Bio Study Guide Exam II Chapters 11, 12, 13, 15, 16, 17
Bio Study Guide Exam II Chapters 11, 12, 13, 15, 16, 17 BIO1107
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Bio Study Guide Exam 1 Chapter 12 The Cell Cycle 1 How is bacterial cell division different from eukaryotic cell division in terms of number of chromosomes involved use of mitotic spindle bers coiling and uncoiling of chromosomes during division amount of DNA that can be handled by cell division process Bacterial cell division uses a process called binary ssion where there is only one chromosome to replicate Protein laments similar to the eukaryotic tubulin attach to the original and replicate Prokaryotic DNA is tightly coiled in a loop with smaller circular DNA molecules within called plasmids Bacterial chromosomes don t have any introns and there is no con ning nucleus that holds the DNA inside Eukaryotic cell division uses processes called mitosis somatic cells daughter cells are identical to the parent cells and meiosis gametes daughter cells have half the number of chromosomes as the parent cell genetic shuf ing occurs 2 What is chromatin What is its composition How does it behave at different stages of the cell cycle Chromatin is a combination of DNA and the protein called histone located within the nucleus of a cell Its function is to package DNA into smaller volumes to t in the cell strengthen DNA to undergo mitosis prevent DNA damage and control gene expression and DNA replication During metaphase chromatin uncoils and forms structured karyotypes 3 What are nucleosomes What is their relation to histone proteins Nucleosomes are the basic unit of DNA packaging in eukaryotes It consists of a segment of DNA wrapped around 8 histone proteins forming a chromosome 4 What events characterizes each of the following cell stages Go 61 S 62 M G0 phase or Interphase is divided into three sub phases 61 S and Gz Go phase resting phase cells that don t divide stay in this phase 0 61 phase cell grows cell conducts inventory make sure there are enough organelles ATP ADP and oxygen to undergo mitosis S phase DNA synthesis 0 G2 phase rapid cell growth protein synthesis cell size regulation 0 M phase mitosis prophase prometaphase metaphase anaphase telophase and cytokinesis 5 What events characterizes each of the following prophase metaphase anaphase telophase and cytokinesis Prophase chromatin condenses into chromosomes nuclear envelope disintegrates Metaphase cells line up in the middle of the cell pulling of opposing kinetochore microtubules occurs Anaphase chromosomes split sister chromatids move to opposite ends of the cell Telophase nuclear membrane and nucleolus reappear Cytokinesis division of the cytoplasm in plant cells Golgi vesicles fuse together to form a cell plate which eventually becomes the cell wall in animal cells Bio Study Guide Exam ll 2 cleavage furrow occurs where a ring of actin laments form in the plasma membrane 6 What are spindle bers made of At what point does the spindle assemble What is the centrosome What are kinetochores Be able to describe the stages by which a spindle assembles and chromosomes attach to it Spindle bers are made up of proteins their job is to separate chromosomes between daughter cells during division they assemble during metaphase Centrosomes are microtubule organizing centers located only in an animal cell Kinetochores are the places on sister chromatids where spindle bers attach to pull them apart 7 What is meant by centromere sister chromatid centriole homologue Centromere is the structure that joins sister chromatids Sister chromatids are the two strands in a replicated chromosome identical genetic material Centrioles are cylindrical structures that contain microtubules located inside a centrosome o A homologue is a chromosome with two sister chromatids that have the same size and shape as another homologue carry the same genes in different versions aka alleles 8 How is entry into the mitotic cycle regulated What role does each of the following play cyclins cyclindependent kinases growth factors anchorage dependence MPF factors are Mphase promoting factors MPF is a complex that consists of a cyclin and a Cdk cyclin dependent kinase Cdk phosphorylates molecules but it needs to bind to cyclin in order to work To activate MPF dephosphorylation of one of the phosphorylation sites on Cdk changes MPF s shape activating it Anchorage dependence is one of the ways that cell division can be controlled if a cell doesn t feel other cells next to them it stops growing to prevent extra growth from the original spot Cancer cells lose their anchorage dependency 9 What changes must occur in a cell in order for it to become cancerous Cell cycle checkpoints have failed and a tumor begins to form Tumor suppressing genes like the p53 oncogene are shut down from the cell cycle 10 What is the difference between a quottransformed cellquot a quotbenign tumorquot and a quotmalignant tumorquot What is metastasis Are all cancers metastatic A transformed cell has the DNA of another cell A benign tumor is a mass of noninvasive noncancerous cells A malignant tumor is an invasive cancerous cell Metastasis is the process of cancerous cells detaching from the original tumor and invading other tissue producing cells of the original tumor in different parts of the body All cancers are metastatic Chapter 13 Meios 1 Distinguish diploid and haploid numbers Which cells carry haploid sets Where are haploid cells created Bio Study Guide Exam ll 3 Diploid 2n contains two alleles of each gene one allele per homologue autosomal cells Haploid n contains one copy of a chromosome and therefore one allele of a gene gametocytes in the ovaries and testes 2 What is a karyotype What kinds of defects can be identi ed from karyotypes A karyotype is an image that shows the number and appearance of chromosomes in the nucleus of a eukaryotic cell all chromosomes are in metaphase Chromosomal diseases can be identi ed by the abnormality of a chromosome s karyotype 3 Contrast mitosis and meiosis In which process do homologous chromosomes pair What is meant by synapsis chiasmata tetrad crossing over nondisjunction Mitosis parent cells produce identical diploid daughter cells Meiosis parent cells split in two four haploid daughter cells are formed Homologous chromosomes form a tetrad or a bivalent in the prophase stage of meiosis Synapsis the pairing of two homologous chromosomes during meiosis Chiasmata formed during meiosis the structure that joins two homologous chromosomes site of crossing over genetic shuf ing between two chromosomes Nondisjunction when homologues or sister chromatids fail to separate 0 Down Syndrome extra 21 Klinefelter s XXY in males Turner s X0 in females Trisomy X XXX 4 How does prophase of mitosis differ from prophase of meiosis l of meiosis II Prophase in Mitosis nuclear envelope disappears chromatin condenses into chromosomes Prophase in Meiosis l synapsis occurs tetrad forms crossing over occurs Prophase in Meiosis ll spindle apparatus forms chromosomes move toward metaphase ll plate 5 How many different chromosome combinations could result excluding crossingover as a result of meiosis in an organism for which N1 N2 N3 N23 Formula is 2quotn Chapter 15 DNA and the Gene Synthesis and Repair 1 Explain what each of the following scientists contributed to the quotstory of DNAquot 0 Hershey amp Chase tried to determine if DNA or proteins were the hereditary material tagged DNA with P32 because DNA contains phosphorus and not sulfur tagged protein with 535 because proteins contain sulfur but not phosphorus concluded that DNA was the hereditary material Watson and Crick discovered the double helix structure of DNA 0 MeselonStahl discovered that DNA replication followed a semiconservative replication aka daughter strand would have old parent strand and one new replicated strand 2 What is a genome What role does complementary basepairing have on the genome Bio Study Guide Exam ll 4 A genome is the entirety of an organism s DNA Complimentary base pairing states that adenine always pairs with thymine and guanine always pairs with cytosine 3 Identify the role of each of the following proteins in DNA replication Origin of Replication DNA polymerase heicase DNA primase DNA ligase Okazaki fragments 0 Origin of replication sequence at which replication is initiated 0 DNA polymerase catalyzes DNA synthesis DNA builds from 5 3 because polymerase only adds nucleotides to the 3 end of a growing DNA chain 0 Helicase catalyzes the breaking f hydrogen bonds between nucleotide bases separates the two DNA strands o SSBPs single strand DNAbinding proteins prevent separated strands from snapping back together stabilizes singlestranded DNAs Topoisomerase enzyme that relieves twisting forces 0 DNA primase type of RNA polymerase that makes the RNA primer that binds to DNA template to initiate DNA replication 0 DNA ligase enzyme that connects Okazaki fragments in the lagging strand of DNA replication catalyzes the formation of a phosphodiester bond Okazaki fragments newly synthesized DNA fragments formed on the lagging template during DNA replication 4 What is meant by quotantiparallel strandsquot in DNA What restriction does this place on replication Antiparallel means that the 5 3 strand joins with the 3 5 strand to form a double stranded DNA The restriction this puts on replication is that DNA can only build in the 5 3 direction 5 Note that because the energy for adding new nucleotides to DNA comes from hydrolysis of phosphate bonds it is only possible to add new nucleotides to a DNA or RNA strand at its 3 terminus Thus all growth of nucleic acids occurs at the 3 end another way of saying this is that new DNA and RNA chains are synthesized in the 5 to 3 direction Using this fact explain what is meant by a quotlagging strandquot in DNA replication What is meant by quotleading strandquot Leading strand the strand of newly made DNA that s being synthesized towards the replication fork Lagging strand the strand that s being synthesized away from the replication fork 6 DNA polymerase also carries out proofreading and repair functions including the excision of incorrectly paired bases and reinsertion of new DNA When does this occur This occurs after the DNA is replicated it scans the DNA strands for mismatched bases 7 What are telomeres and why are they present on linear chromosomes and not circular chromosomes Telomeres are a region of repetitive nucleotide sequence at the end of a chromatid 39ITAGGG they don t code for anything It protects the chromosome from deterioration losing genes They are not present in circular chromosomes because circular chromosomes do not have an end Bio Study Guide Exam ll 5 Chapter 16 How Genes Work 1 What is gene expression Explain the onegene one enzyme hypothesis Gene expression is the process which information from a gene is used to synthesize whatever that gene codes for proteins tRNA mRNA rRNA The one gene one enzyme hypothesis states that each gene produces a single enzyme which carries out its work for it The enzyme is a step in a metabolic pathway 2 How does RNA act as an intermediary DNAmRNAprotein DNA to RNA is called transcription RNA to protein is called translation 3 How is RNA made RNA polymerase makes mRNA from DNA transcription It reads the DNA sequence and calls for free nucleotides to complement the DNA strand 4 Conceptually what is so signi cant about understanding Central Dogma in Biology Central Dogma in Biology explanation of the ow of genetic information within a biological system DNA makes RNA makes protein It is important because it helps us understand organisms at the most basic levels 5 Understand why genotypes are linked to phenotypes give examples Genotype determined by the sequence of bases in an organism s DNA Phenotype physical expression of the product of the protein produced 6 What is the genetic code The set of rules that de nes how information within DNA and mRNA sequences is translated into proteins 7 quotCodonsquot represent a series of 3 bases in DNA or RNA that specify a single amino acid quotAnticodonsquot are found on transfer RNA molecules Theoretically if there are 64 different codons how many anticodons must there be 64 anticodons bring the complementing nucleotides of a codon via tRNA 8 Note that the quotstartquot codon AUG is also the rst amino acid of a protein methionine abbreviated met Does this mean that every protein should start with met Yes 9 Note that the quotstopquot codons do not specify any amino acid but instead cause termination of protein growth What are the 3 stop codons UAA UAG UGA 10 What are the important properties of the genetic code Codons start and stop Mutations Degeneracy redundancy of the genetic code 11 Distinguish between Point Mutations and Chromosomal Mutations Point Mutations a single base change can be a silent mutation thanks to the redundancy of the genetic code can be a missense mutation translates codon into the wrong amino acid because it is a different codon sequence can be a Bio Study Guide Exam II 6 nonsense mutation prematurely inserts a stop codon into the sequence can be a frameshift mutation insertion or deletion of a single base 0 Chromosomal Mutations alters the number of chromosome copies inversion a segment of a chromosome is ipped or rejoined translocation a segment of a chromosome is attached to a different chromosome deletion segment of a chromosome is lost duplication additional copies of a segment are present Chapter 17 Transcription RNA Processing and Translation 1 Describe the various types of RNA Polymerases In prokaryotes there is one type of RNA polymerase In eukaryotes there are four RNA Polymerase I enzyme that transcribes rRNA RNA Polymerase ll catalyzes transcription of DNA RNA Polymerase Ill transcribes DNA to synthesize ribosomal rRNA RNA Polymerase IV synthesizes small interfering RNA in plants 2 What are the steps of Transcription What role does the promoter play in this process 1 Initiation a holoenzyme forms sigmaRNA polymerase sigma binds to promoter region on DNA template strand 10 box and 35 box on bacterial DNA TATA box on eukaryotic DNA 2 Elongation RNA polymerase moves along DNA template strand and synthesizes RNA in the 5 3 direction 3 Termination release of newly synthesized mRNA 3 Explain the role of transcription factors during transcription In eukaryotic cells basal transcription factors bind the polymerase to the DNA strand analogous to sigma in holoenzyme 4 Be able to explain how RNA processing works What does the end product look like For example what is a poyA tail Exons genes expressed in nal mRNA lntrons genes that do not code for anything and must be cut out of nal mature mRNA 539cap modi ed guanine nucleotide 3 phosphate groups added to the 5 end of premRNA polyA tail 100250 adenine nucleotides added to the 3 end of premRNA snRNPS small nuclear ribonucleoproteins assemble to form a splicesosome made up of snRNAs and protein complex 0 mature mRNA has 5cap polyA tail and exons only 5 Be able to describe the process of RNA translation 1 Initiation mRNA binds to small ribosomal subunit called ribosome binding site tRNA carrying Met amino acid binds to start codon large ribosomal subunit binds 2 Elongation peptide bond forms when the P and A sites are occupied E P and A active sites are entirely made up of rRNA translocationl RNA is moved to the E Bio Study Guide Exam ll 7 site tRNA containing growing peptide moves into the P site A site opens up and is exposed to new mRNA codon 3 Termination release factor comes it s a protein that recognizes a stop codon and lls the A site hydrolysis occurs between the bond that links the tRNA in the P site to the polypeptide chain freeing the polypeptide 6 Why do tRNAs have the conformationstructure that they do 0 tRNAs interpret mRNA codons to amino acids during translation 0 has a CCA sequence at the 3 end that acts as a site for amino acid attachment triplet loop on the other end that serves as the anticodon has an upside down L shape 0 aminoacyltRNA synthetase enzyme that attaches amino acids to the tRNA using ATP as energy 7 What is the signi cance of discovering that the ribosome is actually a ribozyme lts discovery showed that RNA could be both genetic material and a catalyst for chemical reactions Ribosomes are actually made up of rRNAs Small subunit holds mRNA in place during translation 0 Large subunit where peptide bond formation takes place 0 E site holds tRNA that will exit 0 P site holds tRNA with growing polypeptide chain attached 0 A site holds an aminoacyl tRNA Chapter 11 CellCell Interactions An Overview of Cell Signalind 1 Compare and contrast the extracellular layers of plant and animal cells 0 Plants rigid cell wall made of cellulose and lled with pectin hydrophilic gelatinous polysaccharide that keeps the cell wall moist serves as a medium for intercellular communication selectively permeable contains plasmodesmata pores that connect adjacent cells where plasma membrane s cytoplasm and smooth ER of the two cells connect 0 Animals no cell wall no plasmodesmata more exible because it contains coHagen 2 What roles do the following substances cellulose and collagen play in the extracellular layers Collagen most abundant protein in extracellular membrane and the human body gives structural support to cells Cellulose what cell walls in plants are composed of 3 What role does a transmembrane protein play Transmembrane proteins are proteins that go from one side of the membrane to another they function as quotloading docksquot denying or permitting the transport of certain substances across the membrane Appear as an alpha helical or a beta barrel which are only found in bacteria and chloroplasts Bio Study Guide Exam ll 8 4 What is the signi cance of quotmulticellularityquot to the study of the structure and communication of living things Multicellularity is based on physical connections between cells For example plant cells are connected together by middle lamella which is continuous with adjacent plant cell s primary cell walls There are three types of connections between animal cells 1 Tight junctions forms a watertight seal between cells preventing solutions from owing through the space between the cells usually found in tissues that for a barrier 2 Desmosomes made up of proteins that link the cytoskeleton to adjacent cells common in epithelial and muscle tissue cadherins are the adhesion proteins in desmosomes which help animal cells attach to each other 3 Gap Junctions act as channels between cells to allow water ions amino acids sugars and nucleotides to move between cells 5 Compare and contrast the roles of tight junctions and desmosomes with hormones during cellto cell communication Hormones are informationcarrying molecules secreted from a cell they circulate the body and act on target cells far from the signaling cells lipid soluble hormones can diffuse through the plasma membrane receptor located in the cytoplasm lipid insoluble hormone large or hydrophilic binds to receptor on plasma membrane Signal Reception and the Initiation of Transduction 6 What is the function of a signal receptor Receptors code for a particular hormones so they can only respond to a speci c hormone Receptors can be blocked or they can change their shape after they bind to a signaling molecule 7 State where signal receptors may be located in target cells 0 For lipid insoluble signal molecules surface of the cell membrane 0 For lipid soluble signal molecules hormones receptor is located in the cytosol Signal molecules affect transcription in the nucleus SignalTransduction Pathways converts the extracellular hormone signal to an intracellular signal original message is ampli ed 0 Receptor protein in membrane spans the membrane 0 Signal receptionsignal transductionsignal ampli cationsignal response transcription 8 List two advantages of using a multistep pathway in the transduction stage of cell SgnaHng 1 Ampli cation increasing the number of signal transductions within the cell 2 Activating second messengers to multiply the effect of the hormone s original signal Bio Study Guide Exam ll 9 9 Explain how an original signal molecule can produce a cellular response when it may not even enter the target cell Gprotein signal transduction or receptor tyrosine kinases signal molecules activate a receptor by changing its conformation receptor starts a phosphorylation cascade and travels through the cell cytoplasm second messengers may be activated to increase the effect of the signal cellular response transcription occurs 10 Describe how phosphorylation propagates signal information Phosphorylation is what activates a protein or an enzyme ex Phosphorylating the G protein activates it 11 Explain why a single cell may require hundreds of different protein kinases Enzymatic cascade occurs when a bunch of protein kinases are phosphorylated and activated 12 De ne the term 39second messenger Brie y describe the role of these molecules in signaling pathways Second messengers are small molecules that diffuse rapidly through a cell You can build a large amount of then in a short amount of time It helps to amplify the hormone signal Second messengers activate protein kinases which phosphorylates multiple kinases this process is known as signal energy transferal cascade cAMP cyclic adenosine monophosphate activates certain protein kinases calcium ions Ca2 found in skeletal muscles and brain 13 Explain how protein phosphatases turn off signaltransduction pathways Dephosphorylation makes a protein useless 14 What would be two examples of a signal response by a cell 1 Transcription 2 Target protein that already exists in the cell is activated or deactivated 15 What role does quotcrosstalk play in signal deactivation Cross talk integrates the diverse signals that a cell receives You can in uence other cells next to you or in uence yourself internally you need it to regulate your transduction pathway The product of one signal transduction pathway can inhibit another transduction pathway and affect that cellular response can stop it or increase it 16 Why would understanding Quorum Sensing in Bacteria be important within the Medical Community Quorum sensing is celltocell communication in bacteria One cell begins to omit a various chemical message and attracts other cells to it they all form a colony Their chemical behavior changes and they start becoming pathogenic The medical community can bene t from this process by preventing the spread of bacteria by disrupting the signal of quorum sensing Bio lms are protective sheets around the community of bacteria Bio Study Guide Exam 10
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