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112 Cards in this Set
- Front
- Back
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colinearity
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crick proposed that genes and proteins are co linear, direct correspondence between the nucleotide sequence of DNA and amino acid sequence of a protein- says the number of nucs in a DNA is proportional to the number of aminos in the protein not a correct thinking
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exon/ intron
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exon: coding regions, intron: noncoding regions- both are initially transcribed to the RNA but after transcription, the intron are removed by splicing
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group 1 intron, group 2 intron, nuclear pre-mRNA intron, transfer RNA intron
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group 1 introns: found in rRNA genes, self splicing
group 2 introns: present in some protein-encoding genes of mitochondria, chloroplasts, self-splicing nuclear pre-mRNA intron: located in protein-encoding genes in eukaryotes, not self splicing but uses snRNAs transfer RNA intron: found in tRNA genes, relies in enzymed to cut and reseal RNA |
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codon
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found in mature mRNA, each amino acid in a protein is specified by a set of three nucleotides called a codon
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5 prime UTR
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chain of noncoding at 5 prime end, in bacterial mRNA it has a sequence called the shine-dalgarno sequence
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shine-dalgarno sequence
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in bacterial mRNA of the 5 prime UTR and serves as a ribosomal-binding site during translation, +7 from first translated codon
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protein-coding region
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mRNA comprised of codons that specify the amino acid sequence of the protein,
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3 prime UTR
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last region of MRNA, called a trailer, affects stability of mRNA and the translation of the mRNA protein-coding sequence
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5 prime cap
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is a posttranscriptional modification to eukaryotic pre-mRNA, it facilitates binding of ribosomes to 5 prime end, increases stability, enhances RNA splicing
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poly (A) tail
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increases stability of mRNA, facilitates binding of ribosome to mRNA, is a posttranscriptional modification to eukaryotic pre-mRNA
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colinearity
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crick proposed that genes and proteins are co linear, direct correspondence between the nucleotide sequence of DNA and amino acid sequence of a protein- says the number of nucs in a DNA is proportional to the number of aminos in the protein not a correct thinking
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exon/ intron
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exon: coding regions, intron: noncoding regions- both are initially transcribed to the RNA but after transcription, the intron are removed by splicing
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group 1 intron, group 2 intron, nuclear pre-mRNA intron, transfer RNA intron
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group 1 introns: found in rRNA genes, self splicing
group 2 introns: present in some protein-encoding genes of mitochondria, chloroplasts, self-splicing nuclear pre-mRNA intron: located in protein-encoding genes in eukaryotes, not self splicing but uses snRNAs transfer RNA intron: found in tRNA genes, relies in enzymed to cut and reseal RNA |
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codon
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found in mature mRNA, each amino acid in a protein is specified by a set of three nucleotides called a codon
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5 prime UTR
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chain of noncoding at 5 prime end, in bacterial mRNA it has a sequence called the shine-dalgarno sequence
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shine-dalgarno sequence
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in bacterial mRNA of the 5 prime UTR and serves as a ribosomal-binding site during translation, +7 from first translated codon
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protein-coding region
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mRNA comprised of codons that specify the amino acid sequence of the protein,
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3 prime UTR
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last region of MRNA, called a trailer, affects stability of mRNA and the translation of the mRNA protein-coding sequence
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5 prime cap
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is a posttranscriptional modification to eukaryotic pre-mRNA, it facilitates binding of ribosomes to 5 prime end, increases stability, enhances RNA splicing
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poly (A) tail
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increases stability of mRNA, facilitates binding of ribosome to mRNA, is a posttranscriptional modification to eukaryotic pre-mRNA
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What are the four modifications of posttranscriptional eukaryotic pre-mRNA?
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1. addition of 5 prime cap
2. 3 prime cleavage and addition of poly (A) tail 3. RNA splicing 4. RNA editing: alters nucleotide sequence of mRNA |
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RNA splicing:
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removes noncoding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced through alternative splicing
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5 prime splice site, 3 prime splice site:
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sites at either end of the intron that indicate moving out, GU and end with AG
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branch point:
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adenine nucleotide that lies from 18 to 40 nucleotides upstream of the 3 prime splice site, this is where the cut 5 prime end attaches to form a lariat
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spliceosome:
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5 RNA molecules that cuts introns out
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lariat:
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after the intron is cut at the 5 prime site, it attaches to the branch point and forms a loop called a lariat, which G-A
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tran-splicing:
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binding together sequences from two different RNA molecules to make an mRNA
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alternative processing pathway:
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to get different proteins, the pre-mRNA must be processed in a different way than the mRNA usually is
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alternative splicing:
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same pre-mRNA is spliced differently to yield multiple mRNAs that are translated into different amino acid sequences and therefore different proteins.
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multiple 3 prime cleavage site:
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another alternative processing pathway where there are two or more options on where a cell can cleave at the 3 prime end to add a poly (A) tail, it could make it long or short
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guide RNA:
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contains sequences that are partly complementary to segments of the preedited RNA so then they base pair and fix
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modified base:
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in tRNA where ribothymine and pseudouridine show up as bases in addition ot the other four
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tRNA-modifying enzyme:
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these are the enzymes that change the bases to make them the weird modified ones, addition of a methyl group can do this
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cloverleaf structure:
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structure of tRNA where there are some complementary and some hydrogen bonded, this makes four arms that are acceptor arm (prime ends), t delta c arm (bases), anticodon arm and DHU arm (modified bases).
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anticodon:
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one of the arms on the cloverleaf tRNA which pairs with the corresponding codon on the mRNA to ensure that the amino acids link in the correct order
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large ribosomal subunit: small ribosomal subunit:
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RNA plus proteins
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RNA interference:
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used by eukaryotes to limit the invasion of foreign genes and to censor the expression of its own genes
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RNA-induced silencing complex:
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made of siRNA and miRNA which keep a faulty base pair from translating
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Do ribosomes carry genetic information?
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no, ecoli grown with heavy, transferred light, babies were heavy
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Can an extract from dead bacterial cells genetically transform living cells?
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Griffiths experiment days yes, where heat killed virulent bacteria genetically transformed the the type two r bacteria into live, virulent type 3s bacteria
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What is the chemical nature of the transforming substance?
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Avery says that it is DNA because he put the bacteria into a filtrate and destroyed RNA, protein and then DNA, only the only with DNA killed did not transform
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What did Hershey and Chase discover?
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that DNA- not protein- is the genetic material for the transforming phage to progeny
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Whats the genetic material for TMV?
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RNA as found by Singer and the tobacco
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Which are purines and which are pyramidine?
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purine: A and G
pyradines: C T U both nitrogenous bases, pair with a deoxyribose or ribose sugar and you get a nucleoside, add a phosphate group and you get a nucleotide |
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What are the different secondary structures of DNA?
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A, B, Z
a=lots of water, right hand b= less water, right hand, wider z= left hand, backbone zig-zags |
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hairpin:
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secondary structure that happens when a sequence of nucleotides on the same strand are inverted complements
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how can the DNA be modified?
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DNA methylation: when methyl groups are added to the bases, pro and eukaryotic can be methylated, related to gene expression.
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What is semiconservative replication?
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-origional nucleotide strands remain intact but may not be combined int eh same molecule, not conservative or dispersive replication
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What were Meselson and Stahl's Experiment?
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they found how to separate the old DNA from the new DA using isotopes of nitrogen and a centrifuge.
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replicons, replication origin:
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individual units of replication, start point
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What are the three types of replication and explain them:
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1. theta: start origin, have replication bubble unwind and are eventually connected and must break, if two forks, called bidirectional replication
2. rolling-circle replication:viruses break of nucleotide strand and uses inner strand that is unbroken as a template 3. linear eukaryotic replication: replicated at many origins, bubble and then spreads until there is one long stretch and then fusion |
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Three requirements for replication:
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1. template consisting of single-stranded DNA
2. raw materials to assemble a new nucleotide strand 3. enzymes and other proteins read the template and assemble the substrate into DNA (the raw materials that new dna is synthesized from is deoxyribonucleoside triphosphates dNTPs) |
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DNA Polymerases:
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enzymes that synthesize DNA add nucleotides to the 3 prime end and allow new DNA strands to elongate int he same 5 to 3 prime direction
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leading strand = continuous replication
lagging strand = discontinuous replication |
true, okazaki fragments are on the discontinuous strand
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What are the four major steps of replication?
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1. initiation:initiator protein causes a short section of DNA to unwind, allows helicase and other ssbproteins to bind
2. unwinding: DNA helicase breaks hydrogen bonds in bases (binds to lagging and moves 5 to 3), can not initiate, but once the initiator protein gets it going its good to go, SSB's keep it open, DNA gyrase keeps the recoil from building up 3. elongation: enzymes use single strand as an enzyme to synthesize DNA, primers are made where the primase synthesized a short strech of nucleotides or primers, then RNA can get a move on, primer on 5 prime of leading strand, DNA polymerase comes in and adds, type iii is the workhorse, it can move 3-5 to correct errors, poly 1 removes RNA primer and ligase seals lagging 4. termination: proofreading by polymerase |
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What are the 7 similarities of all DNA polymerizes:
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1. synthesize any sequence by template strand
2. synthesizes in 5 to 3 by adding to the 3 prime oh group 3. use dNTP to synthesize new DNA 4. require a primer to begin 5. catalyze phosphodiester by joining 5 prime and 3 oh and cleaves off two phosphates 6. new strands are anti parallel 7. associated with other proteins |
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In elongation, what are the five basic components:
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1. helicase to unwind the DNA
2. ssb proteins protect 3. gyrase removes strain 4. primase synthesize primers with 3 prime OH 5. DNA polymearase synthesize leading and lagging strand |
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When/ how is DNA replication terminated?
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when two or more replication forks meet, some have a specific termination sequence,
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What happens when a mistake is made?
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The 3 prime OH group is not in the right spot to add more on and there is a pause in the DNA polymerase, then the 3 to 5 exonuclease activity of the DNA removes the incorrect pair and puts a new one on, or in mismatch repair, the errors are corrected after the replication is complete.
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explain the roles of dNTP:
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dNTPs are the synthesizer of new DNA, there is polymerization of DNA, two phosphate groups are cleaved from a dNTP and the resulting nucleotide is added to the 3 prime OH group of the growing nucleotide strand
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What are ARS?
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autonomously replicating sequences, they are attached to circular pieces of DNA- plasmids, and cause them to replicate on their own
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How does the eukaryotic cell keep the genome from being half or doubly replicated before the entire thing gets replicated?
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the origins must be licensed by the replication licensing factor which attaches to the origin
in eukaryotes: MCM |
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What does DNA alpha do?
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primase activity and initiates nuclear DNA synthesis by synthesizing an RNA primer followed by a short string of DNA nucleotides
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What does DNA polymerase beta do?
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completes replication on the lagging strand
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DNA polymearse E
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takes part in replication of nuclear DNA, replicated leading strand?
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The creation of new nucleosomes requires what three steps?
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1. disruption of original nucleosome on parental DNA ahead of replication fork
2. redistribution of preexisting histones on new DNA 3. addition of newly synthesized histones |
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What happens to histones in eukaryotic DNA replication?
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after DNA replication, the new reassembled octamers are a random mixture of old and new histones
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What does telomerase do?
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It extends the DNA, filling in the gap due to the removal of the RNA primer
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Holliday Junction:
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its a heteroduplex recombination where DNA homologous chromosomes break and migrate to another, they break and migrate and then branch and break, depending on where they break, they can have noncrossover or crossover recombinant DNA
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What does gene sequencing do?
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determines sequence of bases, reads about gene structure and function, sanger did this, ddNTP nucleotide is used as a substrate, they lack the oh 3 prime group a dNTP does they terminate
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When sequencing DNA, what goes in the tube with the DNA copies that you are targeting?
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1. copies of a primer thats complementary to one end of the target
2. all dNTP, the normal precursors of DNA synthesis 3. ddNTP, which terminates as soon as it chins 4. polymerase -then colored dye, gel electrophoresis, and using a wavelength, base pairs are read |
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Life: two things necessary
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1. store and faithfully transmit genetic information during reproduction
2. ability to catalyze the chemical transformations that drive life processes |
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Ribosomes:
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catalytic RNA molecules that cut out parts of thier own sequence, connect RNA molecules and replicate and catalyze formation of peptide bonds between amino acids
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Differences in RNA and DNA:
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1. deoxyribose sugars vs ribose sugars
2. free hydroxyl group on the 2 prime carbon on ribose so that makes it rapidly decay with alkaline conditions 3. RNA is less stable 4. Thymine is replace by uracil in RNA 5. RNA is single strand, DNA double (usually) |
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Three types and functions of RNA:
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1. Ribosomal RNA- make up site of protein assembly
2. Messenger RNA- carries coding instructions for polypeptide chains from DNA to ribosome (leaves nucleus after modification) 3. Transfer RNA- link between coding sequence and amino acid sequence of a polypeptide chain |
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Name some of the small RNAs:
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snRNA- processing m RNA
snoRNA- processing r RNA scRNA- cytoplasm microRNA/siRNA- RNA interference,trigger degradation or stop translation piRNA-sperm |
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What three components does transcription require?
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1. DNA template
2. raw materials (substrate) to build a new RNA molecule 3. transcription apparatus, proteins necessary to catalyze the synthesis of RNA |
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Christmas Tree Miller's diagram, it goes from ____ t ______ of the tree
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top to bottom
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Transcription unit:
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its a stretch of DNA that encodes for an RNA molecule and the sequences necessary for its transcription
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Three critical regions for RNA transcription:
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1. promoter
2. RNA-coding region 3. Terminator- it is copied into RNA |
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if it goes
5'____________3' '3____________5' promoter RNA Coding Terminator how is the RNA transcript and where is upstream and downstream? |
5'_________3'
<- upstream downstream-> apparatus moves downstream |
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What is the overall chemical equation for the growing RNA molecule?
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RNA+rNTP->RNA(n+1) + PPi
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bacterial RNA polymerase has the sigma factor, what is this?
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controls the binding of RNA polymerase to the promoter, with out it there would be transcription starting at any random point. when associated with the core enzyme, it forms a holoenzyme. btw, bacterial transcription only has one polymerase
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Describe what each of the RNA polymerases for eukaryotic RNA do:
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1. RNA polymerase I: transcribes rRNA
2. RNA polymerase II: transcribes pre-mRNA, snoRNA and miRNA and some snRNA 3. RNA polymerase III: transcribes other small RNA molecules, tRNA etc. |
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What are the three steps of bacterial transcription?
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1. initiation: transcription apparatus assembles on promoter and begins synthesis of RNA
2. elongation: DNA threads through polymerase, unwinding DNA and adding new nucleotides to the 3' end of the growing RNA strand 3. termination- recognition of end of unit and separation of RNA from DNA template |
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Initiation of bacterial transcription:
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1. promoter recognition
2. formation of transcription bubble 3. creation of first bonds between rNTP 4. escape of transcription apparatus from promoter |
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In what organism in what function is the -10 consensus sequence, pribnow box TATAAT
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in bacterial promoters to indicate the start of transcription
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Name several things that could be in the promoter of the bacteria transcription template strand of DNA:
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1. TTGACA -35 consensus sequence
2.TATAAT -10 consensus sequence 3. upstream element, A-T pairs -some stimulate transcription and others slow it |
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Name two ways that transcription may terminate; prokaryotic
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1. rho-dependent terminators: DNA sequence produces a pause in transcription, DNA sequence encodes a stretch of RNA upstream from the terminator devoid of secondar
2. rho-independent terminator structures, this is a binding site for the rho protein, when RNA polymerase encounters terminator, pauses and the rho catches up rho-independent: have inverted repeats, hairpin, then seven to nine adenine come and that weak bonds between A and U cause a break off |
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What are the differences between eukaryotic transcription and prokaryotic?
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they have three different RNA polymerases, histone proteins, has core promoter (TATA box)
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Core promoter in euk and regulatory promoter?
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Core: where basal transcription apparatus binds, TATA box
Regulatory promoter: upstream of core promoter, bind to enhancers, |
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How does eukaryotic transcription stop?
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Rat1 binds to the 5' end of the RNA and is an exonuclease, it can degrade, it chews up RNA and cuts it off
1. transcribes past coding sequence 2. cleaves on 3' end of RNA 3. Rat1 exonuclease attaches to trailing end and chew up to end |
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Transcription in Archaea is more _________ to transcription in eukaryotes than to transcription in eubacteria
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similar
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Early life used ____ as both the carrier of genetic information and as biological catalysts
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RNA
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How is initiation in eukaryotes different?
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there must be modification of chromatin structure with histones in the euk.
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Describe what MicroRNA and Small interfering RNA's do differently:
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MicroRNA have an inverted repeat, they fold, they have a dicer come in and break it up, a protein come in and RISC clouds over the imperfection to inhibit translation. The small interfering RNAs just dice up double stranded RNA, a protein comes in and takes a chop, it degrades the mRNA that is imperfect
=they have RNA-induced silencing complex |
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one gene, one enzyme hypothesis:
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genes function by encoding enzymes and each gene encodes a separate enzyme, then modified to be the one gene, one polypeptide hypothesis
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What is a protein?
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its a polymer consisting of amino acids linked by peptide bonds, the amino acid sequence of a protein is its primary structure, it fold to create secondary and tertiary structures according to the instructions given by the genes that make up the primary code
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How was the genetic code cracked?
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1. logic
2. homopolymer testing 3. random copolymers, ratios |
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degenerate code:
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means that there are many codes that will code for one amino acid, codons that code for the same amino acid are said to be synonymous; wobble position allows this (isoaccepting tRNA)
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true or false: there is a nonoverlapping and specific reading frame, the frame is set by the initiation codon
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true
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what are the three stop codons?
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UAA, UAG, UGA, called stop codons, termination codons, nonsense codons
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what is mean to have the genetic code be universal?
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when each codon specifies the same amino acid in all organisms
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What are the four stages that protein synthesis can be divided into?
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1. tRNA charging, tRNA bind to amino acids
2. initiation, components necessary for translation are assembled at ribosome 3. elongation, amino acids are joined to growing chain 4. termination, protein synthesis halts at termination codon and translation components are released from ribosome |
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what is tRNA charging? (requires energy)
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attachment of tRNA to its appropriate amino acid (uses aminoacyl-tRNA synthetases)
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Gene Regulation:
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the mechanisms and systems that control the expression of genes
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How is gene regulation different in eukaryotic organisms and in bacterial organisms?
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In eukaryotic, gene regulation brings about cellular differentiation. In bacteria, gene regulation maintains internal flexibility, turning genes on and off in response to the environment.
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Whats the difference between structural genes and regulatory genes?
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Strucutral genes encode proteins that are used in metabolism or play a role in structure. Regulatory genes and their products, RNA or proteins, interact with other DNA sequences to change transcription or translation of those sequences. (some structural genes are constitutive, and are not regulated)
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Domains:
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60-90 amino acids that are responsible for binding to DNA
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Operon:
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a group of bacterial structure genes that are transcribed together, it regulates the expression of the structural genes by controlling transcription- a regulator gene makes a regulator protein and binds to a region of the operon called the operator to affect whether transcription can take place (regulator gene is not part of the operon)
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What are the three steps of elongation in the eukaryotic translation?
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1. charged tRNA enters the A site
2. peptide bond is created between amino acids in the A and P sites 3. ribosome translocates to the next codon needs GTP |
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Termination of the eukaryotic translation:
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not tRNA enters site, but proteins called release factors bind to ribosome, this makes the release of the polypeptide from the last tRNA, of this tRNA from the ribosome, and of the mRNA from the ribosome.
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