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119 Cards in this Set
- Front
- Back
What does DNA polymerase do?
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Forms phosphodiester bonds at the 3’ end of the growing chain using deoxynucleotide triphosphates (dATP, dCTP, dTTP, dGTP)
Has ability to PROOFREAD previous nucleotide and make sure it is properly basepaired before proceeding. If it is incorrectly paired it will remove the deoxynucleotide triphosphate and replace it with the correct one. |
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Is the formation of phosphodiester bonds at the 3' end of the growing DNA chain an energetically favorable process? Why?
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Yes. Due to hydrolysis of phosphate bonds.
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The error rate of DNA polymerase is:
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1:10^7 nucleotides
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DNA helicase and DNA primase make up:
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the primosome
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The primosome is made up of:
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DNA helicase and DNA primase
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This builds an RNA primer that polymerase uses to start a DNA strand:
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primase
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Primase does this:
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builds an RNA primer that polymerase uses to start a DNA strand
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Does leading strand synthesis require a primer?
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No. Primase builds an RNA primer that polymerase uses to start a DNA strand. This is unnecessary in the leading strand.
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This is a specific DNA sequence approximately 100base pairs long which is rich in adenine and thymine.
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origin of replication
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Origin of replication is:
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A specific DNA sequence approximately 100 base pairs long which is rich in adenine and thymine.
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DNA synthesis cannot begin unless:
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there is a nucleotide to attach to
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Why does replication require primase?
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DNA synthesis cannot begin unless there is a nucleotide to attach to
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What does the single strand binding protein do?
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binds to the lagging strand template to keep it from reforming dsDNA, until the polymerase can begin a new fragment.
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This binds to the lagging strand template to keep it from reforming dsDNA, until the polymerase can begin a new fragment:
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single strand binding protein
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This attaches lagging strand fragments to each other after removal of an RNA primer by a nuclease:
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ligase
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Ligase does this:
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attaches lagging strand fragments to each other after removal of an RNA primer by a nuclease
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Why is replication carried out in the 5’ → 3’ direction?
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If elongation was 3’→ 5’, there could be no PROOFREADING!
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Explain why sickle-cell anemia occurs.
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A single nucleotide is mutated in the β-globin gene. This results in the production of β-globin with a valine instead of a glutamic acid in the sixth amino acid position. This causes it to form polymers of hemoglobin which distort the shape of the cell into sickle shapes. These RBC's do not carry oxygen well and makes the person anemic.
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How does the cell repair DNA?
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mismatch-pair
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This removes replication errors that are missed by polymerase:
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mismatch-pair
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Mismatch pair does this:
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removes replication errors that are missed by polymerase.
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Mismatch repair is carried out by several proteins that scan the new DNA strand for mismatches. T/F
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T
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With mismatch-repair, mistakes are repaired prior to the next round of replication: T/F
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T
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deamination does this:
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mutates DNA by changing C to U resulting in replication making U:A
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depurination does this:
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mutates DNA by the loss of G and A. Will be lost at replication.
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UV Radiation does this:
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mutates DNA by creating Thymine dimers. Interferes with replication
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Each type DNA mutation damage is detected by a different set of enzymes that repair the problem prior to DNA replication: T/F
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T
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What is a genome?
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The entire compliment of genetic material in an organism
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How many distinct chromosomes comprise the human genome?
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24
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How many base-pairs does the human genome span?
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3 x 10^9 nucleotide-pairs
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How many chromosomes are found in a typical human cell?
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46
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How many chromosomes are found in human sperm or egg cells?
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23
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What is chromatin?
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The combination of DNA and histone proteins where the proteins compact the DNA into a coiled and linked structure like "beads on a string"
The compacted DNA structure formed by histone proteins which coil the DNA |
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What is a nucleosome?
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Consists of the DNA wrapped around a histone octamer which consists of two copies each of the core histones H2A, H2B, H3, H4. It also includes the linking DNA which connects it to the next nucleosome to makeup the "beads on a string" structure. The nucleosome has about 200 nucleotide pairs with 146 of them wrapped around the histone octamer. The size of the histone octamer with coiled DNA is 11nm.
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How many nucleotide pairs of DNA are there in a nucleosome?
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about 200
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How many nucleotide pairs of DNA are there wrapped around the histone octamer of a nucleosome?
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about 146
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What is the size of the histone octamer of a nucleosome with the coiled DNA?
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11nm
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How can nucleosomes be dissasembled for study?
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Using nucleases to digest the linker DNA strands and a high concentration of salt to dissociate the coiled DNA and the histone octamer
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Which amino acids are replete in histones? Why?
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Arginine and lysine because they are basic (+ charge). DNA has a negatively charged sugar-phosphate backbone so the basic amino acids attract to it.
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What causes the nucleosome structure to dissociate so that the cell can access the DNA for replication, transcription, etc.? How?
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Histone proteins. They have a long N-terminal amino acid tail which extends out from the DNA-histone core. They are subject to several types of covalent modification that control many aspects of chromatin structure.
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Describe the steps to complete replication.
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Open the DNA
Recruit Proteins Prime DNA Synthesis (PRIMASE) Synthesize DNA (POLYMERASE) Proofread Connect Fragments (LIGASE) |
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Copying of ONE stand of DNA into a complementary strand of RNA:
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transcription
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Describe transcription:
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copying of ONE stand of DNA into a complementary strand of RNA
Done by RNA Polymerase. Energy from nucleoside triphosphates |
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List the Similarities Between Replication and Transcription
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carried out by several enzymes including a POLYMERASE
produces a linear polymer of nucleotides connected by phosphodiester bonds. synthesis is 5’ → 3’ Uses 4 distinct nucleotides: A, U, C, and G |
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List the Differences Between Replication and Transcription
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Nucleotides used are ribonucleotides
Uracil instead of thymine RNA is SINGLE STRANDED Strands of RNA can self-pair RNA itself can function as an enzyme |
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RNA that is TRANSLATED into protein
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mRNA
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Describe mRNA
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RNA that is TRANSLATED into protein
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Describe rRNA
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makes up ribosomes, used for TRANSLATION
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RNA that makes up ribosomes, used for TRANSLATION:
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rRNA - Ribosomal RNA
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RNA that carries amino acids for TRANSLATION:
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tRNA - Transfer RNA
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RNA used for Splicing, transport etc.
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snRNA - Small nuclear RNA
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Describe tRNA
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RNA that carries amino acids for TRANSLATION:
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Describe snRNA
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RNA used for Splicing, transport etc.
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Each type of RNA is synthesized by a distinct RNA Polymerase: T/F
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T
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Each type of RNA is synthesized by:
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a distinct RNA polymerase
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How does the RNA polymerase know where to start and stop transcription of a gene?
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RNA polymerase binds weakly to the DNA strand and slides along it until it finds the promoter region which contains a sequence of nucleotides indicating the starting point for RNA synthesis. Once it reaches the terminator site it will stop and release both the DNA template and the newly made RNA chain.
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How does the RNA polymerase know in which direction to go?
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The promoter indicates the DIRECTION that transcription will proceed because the sequence is asymmetrical.
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Describe promoter
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Sequence of DNA that specifies where transcription will start
indicates the DIRECTION that transcription will proceed because the sequence is asymmetrical. also supplies CONTROL to the process |
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Describe terminator
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Sequence of DNA that specified where transcription will stop
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Why is direction of transcription important?
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During transcription, only ONE strand of DNA is copied.
Once bound to DNA, the polymerase could move either LEFT or RIGHT. Only ONE direction will produce the correct RNA! |
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Describe the transcription process in prokaryotes.
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RNA polymerase finds a DNA strand and binds weakly. It slides down the strand until it finds the promoter and it begins transcribing at the start site of the gene. After about 10 nucleotides the sigma factor comes out of RNA polymerase so that it can continue transcribing. When the RNA polymerase reaches the end of the gene, the terminator stop site, it breaks its bond with the DNA, releasing itself and the newly made RNA strand, then rebonds with the sigma factor.
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Genes can exist anywhere on the DNA strand and can run in opposite directions: T/F
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T
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Bacterial and eukaryotic organisms use essentially the same RNA polymerase for transcription: T/F
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T
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Bacterial and eukaryotic organisms use different enzymes for transcription: T/F
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F
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RNA polymerase and an associated SIGMA FACTOR (protein) slide along the DNA until association at the START SITE. This occurs in:
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prokaryotes
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Transcription in these require Appropriate DNA structure and a binding of specific proteins within the promoter and at other DNA sites.
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eukaryotes
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eukaryotic transcription requires:
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Appropriate DNA structure and a binding of specific proteins within the promoter and at other DNA sites.
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prokaryotic transcription requires:
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RNA polymerase and an associated SIGMA FACTOR (protein) slide along the DNA until association at the START SITE.
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Once a eukaryotic mRNA is synthesized in the nucleus it must be:
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processed
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Once a eukaryotic mRNA is synthesized in the nucleus it must be PROCESSED: T/F
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T
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These are types of processing a eukaryotic mRNA can undergo:
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Capping
Poly-adenylation Splicing |
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Describe Capping:
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Addition of a methyl guanine nucleotide to the 5’ end of the mRNA.
FOR: export from the nucleus and stability. |
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Bacterial mRNAs can contain the instructions for several different proteins whereas eukaryotic mRNA nearly always contains the information for only a single protein: T/F
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T
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Bacterial mRNAs can contain the instructions for only a single protein whereas eukaryotic mRNA contains the information for several different proteins: T/F
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F
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Describe polyadenylation:
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Addition of adenine residues to the 3’ end of the mRNA: poly-A tail.
Usually a few hundred A’s. FOR: export, stability, identification of the transcript as an mRNA. |
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Prokaryotic mRNA must undergo processing before it can be used to translate proteins: T/F
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F
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Describe splicing:
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The REMOVAL of specific mRNA sequences (introns - the non-coding regions)
Carried out by specialized enzymes - small ribonucleoprotein particles (snRNPs) - that recognize “splice signals” in the mRNA sequence. |
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These are marked by specific sequences that are recognized by splicing machinery.
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intron-exon junctions
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What is a spliceosome made up of?
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proteins and snRNAs
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Intron-exon junctions are marked by specific sequences that are recognized by splicing machinery: T/F
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T
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How do snRNAs recognize introns?
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through complementary base pairing
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What does the spliceosome do?
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Recognizes the splicing signals on a pre-mRNA molecule, brings the two ends of the intron together and provides the enzymatic activity for the two reactions necessary to complete the splicing (removal of the intron and joining of the two remaining exons)
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What is the significance of introns?
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make genetic recombination more likely
alternative splicing |
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What is the relationship between exons and protein domains?
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Exons generally specify DOMAINS
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This can produce several different mRNAs from a single gene:
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splicing
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All exons will not be used to build the final mRNA: T/F
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T
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All exons will be used to build the final mRNA: T/F
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F
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This produces several different proteins from the same gene:
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splicing
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Splicing produces several different proteins from the same gene: T/F
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T
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Splicing produces one protein from each gene: T/F
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F
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Multiple transcripts can be produced simultaneously from a gene: T/F
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T
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One transcript at a time can be produced from a gene: T/F
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F
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Describe transcription:
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regions of the DNA (genes) are transcribed into ss RNA
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What is the genetic code?
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The rules specifying the correspondence between nucleotide triplets (codons) in DNA or RNA and amino acids in protein
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The sequence of nucleotides in an mRNA is read how?
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consecutively in groups of three
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Describe codon:
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Each triplet sequence that encodes an amino acid
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Describe anti-codon
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The sequence within the t-RNA that recognizes the CODON
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mRNA is read in this direction:
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5’→ 3’
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In translation this usually specifies the start of the reading frame:
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AUG
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Describe the open reading frame (ORF)
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The sequence of nucleotides that specify a specific protein
Each mRNA has the potential to be “read” in three distinct frames |
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How does the translation machinery know where to start?
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Use a Specific Sequence To
Start All Proteins AUG - methionine |
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What components are needed
for translation? |
tRNA
amino acids ribosome |
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Describe tRNA
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~ 80 nucleotide RNA
contains an anticodon that base-pairs with mRNA “charged” with a specific amino acid a high energy bond between a.a. and tRNA! |
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61 codons encode amino acids, but humans have only 48 different tRNAs. What makes this possible?
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tRNA's recognize more than 1 codon
‘wobble’ base-paring can occur in 3rd codon position |
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What joins an amino acid to tRNA? How?
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Aminoacyl tRNA synthetase
covalently attaches an amino acid to a specific tRNA, by ATP hydrolysis. The high energy bond between the amino acid and tRNA will drive protein synthesis! |
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Where does the energy come from to power protein synthesis?
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The high energy bond between the amino acid and tRNA will drive protein synthesis!
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Describe ribosomes:
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provide the machinery that allows for protein synthesis
Large Subunit 3 rRNAs 49 proteins Small Subunit 1 rRNA 33 proteins Each subunit is constructed in the nucleus. |
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What are the ribosome's tasks?
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Find RNA and know WHERE to start
Associate with tRNA 1 Associate with tRNA 2 Form peptide bond Release the ‘uncharged’ tRNA Cycle along, maintaining FRAME Know where to stop Do all this at 2 peptide bonds/sec! |
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List the ribosomal binding sites:
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RNA binding site
3 tRNA binding sites: A = amino acyl tRNA-binding P = peptidyl tRNA-binding E = exit |
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How does the Ribosome know where to begin translation?
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Initiator tRNA - Special tRNA that Associates with AUG. Carries methionine.
Binds to small subunit along with other initiator proteins BEFORE it associates with RNA. |
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Describe initiator tRNA:
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Special tRNA
Associates with AUG Carries methionine |
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Why is the place where the ribosome begins translation so critical?
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Specifies correct reading frame.
Last point at which the cell can decide to go through with translation. Speed of initiation of translation determines speed of generation of protein. |
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What is the difference between eukaryotic and prokaryotic translation? What does this mean?
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Eukaryotes: 1mRNA = 1 open reading frame. Therefore each mRNA species encodes for one protein.
Prokaryotes: 1mRNA = >1 open reading frame. Therefore each mRNA can encode for several proteins. |
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How does the ribosome know when to stop?
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STOP CODONS:
UAA, UGA, UAG A release factor binds in the A site and the whole complex will be released. |
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Each mRNA will be translated by multiple ribosomes: T/F
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T
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Each mRNA will be translated by multiple ribosomes: Polyribosomes. This means that:
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1 mRNA will lead to the synthesis of many identical peptides.
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1 mRNA will lead to the synthesis of many identical peptides. This is because:
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Each mRNA will be translated by multiple ribosomes: Polyribosomes.
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How is translation controlled?
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Very complicated, but consider that every aspect is REGULATED at some level.
mRNA is broken down Protein is broken down Transcription is turned on and off |
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This sequence of DNA is from the middle of a gene and was used as a template to make mRNA:
5’- T T A C G C G G A T A T C C C - 3’ 1) What is the sequence of the mRNA? 2) What are the amino acid sequences coded? |
5’- G G G A U A U C C G C G U A A - 3’
GISA GYPR DIRV |