution mutations is correct? Nonsense mutations are also called "silent" mutations. In same-sense mutations, usually the third nucleotide in a sequence is changed, resulting in a different codon for the same amino acid. If a base substitution mutation occurs in a protein-coding region of a gene, the resulting protein will always be non-functional. If a base substitution mutation occurs in a protein-coding region of a gene, the resulting protein will always be fully functional. Base substitution mutations occur when large pieces of DNA are inserted into a gene sequence.

In same-sense mutations, usually the third nucleotide in a sequence is changed, resulting in a different codon for the same amino acid.

Which one of the following statements about lysosomes is incorrect? Lysosomes are acidic because they contain acid hydrolases. Resident lysosomal proteins display a mannose-6-phosphate group which targets them to a late endosome. Autophagosomes form in the cytosol around old or broken down organelles; later, the autophagic vesicle fuses with a lysosome. If one of the many types of acid hydrolases found in the lysosome is nonfunctional, a lysosomal storage disease can develop. Proton pumps in the membrane of the lysosome maintain the low pH of a mature lysosome.

Incorrect: Lysosomes are acidic because they contain acid hydrolases. lysosomes are acidic because of the proton gradient.

microvilli

Increase absorptive surface area by 10-20 times extensions of the cytoplams stabilized by regular arrangements of actin bundles

Which of the following statements about the removal of introns is correct? If introns are not removed by snRNPs, catalytic ribosomes are also able to recognize the coding sequence and can cleave out the introns. Although the number of introns to be removed can vary from gene to gene, the size of the excised introns is approximately equal from gene to gene. Since snRNPs cleave in the interior of the primary transcripts to remove introns, this is an example of exonuclease activity. In a spliceosome, introns are removed by enzymatic complexes made up of proteins and DNA. Introns are removed in the nucleus prior to the export of the mRNA into the cytoplasm.

Introns are removed in the nucleus prior to the export of the mRNA into the cytoplasm.

Can alpha tubulin bind GTP? why or why not?

It cannot because its blocked by Beta tubulin subunit

How much time does each cell spend in each of the phases of the cell cycle?

It depends on the organism and the cell type within the organism in the model system: 11 hours is spent in G1, 8 hours in S phase (lots of base pairs to copy), 1 hour in M phase (can't stay long in this phase because no proteins are made here and the cell would be shut down) yeast cells can do the full cell cycle in 1.5 hours

Why isn't it threatening to a cell when a lysosome ruptures?

It releases that lysosome's worth of pH and enzymes so its immediately buffered and enzymes are not active in neutral cytoplasm

How does repair mechanism know which strand to fix?

It's going to look for the strand in hemimethylated DNA that isn't yet methylated. Once DNA gets methylated, enzymes have no way of distinguishing parent from daughter strand: once window closes, it wouldn't even try to guess

What happens to the entire microtubule array when the cell transitions from interphase to M phase?

Its disassembled. This is how dynamic cytoskeleton as a whole can be. built over again into Mitotic microtubule array

What characteristic of a molecule determines how it gets through a pore complex?

Its' size

Difference in pH between the Golgi space and late endosome space makes the MPR molecule do what?

Let go of the materials it was holding on to: releases acid hydrolase to be soluble molecule in lumen of late endosomoe

example of probe molecule working

Let's say we're looking for gene X on chromosome 10. If we know the sequence of gene X then we can prepare a fluorescent probe molecule complementary to a region of gene X. We then add that fluorescent probe molecule onto our glass slide and let it move around trying to find a region of nucleic acid that it is complementary to. If it doesn't find anything it will get washed off. If it does find something that it's complementary to, in other words, when it finds gene X, it will form hydrogen base pairs with gene X because it's complementary to it. And remember, one of our themes this term is any time two single-stranded nucleic acids find each other and are anti-parallel and complementary, they will form complementary base pairs.

How do you gather G actin up to make actin filament?: how much does it rotate, what does it LOOK like, which ends do you line up?

Line up barbed and pointed ends sometimes looks like a double helix: this is incorrect. put one G actin together with the next actin (like putting your right fist on top of your left) only way to make one G actin monomer line up correctly on the one it just went on top of is for it to rotate 166 degrees that makes it look like a helical molecule. consistent diameter down the length of about 7nm (fairly small)

Which one of the following statements about protein modification in the ER is incorrect? Lipid-linked proteins are attached to the membrane via hydrophobic interactions between nonpolar amino acid residues. In N-linked glycosylation, a 14-mer carbohydrate tree is covalently added to an asparagine found in the polypeptide chain. Lipid-linked proteins synthesized in the ER are exposed on the cell surface. BiP molecules as well as enzymes that catalyze disulfide bond formation perform their functions exclusively in the lumen of the ER. Lipid-linked proteins made in the ER will never face the cytoplasm.

Lipid-linked proteins are attached to the membrane via hydrophobic interactions between nonpolar amino acid residues. they're covalent interactions

What is the primary job of the sigma factor of RNA polymerase?

Looking for the promoter region and binding to it, telling the cell that transcription is ready to start. sigma factors are only in bacteria

How do we get recycled material out of lysosomes before they degrade themselves?

Lysosomes have transport channels in them that are used for the export of monomers once a macromolecule has been digested. So even if the lysosome hasn't degraded itself yet, you can still get the amino acids out. You can still get the nucleotides out or the fatty acids out or the monosaccharides out.

Which one of the following statements about animal cell microtubules is correct? GDP-bound tubulin has a high affinity for the minus end of a microtubule. They are composed of 13 tubulin dimers stacked end-to-end. Microtubules are made up of 13 linear protofilaments. In vivo, microtubules exhibit dynamic instability at both the plus and minus ends. Microtubule assembly requires the hydrolysis of GTP molecules bound to both α and β subunits of tubulin shortly after binding to the polymerized structure.

Microtubules are made up of 13 linear protofilaments.

if proofreading doesn't catch the mistake...

Mismatch repair system of enzymes scans recently synthesized DNA: New DNA gets methylated at adenine residues within the sequence 5'-GATC-3' ~10 minutes after replication Brief period of time where parent strand is methylated and daughter strand is not: called Hemimethylated DNA

How do the ribosomes of a mitochondria display one of its similarities to prokaryotic cells?

Mitochondrial ribosomes behave more like prokaryotic than eukaryotic. What's different about mitochondrial ribosomes than even prokaryotic ribosomes is that there's only a single piece of rRNA in the large subunit and a single piece of rRNA in the small subunit. And both of them are coded for on the human mitochondrial genome.

MutH, MutS, and MutL

MutH: looking for hemimethylated DNA and when it finds it it latches on and holds on for a second and waits to see if it gets a signal. once activated it causes a nick that recruits an exonuclease. That exonuclease is going to come in and strip out the region of DNA in the non-methylated strand all the way around the bend past the problem, just past the problem. MutS scans DNA looking for a problem (TG base pairs,etc). doesn't determine which one is wrong but it only finds theres a problem and forms a complex with MutL MutS + MutL: form a complex that links MutL/MutS with MutH and loops out whatever region of DNA lies between the problem and the nearest hemimethylated DNA sequence

Do prokaryotes have actin?

NO, but they do have a molecule thats similar thats believed to be the ancestral molecule

Is it possible for an mRNA that has completed its processing steps to display a nuclear export signal and get taken out into the cytoplasm? Why or why not?

NO. RNA molecules are nucleic acids. Nucleic acids are made of nucleotides. A nuclear export signal is a sequence of amino acids. Only proteins have sequences of amino acids. RNA molecules cannot physically display a nuclear export signal. It's impossible for an RNA molecule like an mRNA to display a traditional NES. So how do we get them out? We bind proteins to the RNA and those proteins display an NES. You have an intermediate, and that's shown in the bottom picture on this page.

What are the Ornaments: Are those ribosomes going ahead and starting translation even before transcription is finished?

NO. impossible because 1. this is in the nucleus and you don't do translation in the nucleus 2. these are rRNA molecules and you don't translate rRNA. 3. you can't do simultaneous transcription and translation in a eukaryote the ornaments are not ribosomes because you don't translate rRNA. they're the processing machinery thats cutting the rRNA molecules but they're not splicing because you're not joining any ends together.

are getting rid of negative regulation and positive regulation the same thing? why or why not?

NO. it turns "dial" up a little bit but lac promoter is fairly weak because -10 and -35 sites deviate from consensus sequence so it needs help the "help" is positive regulation

Do all microtubules remain anchored in the centrosome?

NO. they go to other locations in the cell.

If the main goal of a virus is to replicate its genetic material and package more virus particles, how would an RNA virus make more RNA?

Need nucleic acid synthesizing enzyme: RNA polymerase and primase but primase and RNA polymerase are DNA dependent, RNA synthesizing enzymes if you're an RNA virus you don't have DNA so you need something the cellular hosts don't provide answer: One of the proteins coded for in the viral genome is an RNA-dependent RNA-synthesizing enzyme: Replicase

Is there any degradation of macromolecules in the endocytic vesicles?

No, just a vehicle to bring macromolecules to the acid hydrolyses

Are all genes regulated? If not, which type of genes are not?

No, some gene products are needed at all times, it would actually be wasteful to develop regulatory scheme to turn off something you'll never turn off unregulated genes are constitutively regulated genes

Does the addition of "cold" amino acids change the rate of protein production in a cell?

No, the cell makes the same amount of protein we just aren't going to see them.

Would you expect the amount of smooth ER in testicular tissue to remain relatively constant over the life of a male human? Why or why not?

No. Cholesterol is lipid precursor for steroid hormones, such as testosterone. Lipids are made in the SER. As more testosterone is produced, more SER would be needed.

when a transmembrane structure is formed, does the ribosome know or care if the translocon is opened? what happens to the ribosome?

No. It continues to translation until it's told to stop with stop codon.

Why aren't NLS removed even though a proteins has already made it into the nucleus?

Once you have reformed a small nucleus on one end of the cell and another small nucleus on the other end of the cell and you're in the process of doing cytokinesis, how those nuclear resident proteins get back into the space that they're supposed to be in

How many RNA polymerase do prokaryotes have?

One

termination

One of three stop codons reaches A site No new tRNA involved in termination (no tRNASTOP) Release Factors recognize stop codons, and high energy bond between protein and tRNA is broken

Which one of the following statements about a nuclear pore complex is incorrect? The nuclear pore complex can expand to accommodate molecules up to 40nm in size. Only molecules that contain an A-T rich nuclear localization signal are able to get into the nucleus through a nuclear pore complex. Small molecules that are less than 20 kDa can fit through the central channel of a nuclear pore complex even if the pore is in its most closed state. The nuclear basket aids in recognition of mRNAs that need to be exported into the cytoplasm. Only proteins that have an NLS rich in basic amino acids are allowed into the nucleus.

Only molecules that contain an A-T rich nuclear loacalization signal are able to get into the nucleus through a nuclear pore complex

Lactose Operon: specific example of genetic regulation in E. Coli

Operons are multiple genes under control of a single promoter, transcribed as a polycistronic mRNA set of tools E. Coli needs to use lactose as a food source One of the protein products of the lac operon is an enzyme called beta-galactosidase (or β-galactosidase, or β-gal): direct correlation happens at the level of translation initiation: you don't even make lac permease

Is it the PCM or is it the centreoles that the microtubules emirate from?

PCM: something in the PCM that acts as seed for new microtubules evidence: plants plants have centrisomes but don't have centrioles but can make microtubules: so it must be PCM within animal cell, we can blast out centrioles and cell still makes microtubules the PCM is proteins that surround the centrosome

Explain the experimental reason why Palade did not include mitochondria in what is called the Secretory Pathway.

Palade used pancreatic cells, which secrete a lot of proteins outside of the cell. The bulk amount of proteins made in these cells follow the secretory pathway and he therefore saw the proteins go from RER→Golgi→Vesicles→extracellular space. The proteins that get secreted are all made by membrane bound ribosomes. Mitochondrial proteins, on the other hand, are made by cytosolic free ribosomes and then transported to the mitochondria, and are not part of the secretory pathway.

Is polysome formation possible in eukaryotes? Is co-transcriptional translation possible in eukaryotes? For both questions, explain why or why not.

Polysome is the "assembly-line" production of protein. It involves many ribosomes on the same piece of mRNA translating in a line. This can occur in both prokaryotes and eukaryotes because the final message and ribosomes are located in the cytoplasm. Co-transcriptional translation is not possible in eukaryotes because they are compartmentalized and transcription occurs in the nucleus and translation occurs in the cytoplasm.

In the mismatch repair system in E. coli, which one of the following enzymes does not directly perform a function? Primase MutH Exonucleases Ligase MutL

Primase

Which one of the following statements about the cell cycle is correct? Prometaphase ends when the last pair of sister chromatids arrives at the metaphase plate. The nuclear envelope is disassembled during anaphase A. Interphase is the period of time between telophase and cytokinesis. The metaphase plate is a structure composed of actin. Once a centrosome is positioned at the beginning of M-phase, it remains in that position throughout the rest of M-phase.

Pro metaphase ends when the last pair of sister chromatids arrives at the metaphase plate The nuclear envelope is disassembled during prophase Interphase is the period of time between M phases The metaphase plate is a structure composed of spindle fibers Once a centrosome is positioned at the beginning of M-phase it moves around from that position many times throughout M-phase

3. early gene expression

Production of enzymes needed to replicate viral nucleic acid (and sometimes shut down transcription/replication of host cell's DNA) For some viruses, enzymes for replicating viral nucleic acid aren't made by the host cell, so virus has to provide them Not all virus types have a defined early gene phase! sometimes its skipped

Proteases Nucleases Glycosidases Lipases roll of each of these enzymes? what type of linkage do they degrade?

Proteases (degrade proteins): degrade peptide linkages Nucleases (degrade nucleic acids): degrade phosphodiester linkages Glycosidases (degrade carbohydrates): degrade glycosidic linkages Lipases (degrade lipids): degrade ester linkages many copies of each of these in each lysosome

What did the Pulse-Chase experiment show about how protein production is organized?

Protein production takes place in specific spots in the cytoplasm and it's localized supported the hypothesis that secreted proteins are translated in a central location and moved as a group through some sort of a pathway until they are all exported out of the cell.

The RER plays roles in...

Protein secretion Synthesis of membrane proteins Protein processing

Which one of the following processes is least likely to occur in the Golgi? Protein-bound mannose phosphorylation Cell wall polysaccharide synthesis Protein synthesis Glycolipid synthesis Protein glycosylation

Protein synthesis is least likely to occur in the Golgi

How do cells direct proteins to the proper location?

Proteins that stay and function in the cytoplasm have no additional "targeting" signals Proteins destined for the nucleus have a nuclear localization signal Proteins destined for a mitochondrion have a mitochondrial presequence

What do the smooth and rough ER look like physically?

RER:flattened sacks of membranes with the studded ribosomes binding to them SER: system of connected tunnels

Name of the machinery that removes introns and joins exons together?

RMP

3 types of RNA polymerases in eukaryotes and type of RNA each transcribes

RNA polymerase I: transcribes rRNA genes RNA polymerase II: transcribes mRNA genes RNA polymerase III: transcribes tRNA genes and some rRNA 1:1 correlation between polymerase and type of RNA it creates.

describe the role of each of the RNA polymerases throughout the course of production of a 40S and 60S ribosomal subunit

RNA polymerase I: transcribes the RNA genes RNA polymerase II: transcribes the genes for ribosomal proteins that will be part of ribosomal subunits RNA polymerase III: transcribes the 5s rRNA molecule

which of the three RNA promoters is most complex?

RNA polymerase II: reflection of huge diversity of genes transcribed by this promoter

how does intrinsic transcriptional termination work?

RNA transcript folds into "stem-loop" or "hairpin" which is intra strand base pairing with CG bonds. very stable structure. it interferes with RNA polymerase. AU base pairs are weakest of all and only thing left holding RNA polymerase on so it falls off.

eukaryotic mRNA is exported from the nucleus accidentally prior to the addition of its 5' cap structure. Identify two potential negative consequences.

RNases will recognize the 5' end and begin to degrade the message. This mRNA will not get translated. The ribosome recognizes the 5' cap structure and then starts translation at the next AUG. If there is no 5' cap, the ribosome will not know where to start translation.

why is the cytoskeleton called dynamic?

Reorganizes as cell responds to environment or divides. cell's "skeleton" is not like human skeleton

Elongation step 3 (translocation)

Requires another Elongation Factor (EF-G) and hydrolysis of another GTP Ribosome moves 3 bases toward the 3' end of the mRNA, displacing the uncharged tRNA and opening A site for next charged tRNA

how does rho dependent transcriptional termination work?

Rho protein acts as helicase. Helices unwinds RNA-DNA hydbrid molecule. Finds helicase consensus sequence and binds to it and once its in transcription bubble it unwinds RNA and knocks off RNA polymerase

Which one of the following proteins would be most likely to need an NLS and an NES? Ribosomal proteins Phosphofructokinase Secreted (exported) proteins RNA polymerases DNA polymerases

Ribosomal proteins

Provide a likely explanation for why ribosomes can be found on the outer membrane of the nuclear envelope.

Ribosomes are found on the outer membrane of the RER in order to translate proteins. The outer membrane of the RER is contiguous with the outer membrane of the nucleus and the lumen of the RER is continuous with the lumen of the nuclear envelope. Thus, it's fluid and ribosomes can along the contiguous membrane

What is the path of secretory proteins determined by the Pulse-Chase experiment? A.K.A. secretory pathway

Rough Endoplasmic Reticulum --> Golgi Apparatus --> vesicles --> exterior

Which structures play a direct role in the production and localization of a secreted protein?

SRP, signal peptide, BiP

Describe the similarities and differences between the sigma factor in E. coli and a traditional transcription factor in a eukaryote.

Sigma factor is used in bacteria while transcription factors are used in Eukaryotes. Sigma factor is a component of the RNA polymerase holoenzyme. Sigma factor looks for the promoter regions while it is in complex with the core RNA polymerase. Transcription factors find the promoter region, and then bring in RNA polymerase to the region. There are multiple types of transcription factors, and of each of the three types (I, II, III), is associated with a particular RNA polymerase. Additionally there are many different proteins involved for each type of transcription factor (for example TFIID, TFIIA, TFIIB...). There is only one sigma factor (although there are different types of sigma factors that we haven't talked about yet) that associates with one RNA polymerase. So, more subunits are involved for Eukaryotic transcriptional initiation in comparison to bacterial transcriptional initiation. Both sigma factor and transcription factors recognize specific promoter sequences, but those sequences are not the same, and are different for each type (I, II, or III) of transcription factor. Both sigma and transcription factors orient RNA polymerases at particular transcriptional start sites. In both cases, sigma factor and transcription factors are not used during the actual process of transcription. These factors are left behind or released, leaving RNA polymerase to do its job once transcription has become processive.

SRP

Signal Recognition Particle: 1.recognizes an ER directed signal peptide and binds to it on the emerging protein 2. can also bind to the ribosome itself so it also grabs the ribosome, stopping it from continuing the elongation phase. like hitting the "pause" button 3. makes its way to nearest RER membrane and binds to the SRP receptor. "dock" for SRP. sets ribosomes on the translocon (similar to TIM or TOM) only wide enough for unfolded protein. also makes the SRP molecule let go of the receptor, the ribosome, and newly emerging protein. 4. SRP leaving causes translocon to open and translation resumes but emerging protein goes down through translocon into lumen of ER 5. consensus sequence recognized by signal peptidase that recognizes the junction between the peptide that was acting as your signal and the rest of the protein and chops at that junction. you're sort of feeding in the signal peptide, and it's getting stuck to the inside of the translocon as it goes in. So then the C-terminal end of the peptide is going to be in the lumen, where signal peptidase can chop it.

Steps 1 and 3 during the Elongation phase of Translation require energy in the form of GTP. Why does step 2 not require a GTP as well?

Step 2 is peptide bond formation. Formation of this covalent bond does require energy, but that energy is already "built in" and it does not require GTP hydrolysis. The energy to form the peptide bond comes from breaking the covalent bond (an exergonic reaction) between the amino acid and the tRNA.

Which one of the following statements about transcription in E. coli is incorrect? RNA polymerase is a DNA-dependent, RNA-synthesizing enzyme that reads the template strand in a 3'-5' direction. -10 and -35 promoter sequences are recognized by the sigma (σ) factor. The RNA transcript is complementary to the DNA coding strand. RNA polymerase holoenzyme scans double stranded DNA non-specifically looking for conserved -10 and -35 promoter sequences. RNA polymerase core enzyme transcribes the coding region, and typically the terminator sequence, but does not transcribe the promoter region.

The RNA transcript is complementary to the DNA coding strand.

Which of the following is true regarding the elongation stage of translation? Amino acids are added to the growing protein chain by separation of the large and small subunits of the ribosome. Amino acids are added to the growing protein chain by hydrolysis of GTP. The enzyme, peptidyl transferase, catalyzes the formation of peptide bonds. Amino acids are added to the growing protein chain by forming hairpin structures. The enzyme, EF-G, catalyzes the formation of peptide bonds.

The enzyme, peptidyl transferase, catalyzes the formation of peptide bonds.

Which one of the following statements about T4 is correct? The genes expressed early in its replicative cycle are under the control of a weak promoter. The capsid, tail fiber protein, and base protein are examples of proteins expressed early in its replicative cycle. It expresses nucleases during early gene expression to degrade the host genome, thus diverting resources to viral production. Upon attachment to a cell surface, the capsid injects a double-stranded RNA to the host cytosol. It expresses a replicase enzyme in the early stage of its replicative cycle.

The genes expressed early in its replicative cycle are under control of a strong promoter. The capsid, tail fiber protein, and base protein are examples of proteins expressed late in its replicative cycle. CORRECT: It expresses nucleases during early gene expression to degrade the host genome, thus diverting resources to viral production. Upon attachment to a cell surface, the capsid injects a double stranded DNA to the host cytosol

overview of Ribosomal RNA Genes and the Organization of the Nucleolus

The nucleolus is organized around the chromosomal regions that contain the genes for the 5.8S, 18S, and 28S rRNAs. Eukaryotic ribosomes contain four types of RNA, designated the 5S, 5.8S, 18S, and 28S rRNAs. The 5.8S, 18S, and 28S rRNAs are transcribed as a single unit within the nucleolus by RNA polymerase I, yielding a 45S ribosomal precursor RNA. The 45S pre-rRNA is processed to the 18S rRNA of the 40S (small) ribosomal subunit and to the 5.8S and 28S rRNAs of the 60S (large) ribosomal subunit. Transcription of the 5S rRNA, which is also found in the 60S ribosomal subunit, takes place outside of the nucleolus and is catalyzed by RNA polymerase III.

What ultimately decides the final location of a protein?

The site of translation. Some proteins translated fully out in the cytoplasm

pre RNAs

The tandem arrays of genes for 5.8S, 18S, and 28S rRNAs are transcribed by RNA polymerase I into primary transcripts or pre-rRNAs: Called the pre-rRNA transcriptional unit 45S pre-rRNA is then cleaved into mature 5.8S, 18S, and 28S rRNA

What targets translation to the ER? instead of just allowing it to stay in the cytoplasm?

Theoretically, it could be either the mRNA, ribosome, or protein that's presenting some sort of signal that says, "This shouldn't continue out in the cytoplasm. We need to stop what we're doing right now, move over to the ER, and then we can resume at that point." ribosome: nothing different between ribosome translating in RER versus translating in cytoplasm so thats not it mRNA: NO because all translation initiates on cytosolic ribosomes protein: different after you get started versus before so has the sequence of amino acids that presents 3D shape acting as signal to finish translation on RER

kinases

There are kinases that are very key enzymes during m-phase, that will phosphorylate particular molecules in the nuclear envelope, particular proteins in the nuclear pore complex, and lamin proteins

What do importins do once they let go of their protein and exit back out into the cytoplasm?

They reshape themselves to fit the next NLS. This is energy dependent. GTP hydrolysis GTP ---> GDP + Pi

Why are viruses called mobile genetic elements?

They're just pieces of nucleic acid that happen to be wrapped in a protein coat, and when that information gets inside a living host cell the host cell expresses that information like it does its own information. It makes proteins out of it. What the cell doesn't know is that the proteins it's about to make are going to eventually kill it, but there isn't anything about the virus as an entity that makes it out to getcha

Explain how it is possible for adjacent genes in a chromosome to use different parental strands as the template strand during transcription.

Transcription can only proceed in the 5' to 3' direction. Because the strands are complementary, and NOT identical, each strand has different information. RNA polymerase is oriented in the correct direction based on the location and orientation of the promoter sequences.

2. penetration

Transfer of viral genome into host cell Sometimes just the nucleic acid enters cell, sometimes entire viral particle enters cell Phage usually have to "inject" their genome through cell wall: Capsid is left behind (bacteriophage) Animal viruses follow one of two basic paths: Fusion or endocytosis

Identify if each of the following statements about actin is True or False. Actin is an abundant protein in a human cell. Polymerization of an actin filament will only occur at the plus end. Actin generally polymerizes more rapidly at the barbed end. If the actual amount of available GTP-bound G-actin is below the critical concentration, then the actin filament will depolymerize.

True False: polymerization occurs faster at the plus end, but it can occur at either end True False. If the actual amount of available GTP bound G actin is below the critical concentration, the actin filament will polymerize

Identify if each of the following statements about chromosomal territories is True or False. Each chromosome occupies a distinct territory. If we conduct a chromosome painting experiment with each chromosome painted with a different color, and chromosomes do not occupy their own domains, the colors would mix together and be a grayish-brown color. Chromosome painting is an extension of Fluorescence In Situ Hybridization (FISH). If we do a chromosome painting experiment with each chromosome painted with a different color, and chromosomes do occupy their own domains, there would be a diffuse glow of one color in the nucleus.

True True True False

Identify if each of the following statements is True or False. Even the smallest rRNA molecule is larger than a typical tRNA molecule. In eukaryotes the mRNA message is monocistronic. Ribosomes are identical in eukaryotes and bacteria. The first charged tRNA never occupies the A site.

True True False True

Identify if each of the following statements is True or False. Transcription continues even as a cell has entered S-phase. All chromatin takes an equal amount of time to access for replication. During replication, DNA is collected in regions where replication machinery is located. DNA replication appears to be a well-organized process within the nucleus, but transcription does not appear to have any organization to it.

True False True False

True or False? Having a sequence that could form a stem loop structure doesn't necessarily make you an intrinsic terminator but you can't be an intrinsic terminator without a stem loop structure.

True.

True or False? A given protein can leave the pathway of 11-mer modification at any time?

True. because the enzymes that carry out these modifications don't just recognize the carbohydrates as a substrate, they recognize that protein as wearing that particular "hat" maybe you go through the first step and then you're finished, maybe you go through the first three steps and then you're finished. It's quite simply a matter of you either are a substrate for the next enzyme or you are not. There are some proteins that do need to go all the way through this path, and for them, they had to go through every step, but if a protein is finished and has the appropriate zip code, so to speak, after two of those steps, then it is simply not going to be the substrate for any other enzymes in the Golgi.

Is the machinery for transcription and pre-mRNA processing organized (i.e., accessible and convenient)? How do we know?

Use dye specific to chromatin. Shows difference between interchromsomal domains and chromatin regions Fluorescence microscopy: "brighter" = "more" Electron microscopy: "darker" = "more"

How do we know that microtubules originate at centrosomes?

Use laboratory agents like Colcemid and see what happens if we get rid of the cells microtubules and then allow them to regrow 1. Treat cells with colcemid for 1 hour: long enough to induce depolymerization of microtubules but not long enough to kill the cell 2. After 1 hour, wash away colcemid: now lots of GTP bound tubulin 3. Let cell recover to start forming new microtubules: take another photo showing reformation of microtubules in a region just adjacent to the nucleus

What do plants cells, that lack lysosomes do?

Vacuoles assume the function of lysosomes vacuoles are seemingly empty space in the cell: have degradative molecules in them have multiple within a cell cannot do phagocytosis: don't have lysosomes and cell wall won't fuse out.

lysogenic cycle (lysogeny)

Viral DNA is integrated into host genome, no new virus particles produced, most viral genes turned off cell is "immune" to infection by same type of phage but is to a T4 molecule Phage in lysogeny sometimes called a Prophage: gets into host cell's DNA Active genes within prophage can confer properties to host cell (e.g., non-pathogenic bacteria can make toxins)

lytic cycle (lysis)

Viral DNA is transcribed and replicated, new virus particles produced, cell lysed (broken)

N-linked glycosylation

Virtually every protein that goes through the ER goes through this specific process and in most proteins happens in a variety of different locations the addition of an oligosaccharide tree, or group of sugar molecules, to a specific asparagine residue, or amino acid, within the primary sequence of the protein that is making its way through the translocon 1. protein presents a signal peptide and gets directed to the ER. As it is being inserted through the translocon, a special sequence of amino acids is presented as a signal. This is different than a signal peptide; it's different than a stop-transfer sequence, and it's only three amino acids, one of which is an asparagine. Now that asparagine has a nitrogen in it, which is why this is called N-linked glycosylation 2. build fourteenmer (oligosaccharide) tree on dolichol platform 3. enzyme recognizes asparagine residue and prepared fourteenmer and cuts fourteenmer off dolichol platform and link it covalently to the three amino acid sequence 4. trim fourteenmer down to elevenmer by trimming the glucose off. signal that protein is now ready to go to the next location once its done being translated

How is a protein marked that it's ready to be sent to the Golgi from the ER?

When it presents one or more 11-mers.

Explain why, if most of an intron's sequence is not critical, conserved regions are found at or near the splice sites.

While most of the intron is not important for the the final protein product, there are conserved regions at and near the splice sites. These conserved regions are recognized by snRNPs. snRNPs are the machinery that accurately removes the intron and bring the exons together. There is also a crucial adenine that is near the 3' splice site that plays a role in the process of slicing. If these conserved sequences were not present, it would lead to inaccurate splicing and therefore the mature mRNA would be incorrect which would likely lead to non-functional proteins being made from the incorrect mRNA.

Do some viruses lose the ability to come out of lysogeny and go into the lytic pathway? what are some examples of diseases that arise from this happening?

Yes, due to a mutation sometimes viruses get locked into lysogeny and becomes permanent part of bacterial species Scarlet Fever, diptheria: nothing wrong originally with the bacteria but since it has the virus it now is that didn't hurt it but the phage created protein during lysogenic phase that didn't affect bacteria but got locked in place and became permanent part of bacterial phage

Can one amino acid actually make a difference? give example using sickle cell anemia and how it works

Yes. Sickle cell anemia caused by defective beta globin subunit: changes overall charge of protein with distorted hemoglobin molecule so cells get stuck in blood vessels and limits oxygen delivery causing pain creates sticky sites causing hemoglobin molecules to stick together and precipitate out. pushes red blood cell outward with distorted shape 8% of African Americans are carriers. Why hasn't natural selection gotten rid of it? Parasite infects red blood cells which prevents malaria

Is it possible that a protein that's supposed to stay in the ER accidentally get packaged in a transport vesicle? What does the Golgi do if this happens?

Yes. The Golgi apparatus is smart enough, so to speak, to recognize that there isn't anything to do on this protein, that it was an accident, and it will send it back. moves it from Cis-Golgi back to the ER so it doesn't have to go all the way through the Golgi Stack

Is it acceptable for a vesicle to have both dynein and kinesin on it?

Yes. could have just one or the other too. depends on the needs of the cell

if DNA replication were random, what would the fluorescent experiment color look like? What if it were organized?

You'd see a light color diffused throughout the membrane. If organized there'd be clusters of color

Nuclear Localization Signal (NLS)

a NLS is not a separate object; it's a stretch of amino acids in the primary sequence of that protein. That NLS is recognized and bound to by an importin, and they approach a nuclear pore complex signals the pore complex to let them through mostly positively charged (basic) amino acids

release factor

a PROTEIN recognize stop codons, and high energy bond between protein and tRNA is broken. physically mimics shape of charged tRNA molecule

Svedberg unit

a Svedberg unit takes into account not only a molecule's mass but also its shape Think about the difference between parachuting when you have your arms and legs extended versus when you ball up. When you bring in your arms and legs you move much faster because the resistance is less than it is when you have your arms and legs extended. The same thing is essentially true of molecules when they're being moved through a gradient. If they are stretched out more, so to speak, they will move slower than if they are packed in nice and tight they will move faster. So it's important to understand that a Svedberg unit takes shape into account as well as just size.

ribozyme

a catalytically active RNA molecule. it is the snRNP that makes the cut, but specifically, it's one of the RNA molecules that acts as an enzyme, and that's called a ribozyme.

if we don't want to make new G-actin when we need more and break G-actin down when we don't need it at the moment, how do we tip that equilibrium?

a cell can have up to half a billion G actin cells, so theres a large surplus: it hides whatever G actin it doesn't need using family of proteins that binds to actin: actin binding proteins

Can a cell turn "off" genes it doesn't need? explain example using E. Coli

a cell would use up all of it's ATP if it was making all of its proteins all of the time so YES it is possible ex: E. Coli can use many different sugars to make energy (glucose, lactose, arabinose, maltose, sucrose, etc.) different suites of enzyme needed to utilize each sugar: only needed when that specific sugar is present so if lactose is not available at the moment, those proteins will be turned off

slipped strand mispairing

a nucleotide sequence is present in more than one place on chromosome and copies in homologous chromosomes pair in wrong place. creates a loop in the chromosome

The closer the gene matches the consensus sequence: the better RNA polymerase will do of recognizing it as ____. How does this affect the rate of making RNA?

a promoter. increases the rate of making RNA

what is a gene?

a region of useful information. portion of a chromosome

mitochondrial pre sequence

a sequence of amino acids that comes at the end terminus of the protein that's loaded with basic amino acids.

operon

a single transcriptional unit in prokaryotes that encodes multiple enzymes necessary for a biochemical pathway. clustering them together allows for them to be regulated together

missense mutation (2 classes)

a type of mutation that changes an amino acid in a protein 2 classes: 1.transitions: doesn't change the type of base in the base pair (pyrimidine stays pyrimidine, purine stays purine) 2. transversion:does change the type of base pair.

actin monomers: level of folding?

actin monomers are highly folded globular proteins globular=looks like a globe

I band

actin without overlapping myosin disappears when muscle overlaps because actin and myosin overlap

nuclear ring

acts as a diaphragm: opens and closes

gamma tubulin

acts as seed for formation of new microtubule found throughout the PCM So getting sequentially more specific, it is accurate to say that microtubules emanate from a centrosome. It is more accurate to say that those microtubules emanate from the PCM. And it is more accurate still to say that those microtubules originate from the gamma-tubulin within the PCM

frameshift mutation

addition or deletion of 1 or 2 bases. much worse consequences than a substitution of a base: affects everything downstream from it almost always results in premature stop codon

G0

adult cells stop dividing. they're not dead, they're just not supposed to be replicating anymore ex. liver should not grow past how big it is when you're an adult. if the cells kept dividing it would keep getting bigger and bigger and wouldn't fit anymore at point where G1 is transitioning into S phase Metabolically active, but non-proliferative: still doing transcription, translation, glycolysis, etc. some cells can come out of G0 while others cannot: liver can regenerate itself, nervous system doesn't

cytoplasmic filaments

aid in recognition of protein molecules that need to be imported

Identify if each of the following statements about transcription is True or False. The DNA template is read 5'-3'. The coding strand is complementary to the RNA transcript. The same strand of a double helix serves as the template for transcription of every gene on the chromosome. dNTPs are added onto the primary transcript at the 3' end.

all false

Difference between each type of RNA molecule?

all genes are transcribed the same. The difference among the three is what you use that RNA for, not how you make it.

in single celled organisms, how many of the daughter cells have the mutation?

all of the daughter cells

splicesome

all the snRNPs come together to form splicing molecule

Post translational control. What if the cell needs to quickly shut off an existing protein or enzyme?

allosteric regulation or feedback inhibition: fine tune level of protein actually working for you in the cell

P site and A site

allow a nice complete interaction between the anticodon in the tRNA and the codon in the mRNA.

Why do we get rid of the nucleus during M phase?

allow our newly-formed microtubules to gain access to those condensed chromosomes. We're actually going to have to disassemble the entire nucleus during m-phase, then once those chromosomes have made contact, we're going to, in a way that we'll see soon, separate those sister chromatids to opposite poles of the cell, and then put humpty dumpty back together again.

What do exportins do once they let go of their protein and import back into the nucleus?

allowed back in by nuclear pore complex reshapes itself by hydrolysis of GTP in the cytoplasm GTP ---> GDP + Pi energy not used to get it across the membrane but to reshape it for binding to new proteins

GPI (Glycosylphosphatidylinositol) anchoring

also occurs in the RER: makes lipid linked protein can happen to a protein that's already been N-linked. only small subset of proteins get GPI anchors 1. prepare protein and catch it in the membrane so it doesn't get away from us 2. prepare the GPI anchor. PI stands for phosphatidylinositol, which is a major membrane phospholipid. that phosphatidylinositol molecule is now going to have some sugar groups associated with it, covalently. when you glycosylated a phosphatidylinositol you get a molecule called glycosylphosphatidylinositol. And that's a mouthful, so we just abbreviate it GPI 3. bring together the GPI anchor and the protein. there is an enzyme that recognizes a prepared GPI anchor, recognizes a protein with a specific C-terminal tail that has been held into the membrane. It's going to cut the C-terminal tail off of protein and hold on to the new C-terminus and link it covalently to an ethonolanine groups in the GPI anchor.

Dynamic Instability: what is it critical for?

alternating cycles of growth and shrinkage First shown by Mitchison and Kirschner in 1984 critical for remodeling prior to mitosis

what is the only thing that changes when a sarcomere contracts or relaxes?

amount of overlap between actin and myosin

what does it mean for the genetic code to be redundant/degenerate but not ambiguous?

an amino acid can be specified by more than one different codon, most amino acids are specified by multiple codons degeneracy: lucine might have 6 different ways to specify it ambiguity means that sometimes UUU specifics phenylalanine and sometimes lysine. this is NOT how it works. UUU ALWAYS specifies phenylalanine

Removing an in-frame, 3'-5' ATC sequence in the template strand of the coding region of a protein-coding gene would result in: a true frameshift mutation. an in-frame transition. an insertion mutation. an elongated polypeptide chain. a deletion mutation.

an elongated polypeptide chain

why do no 2 lysosomes look alike?

at any given moment in time, a given lysosome is working on different material than any other lysosome.

How do we get cilium or flagellum to bend or whip

axoneme held together by radial spokes of nexin links if you can't slide you'll have to bend because nexin links are keeping microtubules from freely moving

What does it do for the cell to have spacer DNA?

bacteria have very little spacer DNA. isn't worth our evolutionary time to get rid of...we don't use it for anything.

Why does the first base added in RNA strands get to keep its triphosphate group?

because it's not covalently linked to anything

codon usage bias

because of the degeneracy of the genetic code, not all codons are created equally and one codon will have more charged tRNA molecules, which is the preferred one.

Why can't interphase chromatin usually be observed by light microscopy? What's the exception?

because they're so thin but when you have a thousand of them still stuck together they're still visible under light mitroscopy

Why is an integral membrane protein even though no part of it is embedded in the membrane?

because we can't just float away the protein part. If we were to remove this protein from the membrane, because its connections all the way down to the phosphatidylinositol are all covalent, we'd have to pluck out the phosphatidylinositol, and that would disturb the integrity of the membrane

Why do most mistakes occur during DNA replication?

because were synthesizing huge amounts of DNA

Cytokinesis

begins while telophase is going on M phase finishes when cytogenesis is complete contractile ring pinches using internal contractile ring: forms cleavage furrow use actin filaments and myosin motor proteins rather than microtubules and kinesin/dyenin

just how big is a pore complex (compared to an amino acid)?

bigger than an amino acid, even bigger than polypeptide chains, it's made up of polypeptide chains

MPR (mannose 6 phosphate receptor)

binds to the protein that we are about to send over to the late endosome to be working, not to be degraded. Remember this is an acid hydrolase we're in the process of making. MPR binds that mannose-6-phosphate group, holds onto the protein, and then buds off in a little transport vesicle on its way to a late endosome

Where does the energy for forming the peptide bond in the process of translation most DIRECTLY come from?

by breaking the bond between the tRNA and the amino acid that had been charged onto it.

How do we harness the amount of energy in ATP molecule?

by charging a tRNA. And I mentioned back then when we talked about charging tRNAs, remember that this is a source of potential energy. When you break that bond between an amino acid and that adenine base at the three-prime end of that tRNA molecule that will release energy. You break a covalent bond; you release energy.

How does a ribosome distinguish the initiator codon from an internal methionine codon in bacteria? (include something about 16s rRNA)

by forming a Shine-Dalgarno sequence or ribosome binding site, the ribosome then knows the initiator codon is 10 bases downstream

type I myosin: conventional or unconventional?

called unconventional myosin conventional ones are usually found in pairs and have long tail fibers unconventional ones are found singly and have shorter tails: works as a pair with another type I myosin to move filaments

entry of endocytosis

can be enveloped or naked host cell recognizes theres a particle that needs to brought in and then separated from membrane that came from process of endocytosis then fused with early endosome and use drop in pH as trigger to change conformation of their molecules to escape early endsome now capsid is out in cytoplasm and replicative cycle can continue

What if you were an E. Coli cell that has lactose (with or without glucose present)? How does repressor protein work?

cell wants to make tools necessary to use lactose as a food source so needs to get rid of repressor protein repressor protein has allosteric site on it and when lactose binds to it, it changes the conformation of the repressor protein such that it can no longer hold on to the operator protein so it falls off and promoter is accessible as long as lactose is present you'll have expression of the lac genes

difference between how cilia and flagella move?

cilia are shorter and move slower in wave like fashion flagella are longer and move faster in a whip like fashion but they're built exactly the same way: only difference is how long you make it and how fast you turn it

How many cilia do ciliated cells usually have? what about flagella cells?

ciliated cells have many cilia cells with flagella only have one or two

In every one of these triplets, and there are nine of them around the circle, one of those microtubules is going to grow up into what is to become the axoneme and will become what we call the A tubule. Another one of the three is going to grow out into the axoneme, but along the way it will lose a couple of its protofilaments and become grafted, essentially, to the one next to it. That's going to become the B tubule in every one of these doublets. And then in each of the nine triplets, one of those microtubules simply does not grow up out into the axoneme. So that's how you go from having nine triplets to having nine pairs in the cross-section of the axoneme.filament

circle of tubulins stuck together

lacZ

codes for B-galactasidase protein B-galactasidase breaks down lactose into glucose and galactose

lacY: which protein does it code for and what does this protein do?

codes for lactose permease makes the cell permeable to lactose: without it you would starve because couldn't get any nutrients in the cell

Operon

collection of genes under control of a single promoter though a single terminator that leads to production of polycistronic mRNA that has multiple coding regions for multiple genes Lac has 3: lacZ, lacY, and lacA: under control of the lac promoter

In each pair of microtubules in axoneme, one of the microtubules is a complete microtubule and the other is not? what makes one complete?

complete microtubules have 13 protofilaments A tubule is considered the complete one B tubule is considered incomplete microtubule and has only 10 or 11 protofilaments but central pair are both complete microtubules and not directly connected

critical concentration

concentration of G actin in which the end of an F actin molecule will be stagnant and not be growing or shrinking we know exactly how much G actin is necessary to exhibit no net growth at end of actin. but critical concentration is different at barbed and pointed ends. polymerization occurs 5-10x faster at barbed end (plus) depolymerization occurs 5-10x faster at pointed end (minus) ATP bound G actin has high affinity for other ATP bound G actin. Once ATP hydrolyzed to ADP, G actin doesn't want to be part of actin filament anymore but its stuck in "traffic jam"

how does machinery know where boundaries are for intron removal (RNA splicing)?

conserved sequences at both ends mark splice point: mark the junctions between an intron and exon on both ends.

structure of virus?

consist of nucleic acid, protein coat (Capsid), and sometimes a few enzymes Some animal viruses are surrounded by a lipid/protein membrane acquired during release from host cell

What does the cell use actin filaments for? (3 possibilities)

coordinated efforts with other actin filaments 1. actin bundle: all actin filaments have same directionality and linked together via cross linking proteins acting as a bridge: don't allow for a lot of movement 2. actin network: link 2 or more actin filaments together but use flexible cross linking proteins 3. contractile element: way to move actin filaments relative to other actin filaments using motor protein

2 forms of RNA polymerase in prokaryotes

core polymerase: can synthesize RNA using DNA template but can't initiate synthesis accurately holoenzyme: accurately initiates synthesis

How to get rid of signaling molecule?

destroy the molecule, insulin brought into the cell by outside world and eventually degraded into individual amino acids to be recycled

The human mitochondrial genome is copied by Mitochondrial DNA Polymerase. Trace the path of this enzyme from its production to its function.

encoded by nuclear DNA. transcribed and processed in the nucleus mature mRNA gets transported out into the nucleus Once in the cytoplasm, ribosomes will translate the mRNA to make the Mitochondrial DNA Polymerase protein. This protein will contain a basic (negative) stretch of amino acids called a mitochondrial pre-sequence (or transit sequence). This pre-sequence signals that the protein needs to be transported to a mitochondrion. Chaperone proteins will bind to the protein to keep the protein unfolded and transport the protein to the mitochondrion. Once there, the chaperones will be peeled away. The unfolded protein will go through TOM and then though TIM. The mitochondrial pre-sequence, which has a positive charge, will want to go toward the more negatively charged (more basic) mitochondrial matrix. This is partially where the energy comes from to transport the protein. Once the mitochondrial pre-sequence is inside the matrix, the rest of the protein is ratcheted into the matrix and mitochondrial Hsp70 will keep the protein unfolded until it reaches the chaperonin complex. Once at the chaperonin complex, the Hsp70s are peeled off, and the protein goes inside the chaperonin barrel. This is where the protein is folded in the correct manner (unless it doesn't need to be folded in the chaperonin). Once it is released from the chaperonin, it should be properly folded and functional.

what does "endoplasmic reticulum" mean? use roots of the word

endo= within (the cyoplasm) reticulum= a network a network of membrane bound tubes and sacks

What is a virus called that has an envelope around it? What about a virus without an envelope?

enveloped and naked

monocistronic mRNA

eukaryotes: only carry info for one protein product because each one only has one 5' end and therefore only one 5' cap

Late endosome

eventually works in lysosome. only does so because it displayed mannose-6-phosphate signal

Phenylketonuria (PKU)

every newborn is tested: looking for buildiup of phenylalanine (amino acid): if it's located they have PKU. must go on special diet. caused by change in just ONE amino acid phenylalanine is not allowed to build up in wild type: its turned into tyrosine but buildup of phenylalanine can be toxic for people with PKU

what is happening during S phase?

everything you were doing during G1 phase, you're also doing in S plus DNA replication so cell continues to grow but DNA is also replicated

Huntington's Disease, Hemophilia, Fragile X Syndrome are examples of the consequenes of what type of mutation?

examples of insertion mutations (repeated or inserted sequences of DNA)

The diversity of proteins in humans is primarily a result of: exon variability in mature mRNA. the large size differences in mRNA transcripts. the large amount of DNA compared to other eukaryotes. the vast number of genes compared to other eukaryotic organisms. the existence of 5' caps and 3' poly-A tails.

exon variability in mature mRNA

alternative splicing

exons arranged in different ways for different formations of protein. different mature mRNA = different protein analogy: cookie recipie and list of ingredients. certain ingredients you must have to even be a cookie and others are optional. some exons are necessary and others are optional. alternatively splicing: use different exons to make different proteins especially useful for making different versions of proteins for different types of cells (muscle vs. tissue) explains how the 30,000 genes are able to create the 120,000 different mRNAs in human cells

cAMP receptor protein (CRP or CAP)

facilitates positive gene regulation by greatly increasing RNA polymerase's ability to recognize the lac promoter region and increasing expression of lac but it needs help from cyclic AMP

phosphotase: what does it remove and from where?

family of enzymes that removes phosphate groups. removes the phosphate group from the 5' end of the RNA strand

ABPs

family of proteins that binds to available G actin and hide it making it unavailable for polymerization at the moment hide and reveal G actin based on if you want F actin to be longer or shorter can bind to either type of actin (G or F)

Which end is polymerization faster?

faster at the barbed end (+) than pointed (-) end

G1

first gap phase of interphase. right after mitosis. cell growing and building up nutrient base also checking for mistakes in DNA replication.

How does base substitution become permanent?

first generation: replication error second generation: mutated molecule because parent is always right: adds complementary base, doesn't go back and correct error.

Attachment

first step attaches to specific type of host cell Specific interaction of receptor on host (usually a glycoprotein with its own natural function) and capsid protein (or glycoprotein of enveloped virus)

flipase

flips half of the phospholipds from one leaflet to the other to balance out the number in each leaflet.

T4 (virulent) DNA virus

follows a lytic pathway, resulting in production of new viral particles and release through the bursting of cell has early gene expression period

Temperate DNA virus

follows either a lytic pathway or lysogenic pathway makes molecule decision for which path to take

what do promoters do in transcription?

form a recognition and binding site for RNA polymerase and the actual start site

Fluorescence In Situ Hybridization (FISH)

gives us a chance to visualize mitotic chromosomes using fluorescence. 1.isolate the cells 2. immobilize them on glass slide 3. crack them open 4. remove all non DNA 5. denature DNA (strands are next to each other but not holding on via complementary base pairs)

once protein has left ER what is the next step along secretory pathway?

golgi apparatus

what do chaperone proteins do?

grab on to the protein as soon as it emerges from a ribosome to keep it from folding. Because we're going to have to put it into the mitochondrion in an unfolded state, so let's just keep it unfolded until we get it there.

Mts that leave centrosome and head towards middle of the cell: 2 categories: kinetochore Microtubules and polar microtubules

head towards middle of cell: 2 sub categories ones that do contact kinetochore of MT: kinetochore Mts ones that do no not make contact with kinetochore: (could miss chromosome entirely or contact in a different spot): polar microtubules: extending from one pole of cell to the next

Transcription Factors: who do they "set the table" for?

help with the process of transcription in eukaryotes because eukaryotes do not have sigma factor and therefore only weakly bind to DNA. "set the table" for an RNA polymerase: efficient transcription doesn't happen without them. begin formation of transcription invitation complex and allows RNA polymerase to bind to promoter sequence

What does it mean for an amino acid to be "hot" and "cold"?

hot: it's radioactive. usually with S35 and therefore detectable. labeled version of amino acid cold: not labeled version of amino acid

nuclear pore complex

how large molecules move in and out

gene density

how many genes there are in given unit length of DNA. more genes/unit length of DNA: more dense more gene dense= more likely to be called on by the cell to do transcription of one of those genes, or more than one of those genes. The lower the gene density, the more likely it is for that region DNA to, at that moment in time, exist as heterochromatin, packed up, moved to the periphery.

Bernhard Dobberstein and Günter Blobel

hypothesized that there is a specific amino acid sequence that targets proteins to the ER: referred to as the Signal Hypothesis

Carl Rabl

in 1885 proposed each chromosome probably occupies its own space in the nucleus

Dan Kalderon

in 1984 he discovered the Nuclear Localization Signal (NLS) in the simian virus 40 (SV40) T-antigen found that there's a specific sequence of amino acids that presents a sequence: there are a lot of positively charged (basic) amino acids

How much DNA is in an Mphase or G2 cell?

in both G2 and M, you have a 4n amount of DNA. DNA replication has completed, but cytokinesis has not finished yet, so at some point, that cell is going to divide into two cells and each one of them will be back in G1 with a 2n amount of DNA, but until that instant, it is still either a G2 cell or an m-phase cell, and in this experiment, where the only question you're asking is "How much DNA is in that cell?" G2 cells are indistinguishable from m-phase cells.

Why can transcription and translation occur simaltaneously in prokaryotes but not eukaryotes?

in prokaryotes, the transcription and translation occur in the cytoplasm whereas in eukaryotes, transcription occurs in the nucleus and translation occurs in the cytoplasm

Which one of the following statements about the nucleus is incorrect? The nuclear envelope is porous to small molecules. On the nuclear side of the nuclear envelope there is a network of intermediate filaments attached to the membrane. A nuclear pore complex is a large structure consisting of many polypeptides. The outer membrane of the nuclear envelope is continuous with the RER membrane. The inner membrane of the nuclear envelope is decorated with ribosomes.

incorrect: The inner membrane of the nuclear envelope is decorated with ribosomes correct: the OUTER membrane of the nuclear envelope is decorated with ribosomes

How is a multi-pass transmembrane protein formed?

initiates in same way as single-pass transmembrane proteins depending on where the signal peptide is. if you don't present an additional signal you will continue the status quo...so you must trap the C terminus or N terminus in the membrane by closing the translocon before translation is over by using a stop-transfer sequence

Golgi Stack

interior of Golgi. made of a series of flattened stacks. each stack is separate entity. no way to get from one layer to the next directly. but you can fuse off the side of one and fuse to the next

higher concentration of positive protons in which part of mitochondria?

intermembrane space

introns

intervening sequence: within the genes that does not code for proteins, rRNA, or tRNA vary widely in length

why is it advantageous for the virus to have plasma membrane from the host cell?

it acts as partial camoflouge in order to fuse into other animal cells only partial because it needs some viral proteins on envelope in order to attach to surface of next host cell

What happens to the DNA in M phase?

it gets packed into mitotic chromosomes very tightly and therefore cannot be available for replication or transcription so nucleolus isn't there nucleolus is there every other time.

how does phosphorylation change how each cell interacts with one another?

it'll spread them out more because adding a bulky phosphate group onto it lamina: makes lamina come apart and be broken down into dimers pore complex: change proteins affinity for polypeptides around it membrane of nuclear envelope: fragments into little vesicles: nuclear membrane vesicles don't break up individual pieces, just them and their neighbors so all we have to do to put them back together is de-phosphorylation

How does termination compare between prokaryotes and eukaryotes?

it's essentially the same

Why does the nucleolus appear dark even though there's a lot of DNA there?

it's so busy, there's so much going on and so much material around the DNA to keep the stain from getting to it that it just doesn't stain

by default, is the lac operon gene on or off?

its off lactose is an inducer don't want to make it unless we have to/ its helpful for us to system IS a little bit leaky so there will be a little bit of lac mRNA produced

Proteins fully translated on cytosolic ribosomes (in the cytoplasm) that aren't attached to membranes go to...

just stay in the nucleus (no additional signal) the nucleus, mitochondria chloroplasts peroxisomes

template strand:antisense strand :: coding strand:sense strand

just understand this

tandem repeats

like typing your name over and over but its a copy of an rRNA gene being repeated. this is a small section of the whole chromosomes horizontal line represents the DNA decorations on the branches represents genes being transcribed which means there are RNA polymerase I. branches are getting longer towards right hand side of the gene because thats closer to the terminator

lots of glucose --> low cyclic AMP --> CAP doesn't have helper --> minimum RNA lactose mRNA production

low glucose --> high cyclic AMP --> CAP has helper --> maximum RNA lactose mRNA production

what is the one chemical environment in the cell suitable for disulfide linkages?

lumen of the RER. any protein that has disulfide linkages in it had the disulfide linkages formed in the RER

Requirements for initiation of translation

mRNA Small ribosomal subunit First charged tRNA (always charged with Met*) Accessory proteins called Initiation Factors Energy in form of GTP (equivalent in E to ATP)

translation initiation requires: 4 things

mRNA Small ribosomal subunit (30S in bacteria, 40S in eukaryotes) First charged tRNA (fMet-tRNAfMet in bacteria, Met-tRNAMet in eukaryotes) *Superscript indicates what Amino acid it SHOULD carry. sometimes mistakes are made GTP and various Initiation Factors (number and names differ from bacteria to eukaryotes, but general function is similar)

translation

mRNA ---> protein changing "language" nucleic acid ---> amino acid

mRNA

messenger RNA: not functional by themselves, but carry instructions for making specific proteins. mature mRNA is fed to a ribosome which allows specific protein to be built

dynein

microtbuule motor protein that moves organelles and vesicles toward minus end. works same way as myosin

What is the building block for cilia and flagella?

microtubules. they're extensions of the plasma membrane

M line

middle of the sarcoma where the tail fibers of all the myosin are anchored

Which organelle was believed to have originated by endosymbiosis?

mitochondria

What happens during M phase? (6 main steps)

mitosis=nuclear division cytokinesis=cytoplamsic division 1. Chromosomes condense: limits the risk of breaking them 2. Cytoskeleton reorganizes to form mitotic spindle: 3. Nuclear envelope disappears 4. Chromosomes moved to opposite poles 5. Reformation of nuclear envelope 6. Cytokinesis

How can you tell which phase a cell is in?

mitotic cells are easy to distinguish from others because no nucleolus G1-S-G2 cells must be distinguished biochemically S-phase cells incorporate radioactive thymidine

mitotic spindle pole: how many? what do they grab onto? what do they compare to in interphase?

mitotic version of microtubules in interphase 2 of them grab onto sister chromatids and facilitate their seperation

Why would a virus change the specificity of the host RNA and how does it do it?

modifies sigma factor, modifies specificity of host RNA molecule sigma factor no longer can recognize -10 and -35 sites and theres only handful of promoters capable of being recognized and they're on the viral genome so cell cannot transcribe its own genes only late gene promoters on viral genome can be recognized

Microtubule and actin filaments is road material is moved along, what is doing the moving?

motor proteins myosin work with actin filaments microtubules have 2 types that work with them dynein: uses energy in form of ATP to get closer to - end of microtubules kinesin: move toward plus end move similarly to how myosin moves down actin filament

cell crawling

movement of cell along its substratum (whatever its resting on at the time) 1. push out leading edge of cell by polymerizing actin network (has properties similar to a balloon, must be held in place) 2. attach extended leading edge to substratum so it doesn't snap right back 3. move cell body by having myosin grabbing actin filaments and contracting forward: detach from back and it snaps back in

Anaphase A: what proteins are needed?

movement of sister chromatids away from each other due to motor proteins in kinetochore: get separated move in one direction only: need motor protein that can "walk" along microtubule toward minus end: dyneins

What type of movement does the cytoskeleton allow? What are some examples?

movement of the cell itself and movement of material within an individual cell Macrophages need to be able to engulf material Mitochondria are transported to areas that need ATP Chromosomes must be separated during mitosis

How do we transport material from ER to Golgi?

moving it in little transport vesicles that bud off surface of ER and then they make their way across cell's cytoskeleton to golgi apparatus

polysome formation

multiple ribosomes working on an mRNA molecule simultaneously . allows us to make multiple identical proteins from one RNA: helps with amplification

whats the difference between a muscle cell and a muscle fiber?

muscle fiber: arises from precursor muscle cells, multi nucleated. a bundle of muscle fibers make up a muscle muscle cell --> muscle fiber --> muscle

RNA splicing (intron removal)

must be completed before the mRNA is exported out into the cytoplasm because when the mRNA molecule is exported into the cytoplasm and recognized by a ribosome for translation, ribosomes don't know introns from exons either. So you must get your introns out and bring your exons together before you introduce this molecule to a ribosome or you will be translating a protein product that you did not want to translate. (post transcriptionally) cannot be done by RNA polymerase can happen concurrently with transcription but not during

How do inaccurate splicings lead to defective proteins?

mutations in DNA carried is over to RNA and intron/exon junctions are not recognized by the snRNP that is looking for very specific codes...so the intron isn't removed in nRNP makes on cut and can't find another place to cut, it'll guess and its usually wrong and cuts into necessary exon sequence.

myofibrils: repeating units of____.

myo = muscle small fibers of repeating units of actin and myosin that make up most of the interior of a muscle cell contains repeating units of contraction: some are darker, some are lighter: these are sarcomeres

What does it mean for an amino acid sequence to be necessary and sufficient to allow for a T-antigen to enter the nucleus?

necessary: this sequence is required. A protein that doesn't have a nuclear localization signal isn't going to be allowed into the nucleus. we can remove the amino acids that serve as the NLS and all of a sudden this protein which magically got transported to the nucleus before no longer gets transported to the nucleus and will stay out in the cytoplasm. sufficient: ou can take a cytosolic protein like a glycolysis enzyme, and if you splice on this nuclear localization signal that protein which normally stayed in the cytoplasm its entire life now immediately gets localized to the nucleus (this is all you have to have)

RELATIVE to the inner membrane space, the matrix of the mitochondria is ____ charged

negatively (acidic)

7. release

new virus particles leave from host cell Most phage burst (lyse) cell when released (enzyme made by virus lyses cell wall): pretty much cut their way through cell wall that kills the cell Most animal viruses released by budding: takes small piece of plasma membrane with it and uses it as its own. one virion won't kill the cell but many virions will make the cell burst some cells only release a few at a time on purpose (HIV does this) so it doesn't kill the cell and can keep using it to replicate

are tRNA molecules moving?

no. the "house" (ribosome) moves around them. they find themselves sitting in a different room than they were sitting a moment ago

Let's trace the fate of those ribosomal proteins. Where did they come from? Were they made in the nucleolus?

no; they're proteins. They were synthesized by an existing ribosome out in the cytoplasm. That ribosomal protein was coded for on a messenger RNA gene somewhere else in the nucleus, it depends on what chromosome that gene is on, it got transcribed by RNA polymerase 2, it got capped and tailed and possibly spliced, the mature messenger RNA then got exported through a nuclear pore complex out into the cytoplasm where it got translated into a ribosomal protein, and now that ribosomal protein is going to find its way into the nucleus and incorporate into a new ribosomal particle.

Multi cellular organism somatic mutation: what type of cell is a somatic cell? Which cells are the mutations passed to? how will this affect survivability of species? example of this?

non sex cell: passed to daughter cells in the area. won't affect survivability of the species but can highly affect individual ex: individual exposed to too much ultraviolet light and they get a tumor but you don't pass on cells in skin to your offspring.

whats another name for the strand that isn't the template strand?

non-template strand, coding strand

The anticodon of a tRNA is given as: 5' CUA 3' Which one of the following amino acids should be attached to the 3' end of this tRNA? Val Asp His Met None of the above.

none of the above.

GTP cap

not a physical structure but just describes the state of the nucleotide in the outer layer of tubulin on the end of the microtubule (GTP or GDP) if outer layer has GTP in its binding sites then you have GTP cap if outer layer has had chance to hydrolyze GTP into GDP, you'll have lost your GTP cap

stationary phase

not dividing but not dying either: shifting their metabolism: run out of glucose (preferred food source) so not must use the lactose thats available which means turning the lac operon up

how does the number of nucleotides in an organism compare with the number of genes, or does it? In other words, does more DNA mean that you can make more proteins and therefore be a more complex organism?

not entirely. human genome "only" has 22,000 genes, which is not even twice what nemotodes and fruit flies have. he reason for having introns in the first place is that it gives us the possibility to use those exons in different combinations.

axoneme: structure, what it does

not the same as an axon microtubules here are found in 9 + 2 pattern: 9 pairs around a circle and a central pair of microtubules in the middle functional unit of movement in cilium or flagellum

Difference between interphase microtubule array and mitotic spindle poles?

nothing different in the microtubules specifically some microtubules in mitosis, though, have different designations depending on where they are and which direction they point (astral Mts,

Structurally, what is the nucleus? (3 things)

nuclear envelope: double lipid bilayer nuclear lamina: lamina proteins on inner membrane nuclear pore all 3 of these must be phosphorylated by kinases

nucleoplasm

nucleus equivalent to cytoplasm

S phase

occurs during interphase. synthesis of DNA occurs here. just because you're doing S phase doesn't mean that you stop anything going on in G1 (transcription, translation, glycolysis). you just add DNA replication onto your plate lasts hours.

6. assembly

of new virus particles from replicated genomes and newly synthesized capsid proteins

codon

one codon= 3 bases and codes for a specific amino acid 61 of the 64 codons specify an amino acid other 3 are stop codons

Metaphase

only lasts as long as it takes to get there nothing new going on except breaking down proteins acting as molecule glue holding together sister chromatids: cohesions

lac promoter regions

operator: short sequence of DNA specifically at or near the promoter region for the lac operon: binding site for repressor protein

integrase: how does it do its job?

patches viral DNA into host cell's genome posses its own NLS so when it holds onto the viral DNA, it binds to importin and brings the viral DNA that is now in the nucleus integrase targets a spot and integrates the genome into the host cell: the DNA can sit there for years and not be expressed: only when its called on for transcription

Enzyme that takes Ceramide and turns it into sphingomyelin?

phosphorylate ceramide, add a colein group to the phosphate group, and now you have a phospholipid that isn't based on glycerol as its 3-carbon backbone, but it still has two fatty acid tails and a phosphate group with some other chemical group attached to it. It is a major membrane phospholipid, just not a glycerol-based phospholipid.

what does the breakdown of the nucleus basically boil down to?

phosphorylation and dephosphorylation

Which way do plus and minus ends of a microtubule point?

plus ends face out away from the centromere towards periphery of cell minus ends are anchored in the centrosome

3' cap: name of enzyme that catalyzes this?

polyA tail near the end of the strand there's a conserved sequence. Once that sequence has been transcribed, peeled away from the DNA template, and recognized by the molecules in the cell, it is recognized as a landmark for a nuclease, which is going to cut the mRNA molecule. But it doesn't cut within that sequence. It's a landmark that says recognize here. Recognize the sequence, then reach over, usually about 10 to 30 bases, and then make the cut. then polyA polymerase is recruited in. adds only adenines. creates long polyA tail

nucleation

process of creating actin filament from G actin monomers. has nothing to do with the nucleus. G actin monomers will randomly bump into each other until they form a dimer (2) and then eventually a trimer (3). a trimer is called a nucleus of actin because you've nucleated G actin easier to add on to barbed end but you can add to either end.

What Svedberg unit is assigned to prokaryotic and eukaryotic ribosomes and their subunits

prokaryotic: 70s (50s and 30s subunits) eukaryotic: 80s (60s and 40s subunits) 60 and 40 don't equal 100 in this case because the whole is smaller than the sum of the parts. An 80S ribosome takes up less space than a 60S large subunit and a 40S small subunit.

name some examples of conserved regions

promoter regions, shine delgarno sequences, histones, binding sites

chaperonin

protein folding complexes made up of chaperones. ATP dependent step because chaperones are peeled off the protein when going in. (3rd energy dependent step) door closes on protein and allows it to fold however it needs to. once door opens and protein is pulled out, which is energy dependent. (4th energy dependent step)

cohesion proteins

proteins that hold together sister chromatids, dissasembled during metaphase

nuclear lamina

provides point of attachment for heterochromatin and gives the nucleus its shape just inside the inner membrane made up of rope-like protein fibers called lain proteins 8 repeating units in circle with channel that goes through the middle

How many rRNA and tRNA does mitochondria have?

rRNA: 2: 12S and 16S: 16S the only piece of rRNA in a mitochondrial large subunit. tRNA: 22

Lysosomal storage disorders

range of diseases all caused by loss of SINGLE tool in the tool kit (one acid hydrolase): every loss has disorder associated with most affect neurological function ex: Gaucher's disease, Tay-Sachs disease

Exportins

recognize NES. nuclear pore complex can recognize exporting binds to things and is allowed across membrane by nuclear pore complex

Peptidyl transferase's job

recognizes that a charged tRNA molecule has been allowed to stay in the A site. Then it knows that what it's supposed to do is cut the amino acid off of the tRNA in the P site and move that protein over and link it covalently to the free amino acid that is on the tRNA in the A site gets tricked when there's a release factor in A site: recognizes charged tRNA molecule (even tho its actually not) so it breaks bond between amino acid and tRNA and moves protein over and attach to free amino acid on tRNA but its not actually charged tRNA so it has to let go and polypeptide is released

What are some of the types of proteins in a kinetochore? (3)

regulatory proteins, motor proteins, structural proteins

de-phosphorylation

remove phosphate groups using phosphotase during telophase everyone regains affinity they had before prophase coat each one of your chromosomes on every free available space then vesicles run into each other and fuse together

mitochondrial processing peptidase (MPP)

removes the protein that just came through TIM once the n-terminus emerges into the matrix MPP's job is to chop off just the presequence and leave the rest of the protein, and MPP will act as soon as it recognizes it' substrate.

translocation

requires help and energy. we use that released energy and the help of the elongation factor to move the ribosome three bases closer to the three-prime end of the mRNA, and in the process the uncharged molecule that a moment ago was in the P site now finds itself in the E site and, as mentioned on a previous page, will start to be peel away from the mRNA molecule and then gets kicked out of that E site. So we've now removed the uncharged tRNA, ejecting it out of the exit site, and now the E site will once again be open

What were the first drugs to prevent HIV? Why was HIV able to adapt so quickly?

reverse transcriptase drugs, worked until the virus changed the shape of its reverse transcriptase HIV can change so often because it doesn't proofread: it makes mistakes much more often too could also use protease inhibitor if you give anti virals in combos (cocktail) its far less likely to adapt

Rate of translation regulation

ribosome has already gotten started but slow things down so don't make as many protein molecules use non preferred codons: not all codons are created equal because of degeneracy of genetic code: codon usage bias so cell uses non standard codon and has to wait a moment until one of those tRNA molecules is available making translation slower

Which one of the following statements about ribosomes is correct? The RNA component of a ribosome serves only a structural role, not a functional role. The number of subunits in a ribosome varies between bacteria and eukaryotes. Ribosomes consist exclusively of protein molecules of varying sizes and shapes. Ribosomes consist of two subunits. Ribosomes consist of complexes of DNA, RNA and protein.

ribosomes consist of 2 subunits.

cycle of movement of myosin along actin filament

rigor conformation: where rigor mortis comes from. muscles get locked in place because body has stopped generating ATP to make the myosin let go of the actin. need to bind ATP to make myosin head let go of actin filament ATP binds to binding site ATP is hydrolyzed into ADP and phosphate on binding site so now head group is lined up straight to a different monomer in the filament ADP has attraction to filament group and ejects the phosphate group ejection of phosphate group triggers power stroke making head group return to previous conformation Upon the completion of the power stroke, the ADP is ejected out, basically as the power stroke is occurring the ADP is lost and you're right back where you started from. You're in the rigor confirmation, there's nothing occupying the nucleotide binding site

sarcomere

sarco = muscle functional unit of contraction in a myofibril. lots of sarcomeres in a myofibril span the distance from one z disk to next z disk as muscle contracts, sarcomere also contracts and myosin and actin will interact

order of organization that makes up a muscle starting with sarcomere and ending with a muscle

sarcomere --> myofibril --> cytoplasm of muscle fiber --> muscle bundle --> muscle

Limitations of Transcriptional/Translational control

save most energy when you start regulating as far back as possible but is slower to take affect: doing regulation at level of transcription or translation initiation is better for long-term changes

G2

second gap phase of interphase. making sure you fixed any problems with DNA and you're ready to go through next round of M phase.

Anaphase (A and B)

separate sister chromatids to opposite sides of the cell and push spindle poles away from each other expanding the cell so you don't risk putting two copies of chromosome in one daughter cell A. pull sister chromatids apart and pull to different sides of the cell B. pull spindle poles apart from one another A and B do not indicate time periods, they happen concurrently

what are conserved regions of nucleotides (or amino acids) and what are their consensus regions?

sequence of nucleotides or amino acids that you find the same thing when looking at different places. consensus regions are favored bases or amino acids in every conserved region

If formation of a microtubule is dependent on random interaction between tubulin how do we make a productive interaction? (make them stick to end of microtubule and what would make them want to leave)

similar to what made G actin want to be part of and leave filament. All about nucleotide thats in the binding site. Depends on Beta binding site because only one accessible and can hydrolyze from GTP to GDP GTP bound tubulin has affinity for other GTP bound tubulin so it'll be quickly added onto end. favor polymerization if concentration of GTP bound tubulin is high: before it has a chance to hydrolyze its GTP, the next layer of GTP-bound tubulin has already been added Favor depolymerization if concentration of GTP bound tubulin is low

co-transcriptional translation

simultaneous transcription and translation happens in prokaryotes because transcription and translation both take place in cytoplasm and nothing's stopping translation from getting started

Microtubule associated proteins (MAP): 2 jobs

some occupy end of microtubule to keep from de/polymerization can cut microtubule from its trunk releasing it from the centrosome and allowing it to be transported to another point in the cell

What would be the effect of an in-frame deletion of 3 bases? what is this mutation categorized as?

the loss of an amino acid. the rest of the protein is unaffected. this isn't really a frame shift because it didn't change the reading frame. still can have large affect on amino acid, though very specific event that is thrown into this category because no where else to put it

What if an enzyme that's supposed to be working in a layer of the Golgi stack closer to the cis side accidentally gets packaged in to a transport vesicle and sent in to the next layer close to the trans face?

the molecules in the next layer will recognize the enzyme don't belong there and it will be repackaged and sent right back.

16s rRNA

the one piece of rRNA that is a component of a 30S bacterial subunit. The small ribosomal subunit in bacteria, the 30S subunit, has one piece of rRNA and a bunch of proteins in it. That one piece of rRNA was the 16S molecule, and it has at its three-prime end a stretch of unpaired bases basically just looking for something to hybridize to. So when a 30S ribosomal subunit is scanning an RNA molecule, and in this case let's say it finds an mRNA molecule, what it's looking for is a sequence of bases complementary and antiparallel to the three-prime tail, if you will, of that 16S rRNA. That sequence in the mRNA that is complementary and antiparallel to the three-prime tail of that rRNA molecule is called either a ribosome binding site or a Shine-Dalgarno sequence.

initiator tRNA

the only tRNA in the process of translating a protein by this ribosome that will never occupy the A site. It gets hybridized to the mRNA before there even was an A site, and by the time the large ribosomal subunit has been loaded on, it simply occupies the P site. It never had to come into the A site and then get moved into the P site; it was there before there was an A site. Every other tRNA molecule will have to come into the A site and then eventually make its way into the P and the E sites

Why would acid hydrolyses be inactive if they were floating around in the cytoplasm? Why is this a good thing?

the pH of the cytoplasm is neutral and acid hydrolases are only active in pH environments of around 5 (acidic). If they were active in the cytoplasm, you'd start to degrade components of the cell. So even if they did escape the lysosome, they would not do any damage.

why does plant cell Golgi tend to be darker under EM transmissions than animal cell Golgi?

the plant cell is preparing molecules to be made into a cell wall. make modified cellulose molecules (NOT cellulose) ~80% of plant cell Golgi is dedicated to making these polysaccharides.

what is a 45s molecule?

the primary transcript. gets processed, not spliced, by the snoRNPs into the small pieces, the 18S, the 5.8S, the 28S we call them pre-ribosomal particles, and as they're making their way through the nucleolus out through the rest of the nucleus and out a nuclear pore complex, that's what makes the granular zone look like little grains.

E site

the reason why this is called the exit site is that as soon as a tRNA finds itself hybridized to the mRNA and occupying the E site, it's already beginning to be peeled away from the mRNA. And it will be discharged out of the ribosome.

describe elongation in terms of the sigma factor

the sigma factor becomes displaced and only the core enzyme moves along

What does the roman numeral in a Transcription Factor's name stand for?

the type of RNA polymerase it'll help

how many classes of myosin are there and which end of actin filaments do they generally move to?

there are 18 classes. all but one of them move toward the barbed (plus) end of actin filaments

What keeps the actin filament from sliding back after the myosin moves it along?

there are many other myosin molecules holding it in place

Nuclear Export Signal (NES)

there is also a necessary and sufficient signal to allow something out into the cytoplasm largely Leucines recognized by exportins

What happens if if the cell is not actively transcribing these rRNA genes?

there won't be a nucleolus Transcription of the rRNA genes is very active and very efficiently initiated when needed:

If we need given F actin to be longer/shorter, how do we polymerize/depolymerize it at a moments notice?

theres an equilibrium, certain amount of G actin at which there is no net growth. Can be tipped by changing amount of available G actin add more G actin: favor polymerization remove G actin: favor depolymerization

What do the modifications in the 11-mer act like in comparison to a real life working post office?

these eventual modifications, in the form of adjusting your carbohydrates, act like zip codes for the Golgi to determine where you're supposed to go

What do all protein coding genes in the human mitochondrial genome have in common?

they all have something to do with ETC or oxidative phosphorylation BUT you cannot say that you could build an entire electron transport chain with just what you have in the mitochondria

Why do each of the 4 nucleotides we use for transcription have the same amount of energy in them and what are they?

they are GTP, ATP, CTP, and UTP the energy comes in the triphosphate group so they all have the same amount.

Are ssnRPS randomly scattered or clustered in the nucleus?

they are clustered but can be pushed into inter chromosomal domains because machinery is located there

What property of the ER and Golgi membranes make it possible to transport material?

they are made of the same material so fusing the vesicle in is easy.

what if the 2 tail ends of a pair of myosin are attached? what is this process called? what is it powered by?

they don't move because their movement cancels out as they move closer to the barbed ends of their filaments but they can't move so the actin moves in this case called filament sliding powered by ATP hydrolysis

What if 2 kinesins are connected and pulling with equal and opposite force?

they won't move because equal and opposite so microtubule will move instead of kinesin walking to plus end of microtubule

Why don't microvilli get longer and shorter due to actin changing length because of concentrations of ATP bound G actin?

they would if they weren't occupied. if cell wants a given cytoskeleton element to not change then you just occupy the end. If you don't allow G actin to go on or off the end, it doesn't matter what concentration you're at plus ends are all anchored into actin-binding proteins minus ends are anchored into terminal web, which is an actin network

How do bacterial and eukaryotic ribosomes compare?

they're functionally identical but structurally different in bacteria and eukaryotes

what makes a muscle fiber different from other cells?: what they're made of, shape, where organelles are located, number of nuclei

they're long and cylindrical they have more than one nucleus and other organelles get pushed to the outside made up of mostly actin and myosin

Which position in the nucleotide is usually changed in same sense mutations?

third position

Why is the most common type of virus the linear double stranded-DNA virus?

this is the type that affects bacteria and bacteria are found everywhere in huge numbers

Why do we take apart the nucleus?

to gain access to those mitotic chromosomes for those kinetochore microtubules that are going to be grabbing on to the kinetochores and pulling them apart during anaphase.

DNA polymerase III's job in repairing a mismatch

to pick up at the cleavage site. And remember, the cleavage site, because it's the point of a nuclease activity, would be presenting a free 3' hydroxyl, so you don't need to prime this, you just bring DNA polymerase in, it adds in those bases, and presumably won't make the same mistake again. Even if it did, it's probably going to correct it via proofreading.

only reason you'd make a GPI anchored protein?

to present it to the outside world. so it'll go through secretory membrane through plasma membrane to exposed to the outside world

Trans-Golgi

trans = across: across from ER

The other 95% of those mitochondrial proteins have genes that have been moved to the nucleus. So where are those 95% transcribed? Where are they translated? And if not in the mitochondria, how do they get to the mitochondria?

transcribed in the nucleus. translated in the cytoplasm

tRNA

transfer RNA: small, carry amino acids to ribosomes where the amino acids get added to the growing protein chain

TIM

translocon of the inner membrane. unfolded proteins can be directed into to get into the mitochondria. one way street into the mitochondrian. can close all the way diffuses through TIM due to electron gradient

TOM

translocon of the outermsmbrane. molecule that recognizes the signal a protein puts out to get into a mitochondria. one way street into the mitochondrain. can close all the way takes ATP to bring protein in and peel chaperone off

Identify if the following statement is True or False. Once DNA is fully methylated, the mismatch repair enzymes have no way of distinguishing between the parent and daughter strands.

true

True or False... each sister chromatid has its own kinetochore?

true kinetochores are collections of proteins with very tightly packed material in it

microtubules are hollow true or false?

true, but there are technically some proteins inside the microtubule for support

Telophase

undoing whatever you did during prophase relax chromosomes, break down mitotic spindle array, rebuild nuclear envelope

Why is polymerization and depolymerization fastest at plus end?

unless its been severed, its minus end is anchored into the centrosome

lacI: is it regulated?

upstream of the lac operon itself codes for Lac repressor protein so not actually part of the lac operon Lac repressor can bind to the operator of the lac operon: keeps RNA polymerase from transcribing the structural genes has its own promoter region: constitutively expressed

the promoter lies (upstream/downstream) of the RNA transcript? what is the first base in the promoter region called?

upstream. called -1

Regulation by Translation initiation

use 16s rRNA to form complimentary base pairs with SD sequence in mRNA to initiate translation 16s ribosomes bind to each Shine-Delgarno sequence at different levels because some are farther from consensus sequence: affects how much protein is made from that gene β-gal > permease > transacetylase (partly explains ratio) Also affected by availability of SD, which may be blocked by proteins or folded into 2° structure and unavailable when regions of mRNA are complimentary to each other and form stem loop structures

Autophagy

use existing lysosome to remove organelle within cell itself when its old (mitochondria) cell wraps organelle in membrane that was originally coming from the SER: SER makes a little extra membrane, forming autophagosome autophagy=eating yourself joins with lysosome to create phagolysosome

What happens when an organelle has outlived its nucleus or it needs to degrade bacteria its engulfed?

use lysosome to degrade macromolecules into monomers

How do you keep a lysosome "busy" to prevent it from degrading itself?

uses an extra shell of sugars and carbohydrates and keeps extra proteins in the membrane. If you keep the enzymes busy with busywork, then it's going to be a little longer until they get to the important molecules and rupture the lysosome itself.

How do mitochondria carry out their own translation?

using their ribosomes (2 rRNA and 22 tRNA) They will use a mitochondrial RNA polymerase to transcribe 1 of the 13 protein-coding genes and then those messenger RNAs will be translated by a mitochondrial ribosome. They're transcribed in the matrix; they're translated in the matrix. But only those 13 proteins

describe the process of an amino acid binding to tRNA. (endergonic? exergonic? how does it add?)

very specific and requires input of energy provided by hydrolysis of ATP into AMP and Pi Reaction catalyzed by enzymes called Aminoacyl tRNA Synthetases process is called charging

How do you go from having one lipid bilayer to two?

vesicles fuse and then flatten into outer and inner membrane of nuclear envelope each chromosome gets covered in double lipid bilayer membrane

4. replication

viral nucleic acid is replicated whatever you brought in is what yo need to make copies of

bacteriophage (phage for short)

viruses that affect bacteria viruses can affect all 3 domains but each one has a particular type it can affect. no one virus can infect all 3 domains (yet)

how are kinetochore microtubules used during pro metaphase?

want to line up pair of sister chromatids along metaphase plate in middle of cell moved back and forth by microtubules if we want to pull sister chromatids closer to the microtubule: depolymerize: making spindle pole shorter: dyneins if we want to push sister chromatids farther from microtubule: polymerize: making spindle pole longer: kinesins requires motor proteins

How do we prevent astral microtubules from puncturing the cell membrane while dynein moves it pulls to the cell membrane in anaphase B?

we depolymerize the plus end of astral microtubules that has already passed the dynein.

Why are viruses actually a blessing to the research community?

we have learned a lot about them we can relate to ourselves easy to cultivate and easy to study

When is the transmemberan protein's N terminus in the cytoplasm and C terminus in the lumen INTERNAL SIGNAL PEPTIDE

we must still have a signal to tell us to move to RER but the signal is NEAR the amino terminus signal sequence becomes internal in the membrane folded in with N terminus facing cytoplasm and C terminus facing lumen. but NOT cutting off internal signal sequence N terminus left out in the cytoplasm and ribosome dissociates making the translocon closes and squeezes out anything in it: which in this case is the internal signal peptidase

Nuclear basket structure

we think it aids in recognition of RNA molecules that need to be exported

what does it mean that the genetic code is universal?

what AUG (or any codon) specifies in bacteria, it also specifies in humans and archea

When does Lipid biosynthesis occur/for what reason?

when its time for membrane to get larger or replace lost lipids the smooth ER synthesizes new lipids using machinery located on the cytosolic surface

At what point can we officially call a molecule a lysosome?

when we have completely removed all of the MPR and gotten the pH to 5

A band

where you have myosin some includes overlapping actin filaments from one end of the myosins on one side of the M-line to the other end of the myosins on the other side of that M-line total width of they myosin never changes because length of myosin never changes

where are the 5s genes transcribed?

wherever chromosome 1's territory is. once you transcribe it by RNA polymerase III, then you have 5s molecules recruited into the nucleolus and then are incorporated into the 60s subunit and export them to make them subunits for translation

What do the peaks mean on a DNA fluorescence chart? Why isn't there a peak at S phase?

which phase of the cell cycle its in the probability that you're in a given phase of the cell cycle even though S phase accounts for 1/3 of the cell cycle, S phase replicates DNA so it has much less DNA in it: range instead of a peak

Centrioles: what is it within, what is it made up of and what is the organization of these subunits?

within centrosome A pair of structures made of microtubules in a "nine triplet" arrangement each tube is a microtubule: 27 different ones in each microtubules held together by stabilizing proteins

cyclic AMP: inversely/directly related to glucose?

works with cAMP receptor protein (CAP or CRP) to positively regulate the lac promoter levels of cyclic AMP are inversely proportional to the levels of glucose modified AMP molecule

Is it possible to display both a NLS and NES?

yes,

Is it possible for a molecule without its OWN NLS can get through nuclear pore complex?

yes, if a protein is in the nucleus but we can't find a nuclear localization signal, it paired up with some other protein and that other protein had the NLS

is it possible for a vescicle heading in towards the cell to be on the same microtubule as a vesicle heading out of the cell?

yes, they could be on crash course but cell doesn't want this to happen. the cell can sense they're about to run into each other and they'll move onto opposite sides of the microtubule. no one knows how this works

Can you create a NLS?

yes, when a protein folds. amino acids at c and n terminus alone won't function as NLS but if final 3D conformation

how does protein folding make it difficult to find an NLS?

you don't know whether some amino acids at one point in the protein are going to find other amino acids in a different part of that protein when the protein folds in three-dimensional space.

what if you were an E. Coli cell that has food source but no lactose?

you would not want to be expressing the lac operon because it costs a lot of energy but wouldn't help you you'd want to be keeping the lac operon turned off by using lac repressor to block RNA polymerase from promoter: negative regulation

What is the approximate rate of amino acid formation (translation) in bacteria?

~20 amino acids/second 120 ATP/second

Cis- Golgi

"front door" of Golgi. accepts vesicles cis=same: same side of Golgi as where ER is so also nucleus certain enzymes recognize their substrate, do their work and then send the product on to be the substrate of the next enzyme, which lies in the next layer of the interior of the Golgi called the Golgi stack.

what is the first base in RNA transcript called?

+1 base

describe the process and purpose of N-linked glycosylation.

1. A lipid called dolichol is made, and it is in the membrane of the ER. 2. A 14mer oligosaccharide tree is built one monomer at a time onto a molecule of dolichol. 3. As the protein is being made by a membrane bound ribosome and it is coming through the translocon, there will be a particular stretch of three amino acids, one of them being an asparagine. 4. The 14mer is transferred from dolichol onto the asparagine. Eventually the 14mer is trimmed to an 11mer. This signifies that the protein if fully translated, folded and ready to move on. 5. The 11mer can be further modified; these modifications can act as a signal for where the protein needs to go (for example a phosphate group can be added to the 6th mannose in the golgi, to form mannose-6-phosphate group, which now says "take me to the lysosome").

Prophase (4 things)

1. Disassemble interphase MT array, form mitotic spindle 2. Centrosomes move to opposite poles 3. Chromatin condenses 4. Nuclear envelope dissociates

3 subregions within the nucleolus

1. Fibrillar region or center: collection of naked DNA (no chromatin) because need to be accessible as possible. lightest stain. rDNA is located here. the tandem repeats of the 45S DNA from different chromosome brought to a central location 2. Dense fibrillar region: transcription factors, ribosomal proteins, snoRNPs, all the machinery. shows up darkest stain. directly around fibrillar region. 3. Granular zone: subunits that are ready to send out into nucleus into the cytoplasm. looks like grains of sand. the area in between your columns of fibrillar centers and the dense fibrillar regions that surround them

3 basic shapes of viruses

1. Icosahedral (with or without a tail) looks like a 20 sided die 2. spherical 3. rod shaped

How do we determine how much DNA is in each cell in each phase of the cell cycle?

1. Label liquid culture of cells with fluorescent dye that binds DNA: more DNA=glows brighter 2. Pass cells through flow cytometer, which measures fluorescence: go through one at a time 3. Plot cell number vs. fluorescence intensity

A protein of undetermined molecular weight can be found in the nucleus, but in examining its primary sequence, you find no detectable nuclear localization signal. Provide at least two different explanations for its localization.

1. The protein is smaller than 20 kDa and can passively diffuse through the nuclear envelope 2. The protein binds to another protein that has an NLS. This second protein that has an NLS can then bind to importin. In this manner the protein can piggy-back its way into the nucleus.

Identify the three things that SRP binds to, and provide a reason why each is relevant.

1. The signal peptide: recognizes the signal that says "I need to be translated at the membrane of the RER." 2. The ribosome: Stops the ribosomes from translating the rest of the protein while it is still in the cytosol. 3. SRP receptor: This is the "dock" where the ribosome is now located at the RER. The binding of the SRP to the receptor (and another step that requires GTP) allows the SRP to release the ribosome and the signal peptide, so that it can be used again. This release additionally allows translation to begin again, this time feeding the protein into the translocon (which was opened when the ribosome bound to the translocon).

Arrange the steps in the movement of myosin on an actin filament from earliest to latest, beginning with the rigor conformation. The power stroke occurs and ADP is released. The myosin head group releases from the actin filament. ATP is hydrolyzed into ADP and Pi. ATP enters the nucleotide-binding site of the myosin head. Myosin binds to the actin filament and the Pi group leaves. The lever arm of the myosin head is cocked forward.

1: ATP enters the nucleotide-binding site of the myosin head. 2: The myosin head group releases from the actin filament. 3: ATP is hydrolyzed into ADP and Pi. 4: The lever arm of the myosin head is cocked forward. 5: Myosin binds to the actin filament and the Pi group leaves. 6: The power stroke occurs and ADP is released.

How many ori is each replication focus?

200-300. a replication focus is a cluster of ori

45s pre RNA arrays are found on which 5 chromosomes? how many copies?

25 copies of the 45S gene on each of those molecules, and we've got ten of those molecules, two each of 13, 14, 15, 21, and 22

which end is spliced first? 5' or 3'?

5'

whats the difference between Alpha and Beta tubulin and G actin nucleotide binding sites?

A and B tubulin bind GTP G actin binds ATP

Which one of the following statements about the cytoskeleton is correct? The width of a microtubule represents the approximate width of every cytoskeletal element. Cytoskeletal elements have a common diameter, but differ in type by their lengths. A cell can adjust the lengths of its cytoskeletal elements as needed. Intermediate filaments are wider than microtubules. The width of a cytoskeletal element is directly proportional to its length.

A cell can adjust the lengths of its cytoskeletal elements as needed.

If all proteins are translated in the nucleus, why are some proteins also "translated" on ribosomes on the surface of the endoplasmic reticulum?

A ribosomes in the cytoplasm translates mRNA but the protein, as its made, is threaded into the interior of the endoplasmic reticulum, also known as the lumen. The ribosome never enters the lumen but instead attached to the membrane

Which one of the following statements about translational initiation is correct? Bacteria require ATP for initiation, eukaryotes require GTP. A small ribosomal subunit (30S) recognizes a Shine-Dalgarno sequence in bacteria. The initiator codon is AUG in bacteria, ATG in eukaryotes and archaea. The 30S ribosomal subunit recognizes the 5' cap in eukaryotes. None of the above statements are correct.

A small ribosomal subunit (30S) recognizes a Shine-Dalgarno sequence in bacteria.

What are the general characteristics of an intrinsic terminator?

A stretch of bases near the end of the transcript that form an inverted repeat with a second stretch of complementary, antiparallel bases, separated by only as many bases as needed to do the hairpin turn. Then that stem-loop structure is followed by a short run of A-U base pairing between transcript and template.

Which of the following is true regarding the elongation stage of translation? A tRNA bound to a codon is moved from the E site to the A site of the ribosome. A tRNA bound to a codon occupies the A site of a ribosome first, and then the P site. Charged tRNAs must first enter the E site of the ribosome. Only tRNAs charged with fMet can enter the A site of the ribosome. A tRNA bound to a codon is moved from the P site to the A site of the ribosome.

A tRNA bound to a codon occupies the A site of a ribosome first, and then the P site.

lamin (3 types)

A, B, and C A and C are free floating: never integrated into nuclear envelop B is stuck onto nuclear envelope so when it dissociates it stays with the membrane: have tail that gets added onto them with lipid molecule: stays tethered to nuclear envelope

Enzyme that takes Ceramide and turns it into glycolipids

Adds one or more monosaccharides onto ceramide

If lysosomes eventually degrade themselves, then where do new lysosomes come from?

Arise from maturation of other organelles called endosomes.

Compare and contrast autophagy and phagocytosis.

Autophagy and phagocytosis both eventually fuse with a lysosome to create a phagolysosome that degrade the molecule they engulf. Autophagy, which means eating oneself, is the process used to degrade organelles within the cell that are no longer usuful, like old mitochondria, for example. Phagocytosis, on the other hand, is used to engulf invaders into the cell like bacteria and viruses. Both of these processes degrade the molecules and use their proteins and other macromolecules as recycled material.

subunits of CORE polymerase RNA

B and B' subunits: active site of enzyme a subunit: holds complex together and binds to regulatory molecules

Template driven nucleic acid synthesis must read the template 3' --> 5'. Why are ribosomes seemingly the exception to that?

Because ribosomes are making proteins, not nucleic acid.

Why is there sometimes chromatin pushed out into the interchromosmal domain?

Because the cell needs to work on that region of DNA and in the inter chromosomal territories is the machinery to do transcription and processing. This shows another example of how tis easier to bring DNA to machinery than have machinery scattered.

Describe the similarities and differences between spacer DNA and intron DNA.

Both are regions of DNA that do not code for anything (proteins, rRNA or tRNA). This is called noncoding DNA. Spacer DNA is noncoding DNA between genes. Introns are noncoding DNA within genes. Introns get transcribed and then removed post-transcriptionally. Most spacer DNA does not get transcribed.

types of nucleic acids found in viruses

Can be either DNA or RNA Can be either single- or double-stranded Can be either linear or circular Can be single copy or multiple copies Can be intact or segmented: in tact: all coding regions are on one piece of nucleic acid, segmented: found on different pieces of nucleic acid (this is similar to what humans have: different chromosomes) Most common type is linear double stranded-DNA virus

How is Elongation step 2 (peptide bond formation) catalyzed?

Catalyzed by enzymatic activity in large subunit called Peptidyl Transferase

flow of proteins in the Golgi?

Cis-Golgi --> Golgi Stack --> trans-Golgi

microtubules are so important in mitosis, drugs that affect microtubules can be effective against rapidly dividing cells (in culture) what are these drugs and how do they work?

Colchicine and colcemid are laboratory drugs that block microtubule assembly by binding tubulin: This in turn blocks mitosis: don't discriminate between cells so kill all SOO use related drugs.... Vincristine and vinblastine (FDA approved) selectively inhibit rapidly dividing cells: each has different kind of cancers they're used for: we don't know what makes them target rapidly dividing cells: this is why they get sick and lose their hair because some cells are supposed to be rapidly dividing (hair and stomach cells) Taxol is also a widely used cancer (breast, ovarian) drug, which stabilizes microtubules rather than block formation: won't allow depolymerization of microtubules

Which of the processes that are dependent on correct base pairing is MOST reliable and why?

DNA replication because it is the blueprint for everything else and RNA are temporary

Are humans diploid or haploid?

Diploid. 2n DNA: 23 different chromosomes and 2 copies of each n= number of different types of chromosomes are in the molecule #= number of copies

what is the elongation factor called that is found in bacteria?

EF-Tu: comes in as a group with GTP to A site

Bulk flow goes from _____ to _____ in the cell and within the Golgi?

ER to Golgi Apparatus maybe through ERGIC. within Golgi: from Cis to Stack to Trans

Which phases are skipped in early embryonic cells?

G1 and G2

probe molecule

If you know something about the sequence of the DNA that you have stuck on your slide, then you can prepare in a separate experiment what's called a probe molecule—a fluorescently labeled probe molecule, which is simply single-stranded nucleic acid. It doesn't even matter if it's DNA or RNA, single-stranded nucleic acid which has a dye attached to it. That dye doesn't interfere with its ability to form complementary base pairs, but it's detectable.

The SER plays roles in... (2 things)

Lipid bilayer synthesis Detoxification

Why do we alternate signal peptides and stop-transfer sequences?

Logically you can't open what's already open. You can't close what's already closed, so you would never follow a stop-transfer sequence with another stop-transfer sequence. That doesn't make any sense. You would never follow a signal peptide with another signal peptide.

Why are mistakes in Transcription or Translation not as critical?

Many copies of RNA are produced and RNAs are not heritable over multiple generations.

Regulated Gene Expression

Many genes are turned on and off as the needs of the cell change Adjust metabolism to achieve maximum growth in a given environment: keep it off when you don't need it and turn it on when you do

what does M phase consist of?

Mitosis and cytokinesis

DNA viruses: most common kind and the best studied?

Most common DNA viruses are ds-DNA viruses: infect bacteria Best studied are phage T4 (virulent) and lambda ( λ) (temperate)

Is there any way to tell what direction a vesicle is going if you're looking at a static photo?

No, because vesicles go both to and from ER to Golgi.

During the cell cycle, is one cell influenced by the cells near it?

No, each cell is in its own stage of the cell cycle

What would be the predicted result of a strain of bacteria which lacks splicing machinery? proteins will be synthesized since ribosomes cannot recognize introns vs. exons. The mRNAs will contain introns. Cells will be fine since ribosomes recognize introns and will not translate any non-coding RNA. Nothing will happen; proteins will be accurately translated from the mRNA. Less protein will be synthesized since alternative splicing will not occur.

Nothing will happen; proteins will be accurately translated from the mRNA.

What keeps a lysosome from degrading itself? (what is it made of?)

Nothing, a lysosome will eventually degrade itself. A lysosome is a membrane bound organelle made of protein, lipid, and sugars. It has tools that can degrade each of these.

Do both early and late endosomes contain MPR or only one or the other?

Only late endosomes contain MPR molecules.

5. late gene expression

Production of capsid proteins needed for assembly of viral particles, and enzymes needed for release of virus from host cell things that help you get out of the cell if you didn't have early phase, you don't have "late" phase but you DO STILL HAVE THIS PHASE. instead its called just viral gene expression that happens concurrently with replication

Ways in which prokaryotic gene expression is different than eukaryotic gene expression

Prokaryotic translation begins before transcription is finished. Prokaryotic mRNA can contain multiple genes. Prokaryotes contain operons.

Which one of the following statements comparing the targeting of a mitochondrial matrix protein to the targeting of a protein to the ER is correct? The same signal can be used to direct a protein to either compartment, as long as the appropriate receptor recognizes the signal. Proteins destined for either compartment are likely to retain their amino terminal targeting signals. Proteins destined for either compartment are inserted into their respective compartments in an unfolded state. Proteins translocated into either compartment have an equal chance of ultimately being localized to the outside of the cell. Proteins destined for either compartment are allowed to fold in the cytoplasm and then are unfolded prior to insertion into their respective compartments.

Proteins destined for either compartment are inserted into their respective compartments in an unfolded state.

Replicase: how is it made?

RNA-dependent RNA-synthesizing enzyme either packaged in capsid from previous round of infection and brought along with virus or its the very first thing thats made upon intro of nucleic acid into host cell

Which one of the following enzymes is an RNA virus most likely to use to directly replicate its genome? DNA polymerase I DNA polymerase III Replicase RNA polymerase II Primase

Replicase: RNA dependent, RNA synthesizing enzyme

ERGIC

Stands for: Endoplasmic Reticulum Golgi Intermediate Compartment nothing new is going on here, just a rest stop for vesicles

How does RNA know which one is the template strand?

Strands are complementary NOT identical so the information on each is different. Either can be used as the template strand for a gene but which is chosen depends on location and orientation of the promoter sequence

Basal body: where is it located? Structurally organized? which structures are anchored here?

Structurally similar to a centriole: has 9 triplet arrangements of microtubules basal body is at periphery of cell, centriole is found in centrisome. Basal body does act as origin point for microtubules in the doublets unlike centriole The minus ends of the MTs in cilia and flagella are anchored into this structure

What is the consensus sequence of the -10 region?

TATAAT: in the five prime to three prime direction

True or False... the negatively charged, positively charged, and polar amino acids are hydrophilic so they like being on the outside of an amino acid chain

TRUE

What is the consensus sequence of the -35 region?

TTGACA in the five prime to three prime direction.

hypothesis 1 was that all origins of replication fire off immediately when you go into S-phase and it just takes that long to get them all replicated. Hypothesis number 2 is that maybe some of your origins of replication get fired off early in S-phase and others don't initiate until later during S-phase. which is correct? how do we test this?

Test it using fluorescence with different color dye for early in S phase and late in S phase. has distribution similar to euchromatin vs. heterochromatin. Early DNA replication/High gene density: dispersed throughout nucleus Late DNA replication/Low gene density: clustered around outside and in pockets direct connection between when DNA replication is initiated and how tightly packed it is.

What two membranes is the RER membrane continuous with?

The Smooth ER and the outer membrane of nuclear envelope with one continuous internal space between each ER lumen of ER is continuous with space between outer and inner membrane of nucleus (perinuclear space)

Why is the information in DNA not simply translated directly into protein?

The cell can make multiple copies of RNA from the DNA. From each mRNA transcript, the cell will make multiple copies of protein. This is how the cell can make many copies of protein, thus amplifying the amount of protein made.

Nucleolar Organizing Regions, or NOR

The nucleolus forms around the arrays of the 5.8S, 18S, and 28S rRNA genes on chromosomes 13, 14, 15, 21, and 22

Which one of the following statements about the nucleus is correct? The aqueous environment inside the nucleus is referred to as the nuclear matrix. The perinuclear space is between the inner and outer membranes of the nuclear envelope. The nuclear lamina is typically located in the central region of the nucleus. The intermembrane space is between the inner and outer membranes of the nuclear envelope. The inner membrane of the nuclear envelope is continuous with the endoplasmic reticulum.

The perinuclear space is between the inner and outer membranes of the nuclear envelope.

Determine if each of the following is a possible outcome of a protein coding gene with a missense mutation (and only that missense mutation). If the outcome is a possibility, choose Yes. If the outcome is not a possibility, choose No. The protein is prematurely truncated. The protein is fully functional. The protein is completely inactive. The protein has partial function.

The protein is prematurely truncated. NO The protein is fully functional. YES The protein is completely inactive. YES The protein has partial function. YES

How does a protein get from the ER to the Golgi Appartus considering they're not connected physically? Why does it do it this way?

The protein is taken from the ER to the golgi and shielded along the way: less risky than simply letting the protein swim its way through the cytoplasm by itself

Which one of the following statements about microtubules is incorrect? The tubulin subunits of microtubules have ATP binding sites. In animal cells, microtubules do not enter the nucleus. A sustained GTP cap causes rapid polymerization of microtubules. In vivo, the minus end of a microtubule is anchored most of the time, and therefore does not typically polymerize or depolymerize. Microtubules are very sensitive to a local concentration of GTP-bound tubulin.

The tubulin subunits of microtubules have ATP binding sites.

Which one of the following statements about the genetic code is correct? There are 20 naturally occurring amino acids specified by the genetic code. There are 64 codons, each of which specifies a different amino acid. Every naturally occurring amino acid is specified by at least 2 codons. The only codons for Arginine are CGU, CGC, CGA, and CGG. The genetic code is degenerate because it is ambiguous.

There are 20 naturally occurring amino acids specified by the genetic code.

How does the SER determine which molecule will be made, Sphingomyolin or glycolipid, with Ceramide?

There are two competing enzymes, either one of which can use ceramide as a substrate, and literally whoever gets a given molecule of ceramide first gets to turn it into its product.

A transmembrane protein at the plasma membrane crosses the membrane six times and has both its N- and C-termini in the cytoplasm. Identify the targeting signals, whether present at the plasma membrane or not, that directed the cell to orient the protein in this manner.

There was no amino terminal signal sequence. The first sequence presented was an internal signal sequence. In the plasma membrane there are three internal signal sequences and three stop transfer sequences.

Which one of the following statements about the cells in early human embryonic development is correct? They bypass M-phase altogether. They undergo a full cell cycle, but the number of chromosomes is doubled following cytokinesis. They do not spend much (if any) time in G1. They bypass S-phase altogether. They are most accurately referred to as being in G0.

They do not spend much (if any) time in G1

Why would proteins need to be shuttled to/from the nucleus?

Transcription factors, polymerases (DNA/RNA), histones, ribosomal proteins, etc. any protein whose job is in the nucleus is likely to have displayed a NES

True or False: Theres different contents of DNA in different phases of the cell cycle. If true, how does this help us identify what phase the cell is in?

True. Twice as much DNA after replication has completed

Why do vesicles arriving at the Golgi look much smaller than vesicles leaving the Golgi?

Vesicles leaving the ER to go to the Golgi go as soon as they're ready, you don't stockpile a bunch of protein in order to make it leave, it just goes. But vesicles that leave the Golgi wait to be packaged with other proteins.

Is it possible that a vesicle between the ER and Golgi be carrying an ER resident protein back to the ER?

Yes, like BiP

can signal peptidase tell the difference between internal signal peptide and amino terminal signal peptide? If so which one does it cut?

Yes. the signal peptidase does not touch the internal signal peptidase but cuts the amino terminal signal peptide

Where do we push DNA we're not using at the moment?

You can either push it to the periphery of the nucleus, or you can bury it in the interior of a chromosomal territory. And only when you are needing that region of DNA will you unwind it into euchromatin and pull it to the periphery of the territory.

what is the largest molecule that can get through a nuclear pore complex?

a large ribosomal subunit going from the nucleus to the cytoplasm.

point mutation

a mutation that alters a single base. can be either the substitution of one base for another or deletion or addition of a single base (or small number of bases)

5' cap

additional inverted modified nucleotide (guanine) added to the 5' end of the mRNA to cap it called 7 methyl guanosine cap

How do we get a protein into transmembrane structure?

additional signal. stretches of amino that tells translocon to do something different. called stop-transfer sequence

why is a cytoskeleton especially important for animal cells?

animal cells don't have cell walls like plants

Recycling endosome

another example of a rest stop: material constantly coming in and going out. materials on way to plasma membrane

mitochondrial HSP 70

another form of chaperone protein that folds the protein once its in the mitochondrial matrix

How does (NORS) nuclear organizing regions get its name/ whats its function?

assemble all of your transcription factors, your RNA polymerases, your snoRNPs, your ribosomal proteins we're going to be incorporating in a moment. All of that material gets collected around those genes, and that's why we call those regions of those genes nucleolar organizing regions or NORs.

B-galactasidase

breaks down lactose into glucose and galactose

G actin: size, directionality?

building block to make actin filament. moderate size: 43 kiladaltons has directionality: barbed end: plus end (nothing to do with charge) pointed end: minus end, groove in G actin molecule. binding site for ATP: ATP can be hydrolyzed into ADP under the right conditions G actin hydrolyzes into actin

How do many antibiotics work?

by specifically inhibiting bacterial ribosomes

aminoacyl tRNA synthases

catalyze "charging" of tRNAs different one for each amino acid: given names according to which amino acids they're responsible for charging each enzyme recognizes ends of tRNA, which lets it identify if this tRNA is allowed to add to it

I-cell disease

caused by loss of enzyme that adds manno 6 phosphate groups very fatal never made way into lysosome, can't prepare any tools

Non sense mutation

change in base results in premature stop codon. protein truncated and virtually inactive (null phenotype)

BiP

chaperones that bind to proteins and fold them once they are in the lumen of the ER

Prometaphase

chromosomes are completely condensed new microtubules have access to chromosomes and make contact to collection of proteins in centromeric region when kinetochore and microtubule meet, line up in middle of the cell amount of time it takes for pair of sister chromatins to line up along imaginary line

lacA transcribes...

codes for thyogalactaside transgalctydase (called transgalactydase for short) don't need to know function but if thought to break down toxic products lac premease accidentally lets in

Early endosome

collection of endosytic vesicles that have accumulated over time irregular in shape because constantly having traffic go in and out does not contain any acid hydrolases: even if there were the pH isn't appropriate for them to function usually about 6.5 pH: starting process of lowering pH don't want to degrade everything that has just arrived at early endosome have ability to separate what needs to be degraded and what needs to be recycled: recycled material will bud off and go sideways into their own recycling endosome

What does E. coli RNA Polymerase do?

copies the information in DNA into RNA

The Signal Hypothesis

created by Bernhard Dobberstein and Gunter Blobel proposed that of the 3 molecules innvolved in translation (mRNA, ribosome, and protein), the protein is the one to present a signal in the form of a 3D sequence of amino acids that tells the cell to finish translation on the RER

lariat

created when we take loose 5' end of intron and covalently link it to 2'OH group of the adenine at branch point

What is the model system for eukaryotic cell cycle? How long does it take these cells to go through the cell cycle? How long does each of these phases take?

cultured human cells: human cells with 46 chromosomes being grown in culture go through cell cycle once every 24 hours: consists of M phase (1 hours) and interphase (23 hours)

Which one of the following is not a part of mitosis? Telophase Prophase Prometaphase Metaphase Cytokinesis

cytokinesis mitosis + cytokinesis = M phase

Proteins that start cytosolic stay ______. Proteins that start lumenal stay ______.

cytosolic, lumenal

nucleolus

darkly stained area

Which one of the following types of mutations would disrupt the reading frame in mRNA? Chemical-induced change of cytosine to thymine Same sense mutation Deletion of 1 or 2 bases Insertion of 3 bases Missense mutation

deletion of 1 or 2 bases

Duchenne's Muscular Dystrophy

deletion of exons in dystrophin: muscle fibers degeneration of muscle tissue

If the critical concentration at the plus end of an actin filament is 50, the critical concentration at the minus end is 80, and the actual concentration of available ATP-bound G-actin at both ends is 40, which one of the following describes the behavior of the actin filament? [Note: The description below does not have to be complete, it just has to be accurate for what is described.] Depolymerization at the plus end Polymerization at the minus end Polymerization at the plus end Depolymerization at the minus end while the plus end is at equilibrium None of the above accurately describe the behavior of the actin filament described in the question.

depolymerization at the plus end

DNA polymerase 1 has the ability to ....

do synthesis in the 5' to 3' direction primer removal by a 5' to 3' exonuclease activity proofreading by a 3' to 5' exonuclease activity This one enzyme has three different active sites in it. DNA polymerase 3 and most of the other DNA polymerases simply have the ability to do synthesis in the 5' to 3' direction and proofreading via a 3' to 5' exonuclease activity.

How does a ribosome distinguish the initiator codon from an internal methionine codon in eukaryotes?

don't use 16s rRNA or Shine-Dalgarno sequences. 5' cap structure allows for recognition that this is a translatable molecule. ribosomes look for 5' cap and scan until they find first AUG and use that as start codon

What is the energy used for that comes from breaking the bond between amino acid and adenine base at 3' end of the tRNA molecule?

drive peptide bond formation by peptidal transferase

What is the only time in the cells life when its using thymidine? How does this help us?

during S phase: if you're using thymidine, then you're in S phase using FISH

each doublet has a pair of (dynine/kinesin) arms?

dynine. anchored with tail ends into A tubule in each doublet reaching out to grab the B tubule of neighboring doublet. If and when they make contact and if theres ATP in the area, dynine walk closer to the minus end of the microtubule

How does each polymerase know which type of RNA to transcribe?

each only transcribes what it does because each recognizes specific, unique promoter regions.

Astral microtubules: go from what to what in the cell?

each out away from the centrosome and go towards the cell membrane in the closest direction. Those small microtubules that look like a little starburst around the centrosome astral = star

Is it easier to bring DNA to the machinery or have machinery scattered throughout the cell (in the nucleus)?

easier to bring DNA to the machinery. DNA replication organized so ori are brought out to the periphery of their territories to allow clusters of replication machinery to begin replicating from that point

Is it easier to bring a G actin in and add it to the barbed end than pointed end or vice versa?

easier to bring one in and add it to the barbed end than pointed end (easier to put right fist on top of left fist that bring in left fist and put it under right fist)

exons

expressed sequence: coding region of genes

How do microtubules "get started" in animal cells?

extend from and are initiated in microtubule organizing center (MOC) primary one in animal cell: centrosome: lays outside the nucleus: found anywhere in the cytoplasm: typically extend out towards plasma membrane until they encounter actin network

How do we make compacted cell have an increased amount of surface area?

extend out regions of the cytoplasm and stabilize them by using regular arrangements of cytoskeletal elements use microvilli

Chromosome painting

extension of FISH when you have multiple overlapping probes complementary to regions of particular chromosome makes you able to light up whole regions of a mitotic chromosome. could paint each mitotic/interphase chromosome its' own color.

difference between cilia and microvilli: what are each used for/ stabilized by? which is smaller?

extensions of cytoplasm stabilized by cytoskeletal elements. similar to microvillus microvilli are much smaller than cilia cilia stabilized with microtubules, microvilli with actin filaments. cilia built to move, microvilli just there to increase surface area

What does the vesicle do once it arrives at the Golgi?

fuses with the membrane of the golgi. considered the reverse of budding.

gene- and gene+

gene- : mutated gene (lacI -) gene+/gene : wild type gene. the plus sign can be left out. (lacI+)

Not every cell is making every protein that it can all of the time. So the mechanisms that cells use to say, "I want to make this protein right now" are collectively called _____.

genetic regulation

Lysosomal protein modification

gets the same modification. zip code called mannose 6-phosphate group don't go through regular modification pathway: have their own unique pathway: no other protein goes down this pathway

What do we ned for a new phospholipid?

glycerol a couple of fatty acid tails a phosphate group other chemical group to be covalently linked to the other side of that phosphate

what does it mean that a microtubule is polar?

has nothing to do with charge, it just means one end of it looks different from the other end each individual tubulin has polarity too has plus and minus end as well: assembly and disassembly are fastest at plus end

Importin

helps the nuclear pore complex recognize a signal because the nuclear pore complex is one shape trying to recognize many different types of amino acid signals recognizes and binds to the nuclear localization signal through a protein-protein interaction, and then the importin presents its own signal that's recognized by the nuclear pore complex, and the NPC says, "Oh I recognize you importin; you can come on through, and if you've got anybody with you, they can come through to." So the importin has bound to a cargo protein that we need to localize into the nucleus. They get brought in as a pair into the nucleus, then the importin lets go.

cytoskeleton: what varies and why?

highly dynamic system of protein fibers of varying sizes based on whats needed in cell at that time

how does glucose prevent the "dial" from turning all the way up to 10?

hinders what lac permease was doing if lactose has already gotten in, positive regulation will occur and we will give RNA polymerase some help: cAMP receptor protein

Drosophila and their polytene chromosomes

in 1984, studies of these fruit flies' chromosomes called polytenes proved Carl Rabl's findings correct Normally you have a single chromosome that gets replicated during DNA replication, and now you have two daughter double-helixes, which when the cell is preparing to divide get separated from each other and each daughter cell gets one copy. But in these particular cells in drosophila the DNA molecules get replicated, but they don't get pulled apart. So these polytene chromosomes can have hundreds or even thousands of identical copies of the DNA molecule still stuck together. And this is visible under light microscopy. but these are the exception not the rule so we had to do more experiments to see if other interphase chromosomes also occupy their own space

Are the MTs in axons and dendrites oriented in the same way? Why or why not?

in axon, all microtubules are facing the same direction. plus end away from cell body and minus end toward cell body: long, threadlike part in dendrite, no rhyme or reason which end is facing cell body : short, branched extension we think its because you need to do more rapid rearrangement with dendrites than axons

spacer DNA

in between genes that does not code for proteins, rRNA or tRNA

Where are all proteins translated (at least at the beginning)?

in the cytoplasm

virion

individual viral particle

Primary transcript

introns can be found here because it hasn't been fully processed into mRNA molecules yet. a.k.a pre-RNAs, initial transcript formed with 5' cap and 3' polyA tail

bipartite sequence

it has 2 parts non-relevant sequence: could be any amino acid and positively charged amino acids

What happens if you strip away DNA polymerase's exonuclease activity?

it is 100 times more likely to end up introducing mutations than if that exonuclease activity, that proofreading activity, is there. And this accounts for half of that reduction in the observed overall error frequency. So, 100 times more likely to correct a mistake if you are doing proofreading.

what does the circle on the acceptor end of the iconic representation of tRNA mean?

it means its charged with an amino acid

Active transport

large molecules (more than 40 kiladaltons) requires external energy source average proteins

Insertion/deletion mutations

large scale DNA insertions and deletions considered chromosome level mutations deletion: usually results in null phenotype insertion: results in null phenotype if in coding region, caused by TRANSPOSONS or repetitive sequences

Identify whether or not each of the following structures would shrink upon contraction of a skeletal muscle sarcomere. length of myosin motor proteins length of F-actin I band H zone

length of the myosin proteins would not shrink length of F actin would not shrink I band would shrink H zone would shrink

Endocytosis

like budding but from the outside of the cell's perspective. pull in the cell membrane and pinch it off creating endosytic vesicle: carries cargo molecule inside the cell

Z disk

line between two sarcomeres collection of proteins that allow for anchoring of barbed ends of actin filaments

outer membrane of nuclear envelope

lipid bilayer facing cytoplasm continuous with the membrane of the endoplasmic reticulum

inner membrane of nuclear envelop

lipid bilayer facing the cytoplasm

Dolichol

lipid that gets phosphorylated a couple of times that gets sugar molecules attached to it putting together oligosacchraride tree that has 14 monosaccharides (fourteenmer)

What molecules other than proteins are modified in the Golgi?

lipids

How do we make nerve cell very irregular shape?

loading in microtubules, we can rearrange dendrites of the nerve cell

chromatin

look like beads on a string, DNA + protien

kinetochore

make contact to a collection of proteins at the centromeric region of each of those pairs of sister chromatids microtubules that interact with kinetochores: microtubule kinetochores

lactose permease

makes cell permeable to lactose. without it you would starve because you wouldn't be able to get any nutrients inside the cell

what does tubulin make up?

makes up microtubules its a dimer: composed of two 55 kiladalton polypeptides: alpha and beta tubulin assemble tubulin dimers then build microtubules out of tubulin dimers

Phagocytoisis

means cell eating cell reaches out extension of its cytoplasm and englufs something form the outside world (like bacteria or virus) sort of opposite of endocytosis because extending membrane and englufing rather than pinching and breaking off phagosome then fuses with lysosome forming phagolysome, which degrades the bacteria must continue to pump more protons into phagolysosome in order to keep pH down to 5

kinesin

microtbule motor protein that moves organelles and vesicles toward plus end. works same way as myosin

stop transfer sequence: what type of amino acids usually and what does it do?

mostly hydrophobic amino acids because crosses interior of a lipid bilayer gives a set of instructions to the translocon to eject the protein out of the translocon into the membrane

myosin: type of energy transfer?

motor protein. works along with actin filaments to promote movement in a cell converts chemical energy (ATP) into mechanical energy class II myosins move towards barbed end. walks itself over

Anaphase B: which proteins are needed to complete this?

move spindle poles away from each other to stretch the boundaries of the cell so when its time to do cytokinesis theres lower risk of trapping chromosomes on the wrong side spindle poles are fairly large structures so need both kinesins and dyneins in order to work & lots of them Its minus end is anchored into the centrosome, so it's not only going to be pushing the microtubule, it is helping to push the entire centrosome over dynein can't move either but it gets closer to minus end of astral microtubule its attached to. so microtubule moves and dynein pulls microtubule in towards it, with it pulls entire centrosome towards it

H zone: does it disappear when the muscle contracts?

myosin but no actin brighter part of the A band but darker than I band because myosin are thicker so they show up darker disappears when muscle contracts because actin and myosin overlap

How is a gene name typically written?

name in italics and lowercase first letter

RMP

name of the machinery that removes introns and joins exons together. combination of RNA and protein molecules

How much DNA is in an S phase cell?

no exact measurement because they've all been in S phase for different amounts of time but could say anywhere from 2n+1 to 4n-1 You've added in at least one base during DNA replication, but you haven't finished, so you can't have any more than one base shy of being done

Are viruses cells?

no viruses are not cells, they're particles. they are not alive, they are persisting small genomes

can you transcribe lacA, lacZ, or lacY individually?

no, all part of one operon

Is the nucleolus separated by a membrane from the rest of the nucleus?

no, its just a region.

does the nuclear envelope itself let things through?

no, the pore complexes are the only things that let anything through

is 5s rRNA included as part of the pre-rRNA molecule?

no.

is there a one to one ratio between nucleotide and amino acid?

no. if there were there would only be 4 amino acids in proteins, not 20

Constitutively expressed genes, give some examples

not regulated because needed at all times in the cell ex: respiration enzymes, RNA polymerase, ribosomal RNAs, and proteins

mitochondria now do pretty much nothing but....

oxidative phosphorylation

cytokinesis: what is contractile ring made of?

part of M phase cytoplasmic divison accomplished by a contractile ring of actin and myosin II 1. build a ring of actin filaments around cytosolic leaflet of plasma membrane 2. associate type II myosin with it. they will all be getting closer to barbed end so must all be syntheszied in same direction 3. start inching the "belt" and as you pull more of the belt through the buckle the diameter gets smaller and smaller 4. tails of actin don't dangle in cytoplasm because as soon as region of actin moves past myosin, its depolymerized 5. each daughter cell is back in interphase

snRNP

particular kind of RNA used to remove introns. P is for the protein component assembled at 5' end site and the branch point

G actin is the monomer, so what is F actin?

polymer. or filament of actin

polymerization: where does it occur? reversible?

polymerization can occur on either end and it is reversible so G actin monomers can be lost from either end of the filament and added to either end

How do we make acid hydrolases?

presents mannose 6 phosphate group

Centrosome

primary Microtubule organizing center in animal cells: lay outside the nucleus, DONT go in the nucleus: found anywhere in the cytoplasm: typically extend out towards plasma membrane until they encounter actin network so not all the way to the edge brightly stained on electron micrograph

microtubules during interphase: what do they do?

primary railroad tracks or highway system: material is moved along them largest of cytoskeletal elements diameter wise.

The 45S pre-rRNA is: regulated at the transcriptional level by the abundance of finished ribosomes in the cytoplasm. cut into the rRNA molecules that will comprise the RNA part of a 60S subunit. spliced by snRNPs. processed by snoRNPs. processed into 5s, 5.8s, and 18s rRNA.

processed by snoRNPs

transcription unit

region from promoter to terminator

D-loop

regulatory region. also origin of replication

rRNA

ribosomal RNA. RNA components of a ribosome. complexes with a ribosomal proteins to make ribosomes, which are platforms on which protein synthesis occurs

function of 3' cap (polyA tail)

serves as protection. longer polyA tail = more protein you can make from an mRNA. cell also has ways of extending its poly(A) tail as it gets degraded in order to extend the life of a given mRNA molecule. poly(A) tail allows for the circularization of an mRNA molecule to make it more efficient to make multiple proteins from a single mRNA. when that molecule circularizes, it puts the start signal close to the stop signal. We'll see what those signals are in a bit. But if you put the start signal close to the stop signal then when the ribosome falls off at the stop signal it's right back in the neighborhood of the start signal and can begin another round of translation

Multi cellular organism germ-line mutation

sex cell: passed to new organism. affects survivability of the species: embryo will get mutation

tRNA

short (75-80 nucleotides) single stranded but it folds on itself by intrastrand base pairing 2D resembles clover leaf 2 most important parts are at opposite ends in regions of unpaired nucleotides

What two things form a holoenzyme?

sigma subunit + core polymerase

What keeps a protein in the nucleus from going out into cytoplasm?

signal again. 1995 found to be Nuclear Export Signal (NES)

How do you make a translocon open?

signal peptide

function of 5' cap

signal to the cell that tells it that the RNA is a translatable molecule there are different kinds of RNA, but ribosomes are only supposed to attempt to translate messenger RNAs. So there needs to be some physical structure that acts as a signal that says I am a messenger RNA, go ahead and try to translate me. You don't want that same structure being found on your rRNAs or your tRNAs, or a ribosome would attempt to try to translate them as well. That unique structure that will be found on every mRNA in a eukaryote and none of the other RNAs in a eukaryote is the five-prime cap structure. So the five-prime cap structure, that 7-methylguanosine cap, buys you some time to get some translation done from this mRNA before the nucleases degrade it.

What keeps cytoplasmic proteins out of the nucleus?

signals: only appropriate proteins have the right signal only ones that need to be brought in will present signal

ribosomes

site of protein synthesis complexes of ribosomal RNA (rRNA) and ribosomal proteins Found in cytoplasm of both bacteria and eukaryotes

3 categories of cytoskeletal fiber sizes

size refers to diameter, the length can change within each one. smallest: actin filaments/ actin microfilaments microtubules: largest intermedia filaments: in between (nuclear lamina proteins)

Nuclear speckles are: extensions of chromosome arms in the interchromosomal domain. clusters of snRNPs and RNA polymerases that work on transcriptionally silent genes. likely to be active in all phases of the cell cycle. gold dots that appear as specks or contaminants in fluorescence in situ hybridization experiments. small collections of transcriptional and splicing factors.

small collections of transcriptional and splicing factors.

Passive diffusion

small molecules (less than 9nm in diameter and less than 20 kiladaltons in weight) pass freely with the concentration gradient does not require external energy source

snoRNP

small nucleolar RNP. work on ribosomal RNAs. make cuts but don't join ends together. anything we don't end up with we recycle want to cut 45s into 3 smaller pieces. ( ETS—external transcribed sequences. They're part of the 45S molecule, but they're not going to be one of our finished products) internal transcribed sequences or ITS. Again, they're part of the 45S pre-rRNA transcript, but we aren't going to be using them, so we just cut them out And once you make all of those cuts and you release the ETS and the ITS, then what you're left with are the three pieces in gold—18S, 5.8S, and 28S

perinuclear space

space between outer and inner membrane

multi-pass transmembrane protein

span the membrane several different times and has either its C or N terminus in the lumen and the other in the cytoplasm N and C terminus could both be in either the cytosol or lumen

single-pass transmembrane protein

spans the membrane and has either its C or N terminus in the lumen and the other in the cytoplasm

why is it important to choose correct AUG start codon?

start codon determines reading frame. if you're off by one everything gets shifted creating different proteins kind of like the sentence: The fat cat ate the fat rat. if we started at the h in "The" we wouldn't be able to understand

Proteins translated on membrane bound ribosomes attached to the endoplasmic reticulum go to....

stays in the Endoplasmic reticulum (no additional signal) plasma membrane secretory vesicles: on way outside cell endosome, lysosome golgi appartatus

Structure of Ceramide and what it does and where its made

structure: 3 carbon backbone and 2 fatty acid tails. building block for either sphingomyolin or glycolipid, which are not made in the smooth ER its made in the smooth ER and packaged in transport vesicle to cis-Golgi

base substitution mutation (2 types)

substitution of one base pair for another in DNA. because of the degenerate nature of DNA, this may or may not alter the amino acid encoded. 2 types: 1. silent mutation: new codon from base substitution still encodes the same amino acid 2. missense mutation: base substitution changes an amino acid

the more smooth ER you have.. the more _____ you have to accommodate the enzymes that convert cholesterol into those steroid hormones.

surface area

central sheath

surrounds central pair holding things in place connected to radial spokes

pericentriolar material (PCM): what does it surround, what emanates from it?

surrounds pair of centrioles: just a region, not defined structure An amorphous ("without shape") collection of proteins from which the microtubules emanate Unorganized !!

Nirenberg experiment

synthesized artificial mRNA of 60 uracils and fed it into an in vitro machine that spit out polypeptide of 20 phenylalanine so it proves: genetic code is in fact 3 base pairs (20x3=60) UUU is code for phenylalanine similar experiments uncovered all the other codons

how does the GTP get hydrolyzed

tRNA molecule will rest back in place into that little cavity, cut out part of that ribosome. And when that happens, the elongation factor will push the GTP into a little cleft in that ribosome, and in that cleft there is a GTPase activity, an enzymatic active site that can hydrolyze a molecule of GTP. The energy provided by the release of the phosphate group from that GTP molecule, that's an exergonic reaction remember, that exergonic reaction will give us enough energy to remove the elongation factor, peel it off of the tRNA molecule.

How do we fix the imbalance between the two leaflets after new phospholipids are added to the membrane?

take half of the phospholipids we just made and move them to the other leaflet. this is energy dependent because energetically unfavorable: need enzyme called flipases

Late endosome

tend to lie more towards interior of cell than early endosome vesicles leaving early endosome then fuse with late endosome those proton pumps that are in its membrane have been active for longer, so the pH has dropped even more. If the pH of the early endosome was6.5, then the pH of a late endosome is going to be around 6 still have large collections of material that need to be degraded: this is where we introduce acid hydrolyses to material that needs to be degraded has ability to segregate what needs to be degraded from what needs to be recycled: sends receptor molecules back to the trans face of the Golgi to be recycled

interchromosomal domains

territory in and of themselves, molecules in here carrying out specific functions. surrounds chromosome territories

Shine-Dalgarno sequence or ribosome binding site

that sequence in the mRNA that is complementary and antiparallel to the three-prime tail of that rRNA molecule about 10 bases away is the AUG start codon Bacterial mRNAs can have multiple RBS

Lysosomal acid hydrolases and what pH is it active at?

the "tools" if the lysosome is the "tool box": 40-50 within each enzyme that degrades macromolecules hydrolase= hydrolyze covalent bonds only active under acidic conditions around pH of 5

How does a cell decide whether to lay low for a while (lysogenic pathway) or start replicating now (lytic cycle)

the cell evaluates the conditions in the cell and if they're good because there are a lot of resources available., the virus will start plus when bacterial cell divides, the prophage will be replicated anyway

lumen

the interior compartment. general term. the ER doesn't have a specific name for the inside so just called the lumen

What is the cost of protein synthesis? How does this affect the rate of protein synthesis

very expensive: cell must be selective for which proteins it makes right now ex. lacZ gene in E. Coli. has about 3000 base pairs in it. how expensive is it to make ONE copy? need 3000 ATP (or equivalent like CTP, GTP, or UTP) mRNA will also have 3000 bases in it --> 1,000 amino acids in the protein because triplet code