BIOL 230 Final Study Guide

Explain the process of splicing that produces mature eukaryotic mRNA.

(Pictured is alternative splicing) Introns are removed from the RNA transcripts in the nucleus by RNA splicing, a reaction catalyzed by small ribonucleoprotein complexes known as snRNPs. Splicing removes the introns from the RNA and joins together the exons—often in a variety of combinations, allowing multiple proteins to be produced from the same gene.

Describe the structure of nucleosomes.

-Made up of eight proteins consisting of pairs of four types of histones. DNA makes 1.75 turns around this octomer. -The "string" part is known as the linker DNA They are formed by wrapping DNA around a core protein octamer composed of two subunits each of histones H2A, H2B, H3, and H4

Outline the experiments which led to the discovery that DNA was the molecule of inheritance.

1920- Griffith confirmed that when the S form is killed by heating, it is no longer infectious. But he then discovered that if he injected mice with both the heat-killed S-form pneumococci and with live, harmless bacteria, the animals died of pneumonia. Proved protein is not the genetic material. 1940s- Avery, MacLeod, and McCarty performed an experiment demonstrating that DNA is the genetic material. The researchers prepared extracts from a disease-causing S strain of pneumococcus and showed that the "transforming principle" that would permanently change a harmless R strain into the infectious S strain is DNA. 1952- researchers working with a virus called T2 conducted a different kind of test to determine whether genes are made of DNA or protein. When this virus—which is made entirely of DNA and protein—infects E. coli, it injects its genetic material into the bacterial cell, leaving the empty virus head stuck to the cell surface. 1950s-Rosalind Franklin and Maurice Wilkins studied DNA with x-ray diffraction analysis and determined its 3-D atomic structure. 1953- Their results led to Watson and Crick's model of the double-helical structure of DNA.

Recall the general structure of a G protein and describe how the protein responds when activated by a GPCR.

3 G Protein Subunits - α, β, γ - βγ complex, tethered by γ to plasma membrane - α also tethered to plasma membrane (via short lipid tails) · α - unstimulated, inactive when GDP is bound (attached to βγ) · when receptor binds to GPCR, receptor is activated and changes confirmation · GCPR binds to α, GDP dissociation & exchanged for GTP · Activated α subunit breaks away from βγ (also activated) · Both activated can interact directly with target proteins that relay signals to other destinations in the cell

Describe the post-transcriptional modiications of 5' cap and 3' poly A tail to eukaryotic mRNA.

5' cap modification-protects mRNA from degradation. In addition, initiation factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes. 3' poly A tail modification- protects the mRNA from degradation, aids in the export of the mature mRNA to the cytoplasm, and is involved in binding proteins involved in initiating translation.

List and briefly define three post transcriptional controls.

5' cap modification-protects mRNA from degradation. In addition, initiation factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes. 3' poly A tail modification- protects the mRNA from degradation, aids in the export of the mature mRNA to the cytoplasm, and is involved in binding proteins involved in initiating translation. long noncoding RNAs-The complex silences certain gene expression by cleaving the mRNA molecules coding the target genes. This cleavage results in mRNA fragments that are further degraded by cellular exonucleases.

Summarize how the Fugu genome differs from the human genome in terms of size and approximate number of genes.

A Fugu(pufferfish) genome is about 1/8 the size of a mammilian genome because it is missing nearly all the repetitive DNA, and its introns are shorter. The positions of introns are still perfectly conserved.

Present the components of a typical transposon.

A general name for short segments of DNA that can move from one location to another in the genome. Also known as mobile genetic elements. Bacteria contain DNA- only transposons. They encode a transposase that mediates its movement. These enzymes recognize and act on unique DNA sequences that are present on the mobile genetic elements that code for the transposase.

What are tranposons and what impact do they have on the genome?

A general name for short segments of DNA that can move from one location to another in the genome. Also known as mobile genetic elements.transposons can drive the evolution of genomes by facilitating the translocation of genomic sequences, the shuffling of exons, and the repair of double-stranded breaks. Insertions and transposition can also alter gene regulatory regions and phenotypes.

Use examples to differentiate between somatic and germ line mutations.

A germline mutation occurs before conception. It is present in the zygote. So every cell in the fetus will have it. The offspring of that fetus can inherit it. A somatic mutation occurs after conception. It is in one cell in the body, not all cells. Though that cell can grow and form more cells with it. Usually, it'll be in something like blood, muscle, gut, lung. So it isn't passed on to offspring. Examples of germline mutations include inherited diseases. All cells in the body have a mutation. That includes sex cells, so the mutation's transmitted to the next generation. Examples of somatic mutations include changes in a body cell that causes it to turn cancerous (spontaneous cancer).

Outline the key differences between the synthesis of the leading and lagging strands.

A leading strand is the strand which is synthesized in the 5'-3'direction while a lagging strand is the strand which is synthesized in the 3'-5' direction. ... The leading strand is synthesized continuously while a lagging strand is synthesized in fragments which are called Okazaki fragments.

List several intracellular signaling proteins activated by RTKs.

A phospholipase C that functions in the same way as the phospholipase C activated by GPCRs to trigger the inositol phospholipid signaling pathway. Another intracellular signaling protein is a small GTP-binding protein called Ras.

What is a polyribosome? How does it function?

A polyribosome (or polysome or ergasome) is a group of ribosomes bound to an mRNA molecule like "beads" on a "thread". It consists of a complex of an mRNA molecule and two or more ribosomes that act to translate mRNA instructions into polypeptides.

Contrast the cell signaling systems used by plants and animals.

A spindly weed has hundreds of genes encoding receptor serine/threonine kinases but they are structurally distinct from the ones found in animal cells. In contrast to animal cells, plant cells seem not to use RTKs, steroid-hormone-type nuclear receptors, or cyclic AMP, and they seem to use few GPCRs.

Describe the structure and function of tRNA.

A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long. If it were to be flattened into one plane to reveal its base pairing, a tRNA molecule would look like a cloverleaf. tRNA is a vital component of the translation process that produces polypeptides.

Discuss the various ways that organisms benefit from gene regulation.

A typical eukaryotic cell expresses only a fraction of its genes, and the distinct types of cells in multicellular organisms arise because different sets of genes are expressed as cells differentiate.

Name the classes of enzymes that are the most frequent targets of G proteins, and list the second messenger molecules they produce.

Adenylyl cyclase - cyclic AMP Phospholipase C - inositol triphosphate (promotes cytosolic Ca) & diacylglycerol

List several biological processes triggered by calcium ions.

After fertilization, rise in cytosolic calcium triggers egg to begin development. Muscle cells, signals from nerves cause rise in Ca initiating muscle contraction. Secretory cells (include nerve cells) Ca triggers secretion

Compare how Akt promotes cell survival via Bad and stimulates cell growth via Tor.

Akt promotes cell survival: It phosphorylates and inactivates a protein called Bad. In its unphosphorylated state, Bad promotes apoptosis (form of cell death) by binding to and inhibiting a protein called Bcl2, which otherwise suppresses apoptosis. When Bad is phosphorylated by Akt, Bad releases Bcl2, which now blocks apoptosis, thereby promoting cell survival. The binding of a growth factor to an RTK activates the PI 3-kinase-Akt signaling pathway. Akt then indirectly activates Tor by phosphorylating and inhibiting a protein that helps to keep Tor shut down. Tor stimulates protein synthesis and inhibits protein degradation by phosphorylating key proteins in these processes.

Describe alternative splicing, what is it? Why is it important?

Alternative splicing is a process that enables a messenger RNA (mRNA) to direct synthesis of different protein variants (isoforms) that may have different cellular functions or properties. It occurs by rearranging the pattern of intron and exon elements that are joined by splicing to alter the mRNA coding sequence.

Summarize the factors that determine the duration of a GPCR-stimulated response.

Amount of time either subunit is switched on and able to relay signals is determined by the α subunit. α subunit has intrinsic GTPase activity (ability to hydrolyze GTP to GDP), returning the entire G protein back to original inactive confirmation. This usually occurs within seconds after activation. Inactive G protein is ready to be reactivated by another activated receptor. Activated α activates target protein.

Outline how gene duplication and divergence gave rise to the globin gene family.

An ancestral globin gene encoding a single-chain globin molecule gave rise to the pair of genes that produce four-chain hemoglobin proteins of modern humans and other mammals.

Summarize the molecular events that trigger the separation of sister chromatids at the start of anaphase.

Anaphase begins abruptly with the breakage of the cohesin linkages that hold together the sister chromatids in a duplicated chromosome. This release allows each chromosome to be pulled toward the spindle pole to which it is attached. The cohesin linkage is destroyed by a protease called separase. Before anaphase begins, this protease is held in an inactive state by an inhibitory protein called securing. At the beginning of anaphase, securin is targeted for destruction by APC/C - same protein complex that marks M cyclin for degradation. Once securin is removed, separase is free to sever linkages.

Explain how apoptosis participates in the development of a mouse or a human—or in the metamorphosis of a frog.

Apoptosis is programmed cell death. The amount of apoptosis that occurs in both developing and adult animal tissues can be astonishing. In the developing vertebrate system for example, more than half of some types of nerve cells normally die soon after they are formed. In a healthy adult human, billions of cells in the bone marrow and intestine perish every hour. Cell death balances cell division, unless the tissue is growing or shrinking.

Explain cell memory and the positive feedback loop.

At its simplest, cellular memory is achieved with a positive feedback loop--once activated by some external signal, the feedback loop will continually activate itself, even as the cell divides and the signal is taken away.

Summarize the mechanisms that allow cells to either pause or continue through different transition points in the cell cycle.

At the G1 to S transition, it uses Cdk inhibitors to keep cells from entering S phase and replicating their DNA. At the G2 to M transition, it suppresses the activation of M-Cdk by inhibiting the phosphatase required to activate the Cdk. And it can then delay the exit from mitosis by inhibiting the activation of APC/C, thus preventing the degradation of M cyclin. The control system monitors the cell's internal state and conditions in its environment, before allowing the cell to continue through the cycle. For example, it allows entry into S phase only if environmental conditions are appropriate; it triggers mitosis only after the DNA has been completely replicated; and it initiates chromosome segregation only after the duplicated chromosomes are correctly aligned on the mitotic spindle.

Outline the process of cytokinesis in plant cells.

At the beginning of telophase, after the chromosomes have segregated, a new cell wall starts to assemble inside the cell at the equator of the old spindle. The interpolar microtubules of the mitotic spindle remaining at telophase form the phragmoplast and guide vesicles, derived from the Golgi apparatus, toward the equator of the spindle. The vesicles which are filled with cell wall material, fuse to form the growing new cell wall that grows outward to reach the plasma membrane and original cell wall. The preexisting plasma membrane and the membrane surrounding the new cell wall then fuse, completely separating the two daughter cells.

Review how chromosomes are captured by spindle microtubules, and describe the structure of the point of attachment.

Attachment of microtubules to chromosomes is mediated by kinetochores, which actively monitor spindle formation and prevent premature anaphase onset. Microtubule polymerization and depolymerization dynamic drive chromosome congression. Depolymerization of microtubules generates tension at kinetochores.

Compare and contrast the structure of eukaryotic and prokaryotic chromosomes.

Bacteria carries genes on single circular DNA, Eukaryotic DNA is packaged into multiple chromosomes

Explain how extracts prepared from cells in different phases of the cell cycle have been used to identify components of the cell-cycle control system.

Because of synchrony (cells growing smaller and smaller with each division), it is possible to prepare an extract from frog eggs that is representative of the cell-cycle stage at which the extract is made. They found that an extract from an M-phase egg instantly drives the oocyte into M phase (MPF-maturation promoting factor), whereas cytoplasm from a cleaving egg at other phases of the cycle does not.

Indicate how Ras can fuel uncontrolled proliferation in cancer.

Before Ras was discovered in normal cells, a mutant form of the protein was found in human cancer cells. This mutation inactivates the GTPase activity of Ras, so that the protein cannot shut itself off, promoting uncontrolled cell proliferation and the development of cancer. About 30% of human cancers contain such activating mutations in a Ras gene.

Define bi-orientation and explain its importance for chromosome segregation.

Bi-orientation is the symmetrical attachment of a sister chromatid pair on the mitotic spindle, such that one chromatid in the duplicated chromosome is attached to one spindle pole and the other is attached to the opposite pole. This process generates tension in the kinetochores, which are being pulled in opposite directions. This tension signals to the sister kinetochores that they are attached correctly and are ready to be separated.

Outline the structural features of bacterial and eukaryotic ribosomes.

Both are composed of one large subunit and one small subunit, which fit together to form a complete ribosome. The small ribosomal subunit matches the tRNAs to the codons of the mRNA, while the large subunit catalyzes the formation of the peptide bonds that covalently link the amino acids together into a polypeptide chain. These two subunits come together on an mRNA molecule near its 5ʹ end to start the synthesis of a protein. The mRNA is then pulled through the ribosome like a long piece of tape. As the mRNA inches forward in a 5ʹ-to-3ʹ direction, the ribosome translates its nucleotide sequence into an amino acid sequence, one codon at a time, using the tRNAs as adaptors.

Articulate how viruses differ from mobile genetic elements.

Both are mobile, but viruses can move to other cells and organisms. Viruses are small genomes and their reproduction can lead to the death of host cells.

Assess how retroviruses and retrotransposons are similar.

Both use the reverse transcriptase enzyme to convert RNA to DNA.

Review how cyclin-Cdk complexes are inhibited as cells enter G1.

By eliminating all the existing cyclins, by blocking the synthesis of new ones, and by deploying Cdk inhibitor proteins to muffle the activity of any remaining cyclin-Cdk complexes. The use of multiple mechanisms makes this system of suppression robust, ensuring that essentially all Cdk activity is shut down.

Review how calcium-responsive proteins such as calmodulin propagate a calcium ion signal.

Calmodulin - present in cytosol of all euks; calcium binds to it, protein confirmation changes, it interacts with many target proteins that alters their activities · Ca/Calmodulin dependent protein kinases (CaM-Kinases) when kinase is activated by binding of calmodulin w Ca, they phosphorylate selected proteins Mammalian brains: neuron specific CaM-kinase is abundant at synapses, important part in forms of learning and memory CaM-Kinase activated by pulses of Ca signals that occur during neural activity Mutant mice that lack this kinase have limited ability to remember Structure: calmodulin has dumbbell shape, with 2 globular ends connected by long alpha helix. Each globular end has 2 Ca binding sites (4 total) one on NH2 & one on COOH

What are the three processes in RNA processing?

Capping, Addition of Poly A tail, and removal of introns (splicing) RNA processing is the term collectively used to describe the sequence of events through which the primary transcript from a gene acquires its mature form. Very soon after synthesis by RNA polymerase II begins, transcripts from nuclear protein-coding genes acquire a 5′ cap structure. The 3′ end of the messenger RNA (mRNA) is modified by the addition of a long string of adenosines in a process tightly linked to transcription termination. Finally, maturation of most eukaryotic mRNA precursors requires a process known as splicing, in which internal noncoding segments known as introns are removed and the coding segments, known as exons, are joined to produce functional mRNAs.

Summarize how apoptosis is mediated by a proteolytic caspase cascade.

Caspases are made as inactive precursors, called procaspases, which are activated in response to signals that induce apoptosis. Two types of caspases work together to take a cell apart. Initiator caspases cleave, and thereby activate downstream executioner caspases, which dismember numerous key proteins in the cell.

What is cdc6 and what does it do? What enzymes does it effect?

Cell division cycle 6 (CDC6) is an essential regulator of DNA replication in eukaryotic cells. Its best-characterized function is the assembly of prereplicative complexes at origins of replication during the G1 phase of the cell division cycle.

List the three fundamental cell processes that determine the size of an an animal's organs or body.

Cell growth, cell division, and cell death

Distinguish the appearance of cell necrosis from that of apoptosis.

Cell necrosis: eruption triggers a potentially damaging inflammatory response. By contrast, a cell that undergoes apoptosis dies neatly, without damaging its neighbors. A cell in the throes of apoptosis may develop irregular bulges or blebs on its surface, then it shrinks and condenses.

Differentiate the types of cell responses that occur rapidly with those that take minutes or hours to execute.

Cell response times vary based on if the proper proteins are available within the cell to carry out the response. Acetylcholine on a skeletal muscle cell causes it to contract in milliseconds because the proteins affected by the signal are already present in the cell. Growth and division responses take more time, hours, because the signals require change in gene expression and production of proteins.

Explain the mechanisms that create specialized cell types and promote cell memory.

Cells in multicellular organisms have mechanisms that enable their progeny to "remember" what type of cell they should be. A prominent mechanism for propagating cell memory relies on transcription regulators that perpetuate transcription of their own gene—a form of positive feedback.

Outline the centrosome cycle, indicating how and when it is initiated.

Centrosome duplication begins at the same time as DNA replication and the process is triggered by the same Cdks - G1/S-Cdk and S-Cdk - that initiate DNA replication. Initially, when the centrosome duplicates, both copies remain together as a single complex on one side of the nucleus. As mitosis begins, however, the two centrosomes separate, and each nucleates a radial array of microtubules called an aster. The two asters move to opposite sides of the nucleus to form the two poles of their mitotic spindle.

Recall the type of cells that lack centrosomes.

Centrosomes are not essential in somatic cells in fruit flies, and many animal cells don't have them.

Outline how a comparison of the nucleotide sequences from two closely related organisms can be used to reconstruct the amino acid sequence of a protein from their extinct, common ancestor.

Changes in genomes have produced only minor differences, and a large percentage of nucleotides match.

Contrast how cholera toxin and pertussis toxin exert their effects.

Cholera toxin - protein produced by bacterium that multiplies in intestine · toxin enters cells that line intestine & modifies α (called Gs because it stimulates adenylyl cyclase enzyme · mod prevents Gs from hydrolyzing the bound GTP, locking it in active state, continuously stimulating adenylyl cyclase This results in prolonged & excessive outflow of Cl- and water into gut = diarrhea and dehydration, can lead to death without replacement of water and ions Pertussis toxin - respiratory infection, bacterium colonizes lung, producing toxin, whooping cough · toxin (protein) alters α (Gi because it inhibits adenylyl cyclase) · mod disables subunit by locking it in inactive state (GDP bound) · results in inability to stimulate adenylyl cyclase

Compare cohesins and condensins in terms of structure, function, and how and when they assemble onto chromosomal DNA.

Cohesions: protein complex that holds sister chromatids together. They assemble along the length of each chromatid as the DNA is replicated. This cohesion between sister chromatids is crucial for proper chromosome segregation, and it is broken completely only in late mitosis to allow the sisters to be pulled apart by the mitotic spindle. Condensins: these protein complexes help carry our chromosome condensation, which reduces mitotic chromosomes to compact bodies that can be more easily segregated within the crowded confines of the dividing cell. The assembly of condensin complexes onto the DNA is triggered by the phosphorylation of condensins by M-Cdk. Condensins and cohesions are structurally related, and both are thought to form ring structures around chromosomal DNA. However, whereas cohesions encircle the two sister chromatids, tying them together, condensins assemble along each individual sister chromatid, helping each of these double helices to coil up into a more compact form.

What role does cohesin play in the transition from metaphase to anaphase?

Cohesis are a protein complex that holds sister chromatids together. They assemble along the length of each chromatid as the DNA is replicated. This cohesion between sister chromatids is crucial for proper chromosome segregation, and it is broken completely only in late mitosis to allow the sisters to be pulled apart by the mitotic spindle. Anaphase begins abruptly with the breakage of the cohesin linkages that hold together the sister chromatids in a duplicated chromosome. This release allows each chromosome to be pulled toward the spindle pole to which it is attached. The cohesin linkage is destroyed by a protease called separase.

Review how a technology such as RNA interference or CRISPR can be used to assess the importance of a particular protein in a signaling pathway.

Conversely, the activity of a specific signaling protein can be inhibited or eliminated. In the case of Ras, for example, one could shut down the expression of the Ras gene in cells by RNA interference or CRISPR. Such cells do not proliferate in response to extracellular mitogens, indicating the importance of normal Ras signaling in the proliferative response.

Compare how cyclins and Cdks vary in concentration and activity during the cell cycle.

Cyclins are so-named because, unlike Cdks, their concentrations vary in a clinical fashion during the cell cycle. For example, M cyclin increases during interphase and dramatically drops during mitosis. M-Cdk is very low during interphase and rises at the start of mitosis and dramatically drops at the ends of mitosis.

S-CDK/S-cyclin are very important to proper cell division. Why?

Cyclins drive the events of the cell cycle by partnering with a family of enzymes called the cyclin-dependent kinases (Cdks). A lone Cdk is inactive, but the binding of a cyclin activates it, making it a functional enzyme and allowing it to modify target proteins. The cyclin that acts in G2 to trigger entry into M phase is called the M cyclin, and the active complex it forms with its Cdk is called M-Cdk. Other cyclins, called S cyclins and G1/S cyclins, bidn to a distinct Cdk protein late in G1 to form S-Cdk and G1/S-Cdk, respectively; these cyclin-Cdk complexes help launch S phase. Another group of cyclins, called G1 cyclins, act earlier in G1 and bind to other Cdk proteins to form G1-Cdks, which help drive the cell through G1 toward S phase.

Review how DNA damage can arrest cells in G1.

DNA damage in G1 causes an increase in both the concentration and activity of a protein called p53, which is a transcription regulator that activates the gene encoding a Cdk inhibitor protein called p21. The p21 protein binds to G1/S-Cdk and S-Cdk, preventing them from driving the cell into S phase. The arrest of the cell cycle gives the cell time to repair the damaged DNA.

Explain how DNA damage can occur in cells.

DNA damage occurs continuously as a result of various factors—intracellular metabolism, replication, and exposure to genotoxic agents, such as ionizing radiation and chemotherapy. If left unrepaired, this damage could result in changes or mutations within the cell genomic material.

Describe the cellular mechanisms for repairing DNA.

DNA ligase can seal the nick in damaged or incorrect DNA. DNA mismatch repair removes the replication errors that escape proofreading. Double-stranded DNA breaks require nonhomologous and homologous end joining. nonhomologous end repair results in the loss of some nucleotides at the repair site, but is energetically favorable. homologous end-joining does not lose any nucleotides but expends more energy.

Describe the mechanisms underlying post-transcriptional control (DNA methylation, histone modifications, RNA degradation & translation, miRNA, siRNA, and long noncoding RNAs)

DNA methylation-addition of a methyl (CH3) group to DNA, thereby often modifying the function of the genes and affecting gene expression histone modifications- Addition of acetyl groups to particular lysines in histone tails neutralizes the positive charge and loosens the nucleosome's grip on DNA RNA degradation and translation- occurs on translating mRNA and that mRNA decay factors can inhibit translational elongation as well as affect mRNA degradation. These defects feed into the quality control of translational processes miRNA- bind to the 3'-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing. siRNA- The complex silences certain gene expression by cleaving the mRNA molecules coding the target genes. This cleavage results in mRNA fragments that are further degraded by cellular exonucleases. long noncoding RNAs-(lncRNAs) play important roles in cancer. They are involved in chromatin remodeling, as well as transcriptional and post-transcriptional regulation, through a variety of chromatin-based mechanisms and via cross-talk with other RNA species. can repress target genes through various mechanisms. a | Recruitment of proteins that repress gene expression. The lncRNAs can be transcribed from near the target gene or be brought to its proximity through pre-formed chromatin loops

Explain how the AT/GC rule underlies the ability of DNA to be replicated semiconservatively.

DNA replication produces two daughter DNA double helicies that intertwine with an old parental strand.

Contrast the types of DNA sequences that can accommodate mutations with those that cannot.

DNA that doesn't code for proteins or RNA is only randomly mutated. Deletrious mutations in important genes are not accommodated so easily. when mutations occur, the faulty organism will almost always be eliminated or fail to reproduce.

Describe how cells behave when deprived of mitogens.

Deprived of mitogens, the cell cycle arrests in G1. If the cell is deprived of mitogens long enough, it will withdraw from the cell cycle and enter a nonproliferating state, in which the cell can remain.

Outline an experimental approach to determining the rate at which point mutations accumulate in bacteria.

E. coli divides once every 20-25 minutes, and produces several offspring per day. this increases the probability of causing a point mutation, which is observable and measurable in the lab.

Distinguish the main types of signal-mediated cell-cell communication and identify the type of extracellular signal molecule involved in each.

Endocrine - hormone signaling molecules; long distance signaling; diffusion through the blood stream Paracrine - local mediators; diffuse locally through extracellular fluid in the same cell neighborhood (some cells respond to local mediators they produce themselves, autocrine signaling) Neuronal - neurotransmitters; can deliver long distances, delivered quickly and specifically through axon through electrical signals; axon terminal releases signal at synapse (tiny gap between two cells); the post synaptic cell is one with receptor that receives signal Contact Dependent - signals are bound to cell surface and bind to receptor on other cell surface; important for cell differentiation

Define endocrine, paracrine, neuronal and contact-dependent cell signaling.

Endocrine signaling- the most "public" style of cell-cell communication involves broadcasting the signal throughout the whole body by secreting it into an animal's bloodstream or a plant's sap. Extracellular signal molecules used in this way are called hormones. Paracrine signaling-the signal molecules diffuse locally through the extracellular fluid, remaining in the neighborhood of the cell that secretes them In neuronal signaling a message is delivered quickly and specifically to individual target cells through private lines.Contact-dependent signaling allows adjacent cells that are initially similar to become specialized to form different cell types

Describe how the ethylene signaling pathway regulates ripening of fruits.

Ethylene is a gaseous hormone that regulates a diverse array of developmental processes, including seed germination and fruit ripping. In the absence of ethylene, the empty receptor activates an associated protein kinase that ultimately shuts off the ethylene-responsive genes in the nucleus; when ethylene is present, the receptor and kinase are inactive, and the ethylene-responsive genes are transcribed.

How many RNA-polymerase molecules are there and what does each polymerase do?

Eukaryotic cells contain three distinct nuclear RNA polymerases that transcribe different classes of genes. Protein-coding genes are transcribed by RNA polymerase II to yield mRNAs; ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) are transcribed by RNA polymerases I and III.

Define evolution. This can be done in one sentence.

Evolution is change in the heritable characteristics of biological populations over successive generations.

Express how exon shuffling can facilitate the evolution of new proteins.

Exon shuffling during evolution can generate proteins with new combinations of protein domains. These different protein domains were joined together by exon shuffling during evolution to create the modern-day human proteins.

Compare a signaling pathway in which cyclic AMP produces a response within seconds to one in which the response takes minutes or hours to develop.

Fight or flight - adrenal gland secrets epinephrine, binds to GPCRs called adrenergic receptors to prepare for sudden action · Skeletal muscle, epinephrine increases cAMP to breakdown glycogen by activating PKA (cyclic AMP dependent protein kinase), this active PKA then phosphorylates and activates enzyme [phosphorylase kinase]. This kinase then activates glycogen phosphorylase, an enzyme that breaks down glycogen. These reactions happen quickly because they do not require change in gene transcription or new protein synthesis. cAMP responses that involve changes in gene expression or protein synthesis take minutes or hours · PKA phosphorylates transcription regulators

Outline the main classes of extracellular signal molecules, and describe the types of receptors to which they bind.

First and largest class of signals consists of molecules too large or too hydrophilic to cross the plasma membrane of the target cell. These signals rely on receptors on the surface of the target cell to relay their message across the plasma membrane. The second class of signals consists of molecules that are small enough or hydrophobic enough to pass through the plasma membrane and into the cytosol of the target cell.

P27 and P21, What are they and what is their function?

Following anti-mitogenic signals or DNA damage, p21 and p27 bind to cyclin-CDK complexes to inhibit their catalytic activity and induce cell-cycle arrest. P21 is a cyclin-dependent kinase inhibitor (CKI) that is capable of inhibiting all cyclin/CDK complexes, though is primarily associated with inhibition of CDK2.

Illustrate how selectively neutral mutations, combined with analysis of the fossil record, can be used to construct a phylogenetic tree.

For species that are closely related, it is most informative to focus on selectively neutral mutations because they accumulate steadily at a rate that is unconstrained by selection pressures, these mutations provide a metric for gauging how much modern species have diverged from their common ancestor. Such sequence comparisons allow the construction of a phylogenetic tree.

Summarize how incomplete or incorrect replication can arrest the cell cycle in G2.

For the cell to progress into mitosis, inhibitory phosphates must be removed by an activating protein called Cdc25. If DNA replication stalls, the appearance of single stranded DNA at the replication fork triggers a DNA damage response. Part of this response includes the inhibition of Cdc25, which prevents the removal of phosphates from M-cdk.

Distinguish the two main types of GTP-binding proteins.

G Proteins (large trimeric GTP binding proteins) - relay messages from G protein coupled receptors (GPCRs) GTPases (small, monomeric GTP binding proteins) - help relay signals Switch proteins aided by two sets of regulatory proteins to bind and hydrolyze GTP GEF - guanine nucleotide exchange factors, activate switch, GDP->GTP GAPs - GTPase activating proteins, inactivate, GTP hydrolysis, GTP->GDP

Outline how cyclic AMP is produced in response to G protein activation, and recall how caffeine can potentiate this response.

G protein is activated, switches on adenylyl cyclase, sudden increase in cAMP from ATP To terminate signal, enzyme cyclic AMP phosphodiesterase rapidly converts cAMP to AMP Caffeine inhibits this phosphodiesterase in nervous system, blocking cyclic AMP degradation & keeping concentration of it high

Review how different types of receptors can trigger a rise in the cytosolic concentration of calcium ions.

GPCR and RTKs can both trigger phospholipase C which will in turn cause a rise in Ca.

Review the structure of G-protein-coupled receptors (GPCRs) and describe the types of extracellular signal molecules that bind to them.

GPCRs are the largest family of cell surface receptors. They mediate responses to a variety of signal molecules: hormones, local mediators, neurotransmitters. Signals that bind can be proteins, small peptides, amino acid derivatives, fatty acids, etc. Each one has a different receptor or set of receptors. Still, all GPCRs have similar structure. · Single polypeptide chain that threads back ad forth through plasma membrane *7* times (alpha helices) · Cytoplasmic portion binds to G protein inside cell · For receptors that recognize small signals (acetylcholine & epinephrine), the ligand binds deep within membrane in pocket formed by AAs from transmembrane segments · Receptors that recognize proteins have large extracellular domain that bind protein to ligand One third of drugs used today work through GPCRs.

Articulate how gene duplication can lead to the evolution of genes with new functions or to the generation of pseudogenes.

Gene duplication can lead to the evolution of genes with new functions due to a cell needing a more efficient way to do things.?? There are several duplicated DNA sequences in the a- and B- globin gene clusters that are not function genes. They are similar in DNA sequence to the functional globulin games, but they have been disabled by the accumulation of many inactivating mutations. The existence of pseudogenes makes it clear that not every DNA duplication leads to a new functional gene. In fact, most gene duplication events are unsuccessful in that one copy is gradually inactivated by mutation.

Explain how studies of mutant yeast were used to dissect the cell-cycle control system.

Genes in yeast turned out to encode cyclin or Cdk proteins, which were unmistakable similar-in both amino acid sequence and function- to their counterparts in frogs and clams. Similar genes were soon identified in human cells. A yeast with a defective copy of the gene encoding its only Cdk fails to divide, but it divides normally if a copy of the appropriate human gene is artificially introduced into the defective cell.

Compare the fate of germ-line mutations that are deleterious, selectively neutral, or that provide a selective advantage.

Genes with selective advantage are more likely to be preserved. Deletrious are usually lost, selectively neutral may or may not persist.

Relate the speeds of the responses produced by G proteins activating an ion channel versus activating a membrane-bound enzyme.

Gi protein, βγ binds to intracellular face of K+ channel of pacemaker cell, forcing ion channel to open and allowing K+ to flow out. This increases the membrane's permeability to K+, making it less electrically active, slowing the heart rate. G proteins that interact with ion channels cause immediate change. With enzymes, the reaction is less rapid and more complex because they must produce additional intracellular signaling molecules.

Define chromatin, heterochromatin and euchromatin.

Heterochromatin and euchromatin are two major categories of chromatin higher order structure. Heterochromatin has condensed chromatin structure and is inactive for transcription, while euchromatin has loose chromatin structure and active for transcription.

Compare and contrast mismatch repair and homologous recombination in DNA

Homologous recombination (HR) and mismatch repair (MMR) are inextricably linked. HR pairs homologous chromosomes before meiosis I and is ultimately responsible for generating genetic diversity during sexual reproduction. mismatched nucleotides may be processed by MMR, resulting in nonreciprocal exchange of genetic information (gene conversion).

Define homologous genes and state the percentage of human genes that have clear homologs in species such as the fruit fly and nematode.

Homologus genes are those that are similar in nucleotide sequence due to a common ancestry. 50%of human genes have homologs in species like the fruit fly and nematode.

Illustrate how homologous recombination can lead to gene duplication.

Homologus recombination is the mechanism in which an intact chromosome is used as a template to repair a damaged sequence, but it can also catalyze crossovers that produce hybrid chromosomes.

Describe the process of horizontal gene transfer and state how this form of genetic exchange has significantly impacted human health.

Horizontal gene transfer can take place within an individual organism or organisms of different species. genes that develop resistance to antibiotics area product of horizontal gene transfer.

Compare the number of protein-coding genes present in humans versus Drosophila, C. elegans, and Arabidopsis, and analyze how these values relate to the complexity of the organism.

Humans have 19,000 protein-coding genes; Drosophila has 14,000; C. elegans has 22,000; Arabidopis has 28,000. Organism complexity relates more to the innovations in regulatory DNA sequences than the proteins or functional RNAs.

Recall how apoptosis balances cell division in an adult tissue such as liver.

If a part of the liver is removed in an adult rat, liver cells proliferate to make up the loss. Conversely, if a rat is treated with the drug phenobarbital, which stimulates liver cell division, the liver enlarges.

State what occurs when the DNA damage detected in G1 is too extensive to be repaired.

If the damage is too severe, p53 can induce the cell to kill itself through apoptosis.

Express what conserved synteny between two extant—or living—species indicates about the genome of their common ancestor.

If there is conserved synteny between two species, the genes were neighbors in ancestral DNA and remain neighbors today.

Outline the steps involved in the integration and replication of a retrovirus.

In a double-stranded RNA form, retroviruses infect a host cell with their genome, and then are reverse transcribed into double-stranded DNA, with the DNA integrated into the host cell genome. When integrated into a host genome, a retrovirus is hard to detect and can lay dormant for prolonged periods, having no discernible effect on the host.

Compare and contrast translation in bacteria and eukaryotes.

In a prokaryotic cell, transcription and translation are coupled; that is, translation begins while the mRNA is still being synthesized. In a eukaryotic cell, transcription occurs in the nucleus, and translation occurs in the cytoplasm.

Identify the phases that are shortened during the cleavage divisions of early embryos, and explain the effects of these divisions on cell size.

In an early frog embryo, the first cell divisions after fertilization serve to subdivide the giant egg cell into smaller cells as quickly as possible. In such embryonic cell cycles, the G1 and G2 phases are drastically shortened, and the cells do not grow before they divide.

Compare the changes in the mitotic spindle that underlie chromosome segregation during anaphase A and anaphase B, and delineate the driving forces responsible for each process.

In anaphase A, the sister chromatids are pulled toward the opposite poles as the kinetochore microtubules depolymerize. The force driving this movement is generated mainly at the kinetochore. In anaphase B, the two spindle poles move apart as the result of two separate forces: (1) the elongation and sliding of the interpolar microtubules past one another pushes the two poles apart, and (2) forces exerted on the outward-pointing astral microtubules at each spindle pole pull the poles away from each other, toward the cell cortex.

Compare and contrast transcription in bacteria and eukaryotes.

In bacteria, transcription and translation can occur simultaneously in the cytoplasm of the cell, whereas in eukaryotes transcription occurs in the nucleus and translation occurs in the cytoplasm. There is only one type of bacterial RNA polymerase whereas eukaryotes have 3 types.

Identify where gene regulation can occur in the pathway of gene expression for bacteria and eukaryotes.

In bacteria, transcription regulators usually bind to regulatory DNA sequences close to where RNA polymerase binds. This binding can either activate or repress transcription of the gene. In eukaryotes, regulatory DNA sequences are often separated from the promoter by many thousands of nucleotide pairs. Eukaryotic transcription regulators act in two main ways: (1) they can directly affect the assembly process that requires RNA polymerase and the general transcription factors at the promoter, and (2) they can locally modify the chromatin structure of promoter regions.

Summarize how adaptation in the intracellular signaling cascade of photoreceptors allows the eye to respond to dim or bright light.

In dim light, the signal is enormously amplified as it is relayed across the intracellular signaling pathway. Only a few dozen photons absorbed can be efficient to perceive a signal to be sent to the brain. Bright light, photons flood in large quantities through the photoreceptor cells. This is where the signaling cascade undergoes adaptation, minimizing the amplification. Adaptation depends on negative feedback: intense response in photoreceptor cell decreases the cytosolic Ca concentration, inhibiting enzymes responsible for signal amplification. Adaptation occurs more in intracellular signaling pathways that respond to extracellular signal molecules. This is so cells can respond to fluctuations in the concentration regardless of if the signal is present in small or large amounts, through positive and negative feedback mechanisms. Dim Light: · Absence of light, second messenger cGMP is continuously produced by guanylyl cyclase in cytosol of photoreceptor cell · cGMP binds to cation channels in the photoreceptor cell plasma membrane, keeping them OPEN Light: · Light activates rhodopsin resulting in activation of transducin α subunits · These turn on enzyme cyclic GMP phosphodiesterase, which breaks down cGMP to GMP · Sharp fall in cytosolic [cGMP] reduces amount of cGMP bound to cation channels · Cation channels close, decreasing influx of Na+ & altering voltage gradient across PM

Compare the mechanisms of exon shuffling and gene duplication.

In exon shuffling, eukaryotic genes facilitate the evolution of new proteins by allowing exons from one gene to be added to another. Both mechanisms bring about change in new species and changes in genomes.

Compare and contrast the function of GEF and GAP proteins.

In general, GEFs turn on signaling by catalyzing the exchange from G-protein-bound GDP to GTP, whereas GAPs terminate signaling by inducing GTP hydrolysis. GEFs and GAPs are multidomain proteins that are regulated by extracellular signals and localized cues that control cellular events in time and space.

Compare and contrast RAN and RAS.

In general, the Ras family is responsible for cell proliferation: Rho for cell morphology, Ran for nuclear transport, and Rab and Arf for vesicle transport. Ras proteins function as binary molecular switches that control intracellular signaling networks. Ras-regulated signal pathways control such processes as actin cytoskeletal integrity, cell proliferation, cell differentiation, cell adhesion, apoptosis, and cell migration. Ran is a small 25 kDa protein that is involved in transport into and out of the cell nucleus during interphase and also involved in mitosis. It is a member of the Ras superfamily. Ran is a small G protein that is essential for the translocation of RNA and proteins through the nuclear pore complex.

Explain how regulatory transcription factors are involved in the regulation of transcription.

In multicellular plants and animals, the production of different transcription regulators in different cell types ensures the expression of only those genes appropriate to the particular type of cell.

Contrast the fate of mutations that arise in somatic cells versus germ-line cells.

In sexually reproducing organisms, genetic information is only passed onto the next generation by germ-line cells. somatic cells form the organism's body, but aren't passed on.

What effect can viruses have on the genome? Consider a new to science or novel virus, like Covid-19. What is the potential for covid-19 patients, given this knowledge?

In some cases, scientists are finding, it actually has a beneficial impact. When viruses infect us, they can embed small chunks of their genetic material in our DNA. Although infrequent, the incorporation of this material into the human genome has been occurring for millions of years.

Outline how RTKs activate the MAP kinase signaling module.

In this pathway, MAP kinase is phosphorylated and activated by an enzyme called MAP kinase kinase. This protein is itself switched on by a MAP kinase kinase kinase (which is activated by Ras). At the end of the MAP-kinase cascade, MAP kinase phosphorylates various effector proteins, including certain transcription regulators, altering their ability to control gene transcription. The resulting change in the pattern of gene expression may stimulate cell proliferation, promote cell survival, or induce cell differentiation.

Review how the Notch receptor activates target genes in response to activation by Delta, and explain how this pathway 15. Outline how steroid hormones trigger the transcription of different sets of target genes.

In this simple signaling pathway, the receptor itself acts as a transcription regulator. When activated by the binding of Delta, a transmembrane signal protein on the surface of a neighboring cell, the Notch receptor is cleaved. This cleavage releases the cytosolic tail of the receptor, which is then free to move the nucleus, where it helps to activate the appropriate set of Notch-responsive genes. When a hormone (steroid) binds, the nuclear receptor undergoes a large conformational change that activates the protein, allowing it to promote or inhibit the transcription of specific target genes.

List the many steps required for protein production in prokaryotic cells.

Initiation, elongation, and termination. the only major difference between eukaryote and prokaryotes translation is that, rather than being processed and transported, the mRNA has a 5' strand availible immediately after transcription.

Differentiate the three main classes of cell-surface receptors and provide an example of each.

Ion Channel Coupled Receptors - changes permeability of plasma membrane f or specific ions, alters membrane potential, produces electrical current in proper conditions · Acetylcholine increases contractions in skeletal muscle cell via ICCR GPCRs - activate membrane bound trimeric GTP binding proteins, this activates or inhibits enzymes or ion channels in plasma membrane, begins an intracellular signaling cascade · Acetylcholine reduces contractions in heart pacemaker cells via GPCR Enzyme Coupled Receptors - act as enzymes or associate with enzymes, stimulated enzymes activate variety of signaling pathways

Recall when cytokinesis takes place with respect to mitosis.

It completes M phase. It usually begins in anaphase but is not completed until after the two daughter nuclei have re-formed in telophase.

Explain RNA world and autocatalysis.

It has been proposed that RNA served as both the genome and the catalysts in the first cells, before DNA replaced RNA as a more stable molecule for storing genetic information, and proteins replaced RNAs as the major catalytic and structural components. RNA catalysts in modern cells are thought to provide a glimpse into an ancient, RNAbased world.

Review the contractile ring in terms of its composition, assembly, and mechanism of action.

It is composed mainly of an overlapping array of actin and myosin filaments. It assembles at anaphase and is attached to membrane-associated proteins on the cytosolic face of the plasma membrane. Once assembled, the contractile ring can exert a force strong enough to bend a fine glass needle inserted into the cell before cytokinesis.

State the total size of the human genome, the total number of genes, and the number of chromosomes used to carry this genetic information.

Its 3.2x10^9 nucleotide pairs, spread out over 23 sets of chromosomes.

Compare the general structures of GPCRs and enzyme-coupled receptors such as receptor-tyrosine kinases (RTKs).

Like GPCRs, enzyme-coupled receptors are transmembrane proteins that display their ligand-binding domains on the outer surface of the plasma membrane. Instead of associating with a G protein, however, the cytoplasmic domain of the receptor either acts as an enzyme itself or forms a complex with another protein that acts as an enzyme. Responses to them are typically slow and can act at very low concentrations. - The largest class of enzyme couple receptors consists of receptors with a cytoplasmic domain that functions as a tyrosine kinase, which phosphorylates particular tyrosine's on specific intracellular signaling proteins.

List the four phases of the eukaryotic cell cycle and summarize what takes place in each.

M phase- seen in a microscope, the nucleus divides, a process called mitosis, and then when the cell itself splits into two, a process called cytokinesis. In a mammalian cell, the whole M phase takes about an hour, which is only a small fraction of the total cell-cycle time. Interphase- the period between one M phase and the next. The cell increases in size. Contains 3 phases. S phase- the cell replicates its DNA. G1 phase and G2 phase- the cell continues to grow. The cell monitors both its internal state and external environment. This monitoring ensures that conditions are suitable for reproduction and that preparations are complete before the cell commits to the major upheavals of S phase (which follows G1) and mitosis (following G2). At particular points, the cell decides whether to process to the next phase or pause to allow more time to prepare.

Explain how M-Cdk is activated at the end of G2 and indicate why this activation is sudden and explosive.

M-Cdk complexes accumulate throughout G2. It isn't switched on until the end of G2, when the activating phosphatase Cdc25 removes the inhibitory phosphates holding M-Cdk activity in check. This act of activation is self-reinforcing: once activated, each M-Cdk complex can indirectly turn on additional M-Cdk complexes. The overall consequence is that, once M-Cdk activation begins, it ignites an explosive increase in M-Cdk activity that drives the cell abruptly from G2 to M phase.

Explain how some antibiotics inhibit the growth of bacteria by interfering with translation.

Many of our most effective antibiotics are compounds that act by inhibiting bacterial, but not eukaryotic, gene expression. Some of these drugs exploit the small structural and functional differences between bacterial and eukaryotic ribosomes, so that they interfere preferentially with bacterial protein synthesis

Explain how cells keep the concentration of calcium ions in the cytosol low and how they terminate a calcium ion signal.

Membrane embedded calcium pumps actively remove Ca from cytosol, either to ER or across plasma membrane. This results in steep electrochemical gradients of Ca across both ER & plasma membranes. When signal opens channels, calcium rushes down gradient, this triggers changes in Ca responsive proteins

Explain how membrane-enclosed organelles are distributed to daughter cells during cell division.

Mitochondria and chloroplasts are usually present in large numbers and will be safely inherited if, on average, their numbers simply double once each cell cycle. The ER in interphase cells is continuous with the nuclear membrane and is organize by the microtubule cytoskeleton. Upon entry into M phase, the reorganization of the microtubules releases the ER; in most cells, the released ER remains intact during mitosis and is cut in two during cytokinesis .The Golgi apparatus fragments during mitosis; the fragments associate with the spindle microtubules via motor proteins, thereby hitching a ride into the daughter cells as the spindle elongates in anaphase.

Define the function of MAP-Kinase, MAP-Kinase-Kinase and MAP-Kinase-Kinase-Kinase.

Mitogen Activated Protein (MAP) kinase kinase kinase, MAPKKK (or MAP3K) is a serine/threonine-specific protein kinase which acts upon MAP kinase kinase. Subsequently, MAP kinase kinase activates MAP kinase. Several types of MAPKKK can exist but are mainly characterized by the MAP kinases they activate. MAPKKK is responsible for various cell functions such as cell proliferation, cell differentiation, and apoptosis. Because MAPKKKs are involved in a wide range of cell responses occurring both in the cytoplasm and the nucleus, a mutation in these genes can cause several diseases. Over-expression of the MAPKKK upstream of the ERK 1/2 MAPK and an increase in epidermal growth factor receptor (EGFR) can lead to tumor formation, such as triple negative breast cancer.

Compare the mitotic spindle and contractile ring in terms of composition, location, and the role each plays in cell division.

Mitotic spindle: composed of microtubules and the various proteins that interact with them, including microtubule-associated motor proteins. In all eukaryotic cells, the mitotic spindle is responsible for separating the duplicated chromosomes and allocating one copy of each chromosome to each daughter cell. Contractile ring: consists mainly of actin and myosin filaments arranged in a ring around the equator of the cell. It starts to assemble just beneath the plasma membrane toward the end of mitosis. As the ring contracts, it pulls the membrane inward, thereby dividing the cell in two.

Explain how mobile genetic elements can alter the activity of regulation of a gene or promote gene duplication and exon shuffling.

Mobile genetic elements are DNA sequences that can move from one chromosomal location to another. These cause spontaneous mutations and sometimes novel genes that spread with exon shuffling and gene duplication, like a parasite.

Describe how monomeric GTPases toggle between active and inactive forms.

Monomeric GTPases switch on and off by two sets of regulatory proteins that aid in binding and hydrolyzing GTP GEF - guanine nucleotide exchange factors, activate switch, GDP->GTP GAPs - GTPase activating proteins, inactivate, GTP hydrolysis, GTP->GDP

Explain combinatorial control.

Most importantly is the idea of combinatorial control, which is that any given gene is likely controlled by a specific combination of factors to control transcription. In a hypothetical example, the factors A and B might regulate a distinct set of genes from the combination of factors A and C.

Summarize six basic mechanisms that generate genetic change.

Mutation within a gene, mutation within regulatory DNA sequences, gene duplication and divergence, exon shuffling, transposition of mobile genetic elements, and horizontal gene transfer.

Recall how point mutations typically arise and evaluate how the locations of these mutations can dictate their effects on an organism's appearance or fitness.

Mutations outside the coding sequences of genes can sometimes affect the regulatory DNA sequences, which control the timing, location, and level of gene expression. This can lead to the inhibition of protein production.

Describe an extracellular signal protein that inhibits tissue growth.

Myostatin, for example, is a secreted signal protein that normally inhibits the growth and proliferation of the precursor cells (myoblasts) that fuse to form skeletal muscle cells during mammalian development. When the gene that encodes myostatin is deleted in mice, their muscles grow to be several times larger than normal, because both the number and size of muscle cells is increased.

Compare and contrast necrosis and apoptosis.

Necrosis is the sum of cellular changes that occur after local cell death; it is the process of cellular self-digestion, or autolysis. Cells die long before any necrotic changes are noted by light microscopy. The structural signs that indicate irreversible injury and progression to necrosis are dense clumping and progressive disruption of genetic material and disruption of the plasma and organelle membranes. Apoptosis is an active process of cellular self-destruction implicated in both normal and pathologic tissue changes. When dead cells are observed histologically, necrosis is the correct descriptive term. If the cells have apoptotic structure, then apoptotic necrosis is the correct term.

List some foreign substances that alter physiology by interacting with cell-surface receptors.

Nicotine - stimulates acetylcholine activated ICCRs, resulting in restricted blood vessels and blood pressure elevation · Menthol - stimulates temperature sensitive ICCRs, resulting in: moderate amounts, cool sensation; high doses, burning pain · Barbiturates & Benzos - stimulate GABA activated ICCRs resulting in anxiety relief and sedation · Morphine & Heroin - stimulate G protein coupled opiate receptors, resulting in euphoria and analgesia (pain relief) · Curare - blocks acetylcholine activated ICCRs, results in paralysis by blockage of neuromuscular transmission · Capsaicin - stimulates temperature sensitive ICCRs, results in painful burning; prolonged exposure paradoxically leads to pain relief · Strychnine - blocks glycine activated ICCRs, blocks inhibitory synapses in spinal cord and brain, seizures, muscle spasms

Outline how the gas nitric oxide (NO) can act as a signaling molecule to trigger the relaxation of smooth muscle cells.

Nitric Oxide is small enough and hydrophobic enough to pass through plasma membrane (unlike cAMP and Ca). Acetylcholine binds to GPCR on surface of endothelial cells, activating G protein (Gq) · Active Gq à IP3 à release of Ca inside cell · Ca stimulates nitric oxide synthase, enzyme produces NO from arginine (amino acid) · NO diffuses rapidly from endothelial cell to smooth muscle cell · In smooth muscle cells it regulates activity of specific proteins that relax the cell · Key target protein activated by NO is guanylyl cyclase, catalyzes production of cyclic GMP from GTP Treatment of patients with angina (pain causes by inadequate blood flow to heart muscle) In body, nitroglycerin is converted into NO, relaxing blood vessels

Describe non-coding DNA. What is it and what function does it have?

Non-coding DNA sequences do not code for amino acids. Most non-coding DNA lies between genes on the chromosome and has no known function. Other non-coding DNA, called introns, is found within genes. Some non-coding DNA plays a role in the regulation of gene expression.

State the amount of variation that typically distinguishes one human genome from another and describe the most common form of genetic variation.

Nucleotide sequences differ by 0.1% between people. Genetic variation was mostly inherited from early human ancestors.

Describe the structure of nucleotides, a DNA strand, and the DNA double helix.

Nucleotides- a DNA molecule consists of 2 complementary chains of nucleotides, each of which composed of 4 types of subunits. Phosphodiester bonds hold the nucleotide subunits together. Sequences of nucleotides code for RNA and proteins. DNA strands- composed of 2 long polynucleotide chains, held together by hydrogen bonds. Packaged with protein to form chromatin. Nucleotides inside double helix and phosphate outside.

Review how open reading frames are used in estimating gene number.

ORFs are long sequences missing stop codons that likely encode proteins. computer programs search for ORFs

Explain why the G1-to-S transition in yeast cells is sometimes called "Start."

Once past this critical G1-to-S transition, a cell usually continues all the way through the rest of the cell cycle. In yeasts, the G1-to-S transition is therefore sometimes called start because passing it represents a commitment to complete a full cell cycle.

Differentiate between L1 elements and Alu sequences.

One abundant human retrotransposon, the L1 element (LINE-1, a long interspersed nuclear element), is transcribed into RNA by a host cell's RNA polymerase. A double stranded DNA copy of this RNA is then made using an enzyme called reverse transcriptase, an unusual DNA polymerase that can use RNA as a template. The reverse transcriptase is encoded by the L1 element itself. They constitute about 15% of the human genome. The Alu sequence is present in about 1 million copies, making up about 10% of our genome. Alu elements do not encode their own reverse transcriptase and thus depend on enzymes already present in the cell to help them move.

Recall how a combination of signals can evoke a response that is different from the sum of the effects that each signal can trigger on its own.

One combination of signals is necessary for a cell to survive. The addition of other signals can cause a cell to differentiate or grow and divide. The absence of signals leads to apoptosis.

Describe a method to identify proteins that interact in response to stimulation by an extracellular signal.

One method involves using a protein as "bait." For example, to isolate the receptor that binds to insulin, one could attach insulin to a chromatography column. Cells that respond to the hormone are broken open with detergents that disrupt their membranes, releasing the transmembrane receptor proteins. When this slurry is poured over the chromatography column, the proteins that bind to insulin will stick and can later be eluted and identified. Protein-protein interactions in a signaling pathway can also be identified by co-immunoprecipitation. For example, cells exposed to an extracellular signal molecule can be broken open, and antibodies can be used to grab the receptor protein known to recognize the signal molecule. If the receptor is strongly associated with other proteins, these will be captured as well. In this way, researchers can identify which proteins interact when an extracellular signal molecule stimulates cells.

Review how death receptors can stimulate apoptosis.

One well-understood death receptor called Fas, is present on the surface of a variety of mammalian cell types. Fas is activated by a membrane-bound protein called Fas ligand, present on the surface of specialized immune cells called killer lymphocytes. These killer cells can help regulate immune responses by inducing apoptosis in other immune cells that are unwanted or are no longer needed. The binding of Fas ligand to its receptor triggers the assembly of a death-inducing signaling complex, which inclides specific initiator procaspases that, when activated, launch a caspase cascade that leads to cell death.

Describe how the synthesis and destruction of cyclins regulate progression from one phase of the cell cycle to the next.

Over the course of the cell cycle, the concentration of each type of cyclin rises gradually and then falls abruptly. The gradual increase in cyclin concentration stems from continued transcription of cyclin genes and synthesis of cyclin proteins, whereas the rapid fall in cyclin concentration is precipitated by a full-scale target destruction of the protein. The anaphase-promoting complex or cyclosome (APC/C) tags cyclins with a chain of ubiquitin and they are directed to proteasomes where they are rapidly degraded. The ubiquitination and degradation of the cyclin returns its Cdk to an inactive state. Like cyclin accumulation, cyclin destruction can also help drive the transition from one phase of the cell cycle to the next. For example, M cyclin degradation- and the resulting inactivation of M-Cdk- leads to the molecular events that take the cell out of mitosis.

Review how extracellular signals that promote cell growth and survival activate PI-3-kinase signaling pathways.

PI 3-kinase phosphorylates inositol phospholipids in the plasma membrane. These lipids serve as docking sites for specific intracellular signaling proteins, which relocate from the cytosol to the plasma membrane, where they can activate one another.

What role does securin play in the transition from metaphase to anaphase?

PTTG is a mammalian securin, a key regulator of metaphase to anaphase transition during mitosis, and overexpression or suppression of PTTG results in aneuploidy, and also plays a role in DNA break repair. At the beginning of anaphase, securin is targeted for destruction by APC/C - same protein complex that marks M cyclin for degradation. Once securin is removed, separase is free to sever linkages.

Recall the location and action of the second messenger molecules produced by activated phospholipase C.

Phospholipase C (membrane bound enzyme) when activated increases the second messenger diacylglycerol (DAG), inositol triphosphate, and Ca2+ GCPRs (some) effect G protein (Gq) that activates phospholipase C instead of adenylyl cyclase. · Inositol phospholipid - made by cleavage of a lipid molecule, present in small quantities in cytosolic leaflet of membrane bilayer · Cleavage of membrane to inositol phospholipid by phospholipase C generates 2 secondary messengers: inositol 1,4,5-triphopshate (IP3) and diacylglycerol (DAG) both important for signal relay · IP3 is water soluble sugar phosphate released into cytosol, it binds to and opens calcium channels in ER membrane. Calcium rushes out into cytosol, which signals other proteins · DAG is a lipid, remains in plasma membrane after produced by phospholipase C; it recruits and activates protein kinase (translocates from cytosol to plasma membrane) This enzyme is protein kinase C (PKC) because it needs to bind to calcium to become active and phosphorylate sets of proteins

Review how a point mutation affects our ability to digest lactose.

Point mutations in regulatory DNA sequences affect the ability to digest lactose

Compare positive and negative feedback and contrast the types of responses produced by each.

Positive feedback is when a component downstream in the pathway acts to enhance the response of the initial signal. (can generate all-or-none) Negative feedback is when a component downstream inhibits the response of an earlier component, diminishing the response. (can generate oscillation responses)

List the stages of M phase.

Prophase: duplicated chromosomes condense; mitotic spindle assembles between centromeres. Prometaphase: breakdown of nuclear envelope; chromosomes now attach to spindle microtubules; undergo active movement. Metaphase: chromosomes are aligned at equator; kinetochore microtubules on each chromatid attach to opposite poles of the spindle. Anaphase: sister chromatids separate and pull towards the poles; kinetochore gets shorter. Telophase: new nuclear envelope reassembles; division of cytoplasm begins with assembly of contractile ring.

Describe proteasomes and their regulatory function in the cell.

Proteasomes are large protein machines that break down proteins. They are present in both the cytosol and the nucleus. Proteasomes bind the proteins destined for degradation (marked by the covalent attachment of ubiquitin) and use ATP-hydrolysis to unfold the proteinasnd thread them into the inner chamber of its cylinder to chop them into short peptides.

Please explain the function of the polyubiquitin targeting. Be complete and precise.

Proteins that are meant to be short-lived often contain a short amino acid sequence that identifies the protein as one to be ubiquitylated and degraded in proteasomes. Damaged or misfolded proteins, as well as proteins containing oxidized or otherwise abnormal amino acids, are also recognized and degraded by this ubiquitin-dependent proteolytic system. The enzymes that add a polyubiquitin chain to such proteins recognize signals that become exposed on these proteins as a result of the misfolding or chemical damage—for example, amino acid sequences or conformational motifs that are typically buried and inaccessible in a "healthy" protein. Proteins marked by a polyubiquitin chain are degraded by the proteasome.

Explain how purifying selection leads to the conservation of functionally important DNA sequences and characterize the roles that these conserved sequences might play.

Purifying selection is the elimination of individuals carrying mutations that interfere with important functions. By observing where the human and mouse sequences have remained nearly the same, one can thus see very clearly the regions where genetic changes are not tolerated. these sequences have been conserved by purifying selection.

Explain how Rb blocks cell proliferation and how mitogens reverse this inhibition.

Rb is abundant in the nuclei of all vertebrate cells, where it binds to particular transcription regulators and prevents them from turning on the genes required for cell proliferation. Mitogens release the Rb brake by triggering the activation of G1-Cdks and G1/S-Cdks. These complexes phosphorylate the Rb protein, altering its conformation so that it releases its bound transcription regulators, which are then free to activate the genes required for entry into S phase.

Express how changes in regulatory DNA sequences can contribute to the evolution of species.

Regulatory DNA sequences dictate each organism's developmental program: the rules its cells follow as they proliferate, assess their positions in the embryo, and specialize by switching on and off specific genes at the right time and place.

Explain how the same signal molecule can induce different responses in different target cells.

Responses to a signal molecule depend on the receptor and the type of cell. Both heart pacemaker cells and salivary gland cells have the same receptor for acetylcholine. When exposed to acetylcholine, the heart peace maker cell decreases firing, while the salivary gland cell secretes saliva through exocytosis of vesicles. Skeletal muscle cells have a different receptor that receives two acetylcholine signal molecules, causing the cell to contract.

Compare the movement of DNA-only transposons and retrotransposons.

Retrotransposons appear to only be in eukaryotes. one type of R.T., the L1 element, is transcribed into RNA by a host cell's RNA polyamerase. A double-stranded DNA copy is then made via reverse-transcriptase, an unusual DNA polyamerase that uses RNA as the template. the DNA copy is then free to reintegrate into another site in the genome.

Outline how GPCRs in the photoreceptors of the retina transmit an extremely rapid signal in response to stimulation by light.

Rhodopsin, a G protein coupled light receptor, when stimulated by light, activated the G protein transducin. The activated α subunit of transducin activates an intracellular signaling cascade, causing cation channels to close in the plasma membrane. A voltage change is produced across the membrane, altering neurotransmitter release and leads to nerve impulses sent to the brain. Rod is stimulated by light, signal is sent from rhodopsin through the cytosol, to ion channels that allow the positive ions to flow through PM of outer segment. Cation channels close in response to cytosolic signal, this produces a change in membrane potential of rod cell.

SHORT ANSWER QUESTIONS

SHORT ANSWER QUESTIONS

Summarize what has been revealed by the comparison of human and Neanderthal DNA.

Scientists have discovered which genomic regions have undergone change.

What do cyclic AMP, Calcium and Nitric Oxide have in common? Explain.

Second messengers are molecules that relay signals received at receptors on the cell surface — such as the arrival of protein hormones, growth factors, etc. — to target molecules in the cytosol and/or nucleus. But in addition to their job as relay molecules, second messengers serve to greatly amplify the strength of the signal. Binding of a ligand to a single receptor at the cell surface may end up causing massive changes in the biochemical activities within the cell.

Define signal transduction and list the basic components involved in this process in cells.

Signal transduction is the conversion of an impulse or stimulus from one physical or chemical form to another. The signals that pass between cells are simpler than the sorts of messages that humans exchange. In typical communication between cells, the signaling cell produces a particular type of extracellular signal molecule that is detected by the target cell. Target cells possess proteins called receptors that recognize and respond specifically to the signal molecule. Signal transduction begins when the receptor on a target cell receives an incoming extracellular signal and then produces intracellular signaling molecules that alter cell behavior.

Summarize how phosphorylation can act as a molecular switch, and identify the types of proteins that add and remove this chemical modification.

Signaling by protein phosphorylation - the signal protein is off until a protein kinase phosphorylates it through ATP hydrolysis. The addition of the phosphate to the protein switches it "on", sending out a signal. Protein phosphatase hydrolyzes the protein, removing the phosphate, switching it "off". Many switch proteins are protein kinases - phosphorylation cascades. One PK phosphorylates the next in a sequence. This amplifies, distributes, and regulates the transmission of the signal. Protein kinases 2 main types: serine/threonine kinases (phosphorylate proteins on serines and threonines) and tyrosine kinases (phosphorylate proteins of tyrosines)

List the three specialized DNA sequences and explain their functions.

Specialized DNA sequences are required for DNA replication and chromosome segragation. Replication Origins: Controls the beginning of DNA synthesis. Centromere: permit one copy each of the duplicated chromosomes to be pulled into each daughter cell at division. Telomere: allow ends to be efficiently replicated and also prevent chromosome ends from being recognized as breaks in need of repair.

Explain how mutant proteins can be used to determine the order in which proteins participate in a signaling pathway.

Such classical genetic screens can also help sort out the order in which intracellular signaling proteins act in a pathway. Suppose that a genetic screen uncovers a pair of new proteins, X and Y, involved in the Ras signaling pathway. To determine whether these proteins lie upstream or downstream of Ras, one could create cells that express an inactive, mutant form of each protein, and then ask whether these mutant cells can be "rescued" by the addition of a continuously active form of Ras. If the constantly active Ras overcomes the blockage created by the mutant protein, the protein must operate upstream of Ras in the pathway. However, if Ras operates upstream of the protein, a constantly active Ras would be unable to transmit a signal past the obstruction caused by the disabled protein.

Describe how the ends of eukaryotic chromosomes (telomeres) are replicated.

Telomerase adds complementary RNA bases to the 3′ end of the DNA strand. Once the 3′ end of the lagging strand template is sufficiently elongated, DNA polymerase adds the complementary nucleotides to the ends of the chromosomes; thus, the ends of the chromosomes are replicated.

What is the Bad-protein how does it function, when phosphorilated, when dephosphorilated?

The BCL2 associated agonist of cell death (BAD) protein is a pro-apoptotic member of the Bcl-2 gene family which is involved in initiating apoptosis. BAD is a member of the BH3-only family, a subfamily of the Bcl-2 family. Dephosphorylated BAD forms a heterodimer with Bcl-2 and Bcl-xL, inactivating them and thus allowing Bax/Bak-triggered apoptosis. When BAD is phosphorylated by Akt/protein kinase B (triggered by PIP3), it forms the BAD-(14-3-3) protein heterodimer. This leaves Bcl-2 free to inhibit Bax-triggered apoptosis. BAD phosphorylation is thus anti-apoptotic, and BAD dephosphorylation (e.g., by Ca2+-stimulated Calcineurin) is pro-apoptotic. The latter may be involved in neural diseases such as schizophrenia.

Compare and contrast GRCR and RTKs (receptors).

The ability of a single ligand-binding event to trigger so many pathways is a key difference between receptor tyrosine kinases and G protein-coupled receptors. Notice that each has an extracellular ligand-binding site, an "alpha" helix spanning the membrane, and an intracellular tail containing multiple tyrosines.

Describe the role of chromosomes in assembly of the mitotic spindle.

The assembly of a mitotic spindle requires the interaction of microtubules with chromosomes. As a cell enters mitosis, long microtubules are converted to short ones, as microtubules become unstable. Dynamic microtubules are then stabilised by chromosomes, forming a bipolar spindle.

Explain why studies of yeast can lead to insights into the biology of human cancers.

The basic organization of the cycle is essentially the same in that all eukaryotes appear to use similar machinery and control mechanisms to drive and regulate cell-cycle events. The proteins of the cell-cycle control system first appeared more than a billion years ago, and they have been so well conserved over the course of evolution that many of them function perfectly when transferred from a human cell to a yeast.

How does Cholera toxin function, be precise

The catalytic portion of cholera toxin performs a single function: it seeks out the G proteins used for cellular signaling and attaches an ADP molecule to them. This converts the G-protein into a permanently active state, so it sends a never-ending signal.

Indicate how Cdk inhibitors can help regulate progression through the cell cycle.

The cell cycle uses these inhibitors to block the assembly or activity of certain cyclin-Cdk complexes. Some Cdk inhibitor proteins, for example, help maintain Cdks in an inactive state during the G1 phase of the cycle, this delaying progression into S phase. Pausing at this transition point in G1 gives the cell more time to grow, or allow it to wait until extracellular conditions are favorable for division.

Explain how the spindle assembly checkpoint ensures that all chromosomes are attached to the spindle and why this checkpoint can delay the onset of anaphase and the exit from mitosis.

The cell makes use of a negative signal: the kinetochores of unattached chromosomes send a "stop" signal to the cell-cycle control system. This signal inhibits further progress through mitosis by blocking the activation of APC/C. Without active APC/C, the sister chromatids remain glued together. Thus, none of the duplicated chromosomes can be pulled apart until every chromosome has been positioned correctly on the spindle. The absence of APC/C also prevents the destruction of cyclins, so that Cdks remain active, prolonging mitosis.

Contrast cut-and-paste and replicative transposition for DNA-only transposons.

The cut-and-paste mechanism occurs when the element is excised from the genome and inserted into a different site. Replicative transposition replicates first, and the new copy of the transposon inserts into a second chromosomal site, leaving the original intact.

Recall why different cyclin-Cdk complexes trigger different events in the cell cycle.

The cyclin that acts in G2 to trigger entry into M phase is called the M cyclin, and the active complex it forms with its Cdk is called M-Cdk. Other cyclins, called S cyclins and G1/S cyclins, bidn to a distinct Cdk protein late in G1 to form S-Cdk and G1/S-Cdk, respectively; these cyclin-Cdk complexes help launch S phase. Another group of cyclins, called G1 cyclins, act earlier in G1 and bind to other Cdk proteins to form G1-Cdks, which help drive the cell through G1 toward S phase.

Recall how dephosphorylation helps trigger the abrupt activation of cyclin-Cdk complexes.

The cyclin-Cdk complex contains inhibitory phosphates, and to become active, the Cdk must be dephosphorylated by a specific protein phosphatase. Thus protein kinases and phosphatases act together to regulate the activity of specific cyclin-Cdk complexes and help control progression through the cell cycle.

Recall why nitric oxide acts as a paracrine signal only on cells near its site of synthesis.

The distance NO diffuses is limited by its reaction with oxygen and water in the extracellular environment, which convert NO into nitrates and nitrites quickly Target cells; NO binds and activates guanylyl cyclase, stimulating formation of cyclic GMP from GTP. Cyclic GMP is a second messenger in the NO signaling chain. Viagra enhances erection by blocking the enzyme that degrades cyclic GMP, prolonging the NO signal

Describe chromatin remodeling. How does this occur and why?

The dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression.

Differentiate between the amount of the human genome that codes for proteins versus the amount that consists of mobile genetic elements.

The first striking feature of the human genome is how little of it- less than 2% codes for proteins. In addition, almost half of our DNA is made up of mobile genetic elements that have colonized our genome over evolutionary time.

Define the cleavage furrow and explain how its position is determined.

The first visible sign of cytokinesis in animal cells is a puckering and furrowing of the plasma membrane that occurs during anaphase. The furrowing invariably occurs along a plane that runs perpendicular to the long axis of the mitotic spindle. The positioning ensures that the cleavage furrow cuts between the two groups of segregated chromosomes. If the mitotic spindle is deliberately displaced as soon as the furrow appears, the furrow will disappear and a new one will develop at a site corresponding to the new spindle location.

Present evidence that supports the occurrence of whole genome duplication events.

The frog, xenopus, includes species that differ dramatically in DNA content. some are diploid, some are tetraploid or octoploid. whole genome duplication is also shown in several plants, such as sugarcane.

Review the structure of genes in the genomes of human, fly, and yeast, and compare how densely genes are distributed in the chromosomes of each organism.

The human genome is less dense with genes. The genes of a fly and yeast are more compact with fewer introns.

Describe the organization of the lac operon and how it is under negative and positive control.

The lac operon exhibits both systems. It is a negative control system because expression is typically blocked by an active repressor (the lac repressor) that turns off transcription. However, when CAP (catabolite gene activating protein) binds upstream of this operator region near the promoter and transcription increases, this is an example of a positive control system. We see this positive control of transcription happen when glucose levels decline.

Indicate which phases of the cell cycle vary the most in length to influence the rates of cell division in the adult body.

The length of S phase varies according to the total DNA that the particular cell contains; the rate of synthesis of DNA is fairly constant between cells and species. Usually, cells will take between 5 and 6 hours to complete S phase. G2 is shorter, lasting only 3 to 4 hours in most cells.

Describe the structure of the mitotic spindle and explain how and when it begins to form.

The mitotic spindle begins to form in prophase (first stage of mitosis, during which the duplicated chromosomes condense and spindle forms). The assembly of this structure depends on microtubules. As stated before, microtubules continuously polymerize and depolymerize by the addition and loss of their tubulin subunits, and individual filaments alternate between growing and shrinking (dynamic instability). At the start of mitosis, dynamic stability rises - in part because M-Cdk phosphorylates microtubule-associated proteins that influence microtubule stability.

Contrast the differences between the chimp and human genomes with those between the human and mouse genomes.

The mobile genetic elements found in mouse and human DNA, although similar in nucleotide sequence, are distributed differently, as they have had more time to proliferate and move around the two genomes after these species diverged. The large scale- organization of the human and mouse genomes have been scrambled by many episodes of chromosome breakage and recombination over the past 75 million years: it is estimated that about 180 such "break and join" events have dramatically altered chromosome organization. For example, in humans most centromeres lie near the middle of the chromosome, whereas those of mice are located at the chromosome ends.

Explain how multiple signaling pathways can integrate information to produce a coordinated cell response.

The most extensive links among the pathways are mediated by the protein kinases present in each. These kinases often phosphorylate, and hence regulate, components in other signaling pathways, in addition to components in their own pathway. Many intracellular signaling proteins have several potential phosphorylation sites, each of which can be phosphorylated by a different protein kinase. These proteins can thus act as integrating devices. Information received from different intracellular signaling pathways can converge on such proteins, which then convert a multicomponent input to a single outgoing signal. These integrating proteins, in turn, can deliver a signal to many downstream targets. In this way, the intracellular signaling system may act like a network of nerve cells in the brain—or like a collection of microprocessors in a computer— interpreting complex information and generating complex responses.

Contrast the arrested state G0 with the cell-cycle withdrawal that occurs during terminal differentiation.

The most radical decision that the cell-cycle control system can make is to withdraw the cell from the cell cycle permanently. This decision has a special importance in multicellular organisms. Many cells in the human body permanently stop dividing when they differentiate. In such terminally differentiated cells, such as nerve or muscle cells, the cell-cycle control system is dismantled completely and genes encoding the relevant cyclins and Cdks are irreversibly shut down. Other cell types withdraw from the cycle only temporarily, entering G0. They retain the ability to reassemble the cell-cycle control system quickly and to divide again.

Compare the point mutation rates of E. coli and humans and assess the significance of these relative values.

The mutation rate in humans is about 1/3 of that in E. coli, which suggests that our mechanisms ensuring genome integrity evolved at a rate similar to that of E. coli.

Summarize how and when the nuclear envelope breaks down.

The nuclear envelope disassembly begins in prometaphase. It breaks up into small membrane vesicles. This process is triggered by the phosphorylation and consequent disassembly of nuclear pore proteins and the intermediate filament proteins of the nuclear lamina, a network of fibrous proteins that underlie and stabilize the nuclear envelope

Explain how the genetic code specifies the relationship between the sequence of codons in mRNA and the amino acid sequence of a polypeptide.

The nucleotide sequence in mRNA is read in consecutive sets of three nucleotides called codons; each codon corresponds to one amino acid. The correspondence between amino acids and codons is specified by the genetic code. The possible combinations of the 4 different nucleotides in RNA give 64 different codons in the genetic code. Most amino acids are specified by more than one codon.

Evaluate how RNA sequencing can provide a more accurate estimate of the number of genes in a genome than DNA sequencing.

The number of predicted protein-coding genes has dropped because the technique detects only those genes that are actively transcribed. The approach allowed the detection of genes that do not code for proteins, but instead encode functional or regulatory RNAs

Contrast the origin recognition complex (ORC) and the prereplicative complex in terms of composition and when each assembles on the DNA.

The origin recognition complex (ORC) remains perched on the replication origins throughout the cell cycle. To prepare the DNA for replication, the ORD recruits a protein called Cdc6, whose concentration rises early in G1. Together, these proteins load the DNA helicases that will ultimately open up the double helix at the origin of replication. Once this prereplicative complex is in place, the replication origin is loaded and ready to go.

Describe how the synthesis of new DNA strands begins at an origin of replication.

The process of DNA synthesis starts by initiator proteins that bind to specific DNA sequences called replication origins. the initiator proteins pry the two DNA strands apart, breaking the hydrogen bonds between the bases. Once an initiator protein binds to DNA at a replication origin and locally opens up the double helix, it attracts a group of proteins that carry out DNA replication. These proteins form a replication machine, in which each protein carries out a specific function.

steps of gene expression

The process of gene expression includes 1) transcription, the conversion of DNA to RNA, and 2) translation, the conversion of RNA to proteins.

Name the basic components needed for an extracellular signal molecule to change the behavior of a target cell, and identify the site at which the primary step in signal transduction takes place.

The signal molecule needs a receptor protein to start the primary step of signal transduction: The receptor recognizes the extracellular signal, generates a new intracellular signal, this signal is passed downstream from one signal molecule to the next. Each transition activates or generates a the next signaling molecule in the pathway. The final response is usually a metabolic enzyme, a change in cytoskeleton confirmation, or a gene switched on or off. Intracellular signaling molecules leads to effector proteins (metabolic enzymes, cytoskeletal proteins, transcription regulators, etc) that generate the response (altered metabolism, altered shape or movement, altered gene expression, etc)

Describe how chromatin modifying proteins help regulate transcription.

The structure of chromatin (DNA and its organizing proteins) can be regulated. More open or "relaxed" chromatin makes a gene more available for transcription. Sets of transcription factor proteins bind to specific DNA sequences in or near a gene and promote or repress its transcription into an RNA.

Describe the trp operon and how it is under negative control.

The trp operon, found in E. coli bacteria, is a group of genes that encode biosynthetic enzymes for the amino acid tryptophan. The trp operon is expressed (turned "on") when tryptophan levels are low and repressed (turned "off") when they are high. Like the lac operon, the trp operon is a negative control mechanism. The trp operon responds to a repressor protein that binds to two molecules of tryptophan. When the tryptophan is plentiful, this repressor-tryptophan complex binds to the trp operator. This binding prevents the binding of RNA polymerase, so the operon is not transcribed.

Summarize how cells change in shape and attachment throughout the cell cycle.

These changes result, in part, from the reorganization of actin and myosin filaments in the cell cortex, only one aspect of which is the assembly of the contractile ring. Mammalian fibroblasts in culture, for example, spread out flat during interphase, as a result of the strong adhesive contacts they make with the surface they are growing on. The change in shape takes part because some of the plasma membrane proteins responsible for attaching the cells to the substratum become phosphorylated and thus weaken their grip.

Review the main functions of an intracellular signaling pathway and identify the steps at which each can take place.

They can relay the signal to help it spread · Amplification of signal received, makes it stronger; few molecules can evoke a large response · Detect signals from multiple intracellular signaling pathways and integrate them · Distribution of the signal to multiple effector proteins; complex response · Module the response of signal by regulating the activity of upstream components via feedback

Explain why chromosomes align at the spindle equator during metaphase, and present experimental evidence for this mechanism.

They form halfway between the two spindle poles, forming the metaphase plate. This event defines the beginning of metaphase. Both the continual growth and shrinkage of the microtubules and the action of the microtubule motor proteins are required.

Describe the type of signal transduction carried out by ion-channel-coupled receptors.

They transduce a chemical signal into an electrical signal. Neurotransmitter binds to ICCR on the target cell surface, the receptor's confirmation is altered, opening a channel on the target cell membrane for specific types of ions. Without the neurotransmitter signal bound to the receptor, the ion gated channel is closed. When open, the ions migrate based on their electrochemical gradients, from high concentration to low concentration. This changes the membrane potential (very fast, milliseconds) Membrane potential change might trigger nerve impulse or alter the ability (easier or harder) for other neurotransmitters to do so.

Detail how S-Cdk initiates replication and prevents re-replication during the same cell cycle.

This kinase phosphorylates helicase, activating it. It also promotes the assembly of proteins at the replication fork. It prevents re-replication by inactivating cdc6 or ORC.

Summarize the function of the cell-cycle control system and describe the transition points at which progression through the cycle is regulated.

This system guarantees that the events of the cell cycle- DNA replication, mitosis, and so on- occur in a set sequence and that each process has been completed before the next one begins. At the transition from G1 to S phase, the control system conforms that the environment is favorable for proliferation before committing to DNA replication. At the transition from G2 to M phase, the control system confirms that the DNA is undamaged and fully replicated, ensuring that the cell does not enter mitosis unless its DNA is intact. Finally, during mitosis, the cell-cycle control machinery ensures that the duplicated chromosomes are properly attached to a cytoskeletal machine, called the mitotic spindle, before the spindle pulls the chromosomes apart and segregates them into the two daughter cells.

Outline how a set of mutant RTKs can be used to determine which tyrosines serve as docking sites for the intracellular signaling proteins that propagate the signal.

To determine which tyrosine binds to a specific intracellular signaling protein, a series of mutant receptors is constructed. In the mutants shown, tyrosines Tyr2 or Tyr3 have been replaced, one at a time, by phenylalanine, thereby preventing phosphorylation at that site. As a result, the mutant receptors no longer bind to one of the intracellular signaling proteins. The effect on the cell's response to the signal can then be determined. It is important that the mutant receptor is tested in a cell that does not have its own normal receptors for the signal molecule.

Recall how signals transmitted by RTKs can be terminated.

To help terminate the response, the tyrosine phosphorylation's are reversed by adding tyrosine phosphatases which removes the phosphates that were added to the tyrosines of both the RTKs and other intracellular signaling proteins in response to the extracellular signal. In some cases, activated RTKs are inactivated in a more brutal way: they are dragged into the interior of the cell by endocytosis and then destroyed by digestion in lysosomes.

Outline the steps of transcription, and the role of RNA polymerase in this process.

Transcription involves four steps: Initiation-DNA unwinds and separates, and RNA polymerase binds to the leading strand. Elongation-RNA polymerase moves along the template strand, synthesising an mRNA molecule Termination-additional adenine nucleotides are added at the 3' of the RNA transcript Processing- After transcription the RNA molecule is processed in a number of ways: introns are removed and the exons are spliced together to form a mature mRNA molecule consisting of a single protein-coding sequence

Describe the three stages of translation.

Translation takes place in a four-step cycle, which is repeated over and over during the synthesis of a protein. In step 1, a charged tRNA carrying the next amino acid to be added to the polypeptide chain binds to the vacant A site on the ribosome by forming base pairs with the mRNA codon that is exposed there. Only a matching tRNA molecule can base-pair with this codon, which determines the specific amino acid added. The A and P sites are sufficiently close together that their two tRNA molecules are forced to form base pairs with codons that are contiguous, with no stray bases in-between. This positioning of the tRNAs ensures that the correct reading frame will be preserved throughout the synthesis of the protein. In step 2, the carboxyl end of the polypeptide chain (amino acid 3 in step 1) is uncoupled from the tRNA at the P site and joined by a peptide bond to the free amino group of the amino acid linked to the tRNA at the A site. This reaction is carried out by a catalytic site in the large subunit. In step 3, a shift of the large subunit relative to the small subunit moves the two bound tRNAs into the E and P sites of the large subunit. In step 4, the small subunit moves exactly three nucleotides along the mRNA molecule, bringing it back to its original position relative to the large subunit. This movement ejects the spent tRNA and resets the ribosome with an empty A site so that the next charged tRNA molecule can bind

Compare and contrast monmeric and trimeric G-proteins

Trimeric G Proteins are made up of alpha, beta and gamma subunits; trimeric G-proteins can self GTP-hydrolyse whereas in monomeric G-proteins a GAP (GTPase Activating Protein) is required as it possesses weak intrinsic GTPase activity

Outline how apoptosis is regulated and initiated by the Bcl2 family of proteins.

Two of the most important death-inducing family members are proteins called Bak and Bax. These proteins - which are activated in response to DNA damage or other insults- promote cell death by inducing the release of the electron-transport protein cytochrome c from mitochondria into the cytosol. Other members of the Bcl2 family inhibit apoptosis by preventing Bax and Bak from releasing cytochrome c.

UNIT 3 STUDY GUIDE

UNIT 3 STUDY GUIDE

Review how the binding of a signal molecule activates RTKs to trigger the assembly of an intracellular signaling complex.

Unlike GPCRs, enzyme coupled receptor proteins usually only have one transmembrane segment, which spans the lipid bilayer as a single alpha helix. Because a single alpha helix is poorly suited to transmit a conformational change across the bilayer, enzyme coupled receptors have a different strategy for transducing the extracellular signal. In many cases, the binding of an extracellular signal molecule causes two receptor molecules to come together in the plasma membrane forming a dimer. This pairing brings the two intracellular tails of the receptors together and activates their kinase domains, such that each receptor tail phosphorylates the other. In the case of RTKs, the phosphorylation's occur on specific tryosines. T-phosphorylation then triggers the assembly of transient but elaborate intracellular signaling complex on the cytosolic tails of the receptors. A new phosphorylated tyrosine serves as a docking site for a whole zoo of intracellular signaling proteins.

Describe how the nuclear envelope reassembles during telophase.

Vesicles of nuclear membrane associate with the clustered chromosomes and then fuse to re-form the nuclear envelope. During this process, the nuclear pore proteins and nuclear lamins that were phosphorylated during prometaphase are now dephosphorylated, which allows them to reassemble and rebuild the nuclear envelope and lamina.

Review how and why viruses use the host's biochemical machinery to reproduce themselves.

Viruses need a host due to their small size and inability to reproduce.

Describe how the early estimate of 100,000 human genes was derived.

Walter Gilbert estimated this number based on the average size of the few known human genes in the mid-1980s, as well as the size of the human genome.

Briefly explain the Delta-Notch cell signaling system.

When the cell-surface receptor Notch interacts with a ligand (e.g., Delta), its intracellular domain is cleaved and travels to the nucleus to regulate transcription. The Notch pathway regulates cell proliferation, cell fate, differentiation, and cell death in all metazoans.

Describe how asymmetric divisions are set up during embryonic development.

When the mitotic spindle is located centrally in the cell - the usual situation in most dividing cells - the two daughter cells will be of equal size. During embryonic development, however, there are some instances in which the dividing cell moves its mitotic spindle to an asymmetrical position, and, consequently, the furrow creates two daughter cells that differ in size. In most of these asymmetric divisions, the daughters also differ in the molecules they inherit.

Contrast the causes of necrosis and apoptosis and describe the consequences of each on nearby cells and tissues.

While apoptosis often provides beneficial effects to the organism, necrosis is almost always detrimental and can be fatal.

Give a molecular definition of the term gene.

at the molecular level, a gene is defined as an organized unit of DNA sequences that enables a segment of DNA to be transcribed into RNA, resulting in the formation of a functional product.

Describe function of the contractile ring during cytokenesis.

consists mainly of actin and myosin filaments arranged in a ring around the metaphase plate; as the ring contracts, it pulls the membrane inward, thereby dividing the cell in two

List the functions of helicase, topoisomerase, single-strand binding proteins, primase, and DNA polymerase at the replication fork.

helicase- unwinds the helix topoisomerase- prevents the DNA from becoming too tightly coiled ahead of the replication fork single-strand binding proteins- prevent the helix from re-forming primase- forms an RNA primer DNA polymerase- an enzyme that catalyzes the addition of nucleotides to the 3' end of a growing DNA strand.

Why is the transition from metaphase to anaphase so important?

if chromosomes are not lined up properly on the metaphase plate before separation, one daughter cell could receive a surplus or incomplete set of chromosomes; both situations are lethal

What two molecules does inositol phospholipid form, what enzyme catalyzes that production?

made by cleavage of a lipid molecule, present in small quantities in cytosolic leaflet of membrane bilayer. Cleavage of membrane to inositol phospholipid by phospholipase C generates 2 secondary messengers: inositol 1,4,5-triphopshate (IP3) and diacylglycerol (DAG) both important for signal relay

Compare and contrast small interfering RNA and micro RNA. Define gene duplication and divergence.

miRNA- bind to the 3'-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing. siRNA- The complex silences certain gene expression by cleaving the mRNA molecules coding the target genes. This cleavage results in mRNA fragments that are further degraded by cellular exonucleases. gene duplication-the process by which a region of DNA coding for a gene is copied. Gene duplication can occur as the result of an error in recombination or through a retrotransposition event. Duplicate genes are often immune to the selective pressure under which genes normally exist. followed by divergence is a source of new genes in genomes. Divergence literally means to go in different directions. In this context, we mean that the sequences of the gene copies are becoming different from each other because of the accumulation of mutations.

What is a phragmoplast and what is its function?

phragmoplast: structure that is formed in plant cells between two daughter nuclei during cytokinesis; made up of actin and myosin filaments functions: help in partitioning the two daughter cells during cytokinesis; helps the cell plate to fuse with the parent cell and two daughter cells separate with individual cell components

Recall why a ribosomal RNA gene was selected to construct a phylogenetic "tree of life."

rRNA is used because its genetic information has been conserved since the beginning of life.

Explain how aminoacyl-tRNA synthetases attach amino acids to tRNAs.

tRNAs act as adaptor molecules in protein synthesis. Enzymes called aminoacyl-tRNA synthetases covalently link amino acids to their appropriate tRNAs. Each tRNA contains a sequence of three nucleotides, the anticodon, which recognizes a codon in an mRNA through complementary base-pairing.

What is the difference between viruses and retroviruses?

the main difference between the two is how they replicate within a host cell. All viruses need to make messenger RNA (mRNA) to produce their proteins. Viruses do not have full instructions for producing proteins from DNA/RNA so they are dependent on the translational chemistry of the host cell. Retroviruses have an RNA genome, but not all RNA viruses are retroviruses. Retroviruses also have the enzymes, reverse transcriptase and retroviral integrase, these enzymes have the unique property of transcribing their RNA into DNA after entering a cell. The retroviral DNA can then integrate into the chromosomal DNA of the host cell where it is called a provirus.

Define epigenetics precisely

the study of heritable phenotype changes that do not involve alterations in the DNA sequence. The pattern of DNA methylation can be transmitted from one cell generation to the next, producing a form of epigenetic inheritance that helps a cell remember the state of gene expression in its parent cell. There is also evidence for a form of epigenetic inheritance based on transmitted chromatin structures.

Outline the general steps of pluripotent cell induction, and the use of the techniques for human health.

these reprogrammed cells behave much like naturally occurring ES cells, and they can be directed to generate a variety of specialized differentiated cells. This approach, initially performed using cultured fibroblasts, has been adapted to produce iPS cells from a variety of specialized cell types, including those taken from humans. Differentiated cells produced from human iPS cells are currently being used in the study or treatment of disease.

Shinya Yamanaka was awarded the Nobel Prize in Physiology or Medicine, 2012, for the discovery of induced pluripotent stem cells. Explain what these cell are and how they are produced. What cell function is manipulated?

these reprogrammed cells behave much like naturally occurring embryonic stem cells, and they can be directed to generate a variety of specialized differentiated cells. This approach, initially performed using cultured fibroblasts, has been adapted to produce iPS cells from a variety of specialized cell types, including those taken from humans. Differentiated cells produced from human iPS cells are currently being used in the study or treatment of disease. When somatic cells were reprogrammed by transferring their nuclei into oocytes or by fusion with ES cells, genome-wide transcriptional activity and DNA methylation patterns were converted from the somatic state to an embryonic state.