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DNA and Protein Synthesis

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icer215's version from 2016-08-24 04:33

Section 1

Question Answer
DNAis two strands in opposite directions next to each other (due to hydrogen bonds), twisted into a double helix. deoxyribonucleic acid
DNA codesfor the living material that will be built, it regulates living cells, programs death of other cells, turns genes on or off, carries traits through generations, results in survival of the species through evolution.
Double-Helix Structure The sugar is the 3' carbon and the phosphate is the 5' carbon.
RNA and DNA polymeraseread from the 3' end and made from the 5' end.
The double-helix can unzip like a zipper then be copied from the 3' side.
Transmission of genetic informationComplementary base pairing property allows for DNA replication. RNA is created via a process called transcription. RNA strands are translated into amino acids
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DNA has Purinesadenine and guanine
DNA has Pyrimidinesthymine and cytosine
Deoxyriboseis a 5 carbon sugar
Phosphateon the 5' covalently bonds with sugar on the 3'
Adenine & Thymine2 hydrogen bond
Guanine & Cytosine3 hydrogen bonds
polypeptide with a net positive charge at physiologic pH most likely has a basic R group.
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Nucleic acidsare crucial for all living organisms. Two types of nucleic acids are DNA and RNA, which are made up of nucleotides. Genetic information is transferred using nucleic acids.
NucleosidesSugar + base (= glycosylamines), Examples include cytidine, uridine, adenosine, guanosine, thymidine and inosine, Made in the liver from consumed food (contains nucleic acids), Used as antiviral and anticancer agents, Can be phosphorylated to produce nucleotides
Nucleotidesthe monomers of nucleic acids. Includes cytosine, thymine (found in DNA), adenine, guanine and uracil (found in RNA). Made up of a five-carbon sugar, a nitrogenous base and a phosphate group.Building blocks of nucleic acids. Data storage: DNA/RNA. Energy currency: ATP. Cellular communication: cAMP. Co-enzyme catalysis
Sugar phosphate backboneComposed of alternating sugar and phosphate groups
The sugar base of one nucleotideis linked with an adjacent nucleotide’s phosphate group by ester bonds. The sugar is at the 3’ end and The phosphate at the 5’ end
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DNA is not justan arrangement of nucleotides spiraling around each other. DNA holds all of our genetic information.
Segments of DNAthat influence certain traits or characteristics are known as genes. These genes provide information on the type of proteins that our body should produce. The actions of these proteins shape the organism physically.
DNA contains the blueprintfor for an organism, and is therefore capable of transmitting genetic information.
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Section 2

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Function in Transmission of Genetic InformationDNA is a code for production of tissue (proteins) and control of cells and genes.
Function in Transmission of Genetic InformationDNA is the basis for all genetic information, as it's order of base pairs is the blueprint for all structures built by the body and all control of use of genes as well.
DNA ReplicationDNA unzips itself, the 3' gets new nucleotides bonded to it one at a time. 5' is written first.
EukaryotesDNA polymerase alpha/delta (lagging/leading).
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Prokaryotes DNA polymerase III
DNA Strands SeparateDNA gyrase, Helicase, Single-Stand Binding Protein
DNA gyrase (class II topoisomerase) uncoils DNA ahead of the replication fork
Helicaseis responcible for unwinding DNA at the replication fork
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Single-Stand Binding Protein stabilizes single-strand DNA by binding to it
DNA Gets Primed Primase & DNA Polymerase
The primary structure of a protein is least likely to be affected by changes in pH. the amino acid sequence of a protein plus the peptide bonds joining them together.
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Section 3

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Primaseputs an RNA primer onto the DNA
DNA Polymerasestarts making DNA complementary to the unwound DNA (AT-GC)
RNA Primers ReplacedDNA Repair Complex & DNA Ligase
DNA Repair Complex with DNA Polymerase I Replaces the RNA Primer (leading)
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DNA Ligaseconnects Okazaki fragments (lagging)
Semiconservative Nature of ReplicationNew DNA is made of one old (conservation) and one new strand.
Repair of DNARepair is a normal process. Different errors or amounts of errors lead to different repairs.
Repair During ReplicationDNA polymerase proof-reads 3'-5' and removes and replaces 5'-3' when there are errors.
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Repair of MutationsMismatch repair, Base-excision repair, Nucleotide-excision repair, Nick translation
Mismatch repairenzymes recognize incorrectly paired base-pairs and cuts out the stretch of DNA containing the mismatch. Then polymerase re-adds the correct nucleotides in.
Base Excision RepairSome single damaged bases (especially uracil) are removed by a glycosylase enzyme, then the sugar and phosphate and surrounding nucleotides are removed.
Nucleotide Excision Repair (Ex. Thymine Dimers)One strand is damaged and the other is not, methylation of the older strand determines which stand is used to rebuild the damaged strand. Mismatch Repair works the same way, but it is triggered by mismatch (not damage)
Nick Translation (Ex. RNA Primer Replacement)The proof-reading (exonuclease activity) of polymerase.
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Section 4

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Restriction Enzymescut double stranded DNA at palindrome sequences. The resulting fragments are called restriction fragments which may have sticky ends (1:5 to hybridize) or blunt ends (3:3 can not hybridize)
Recombinant DNARestriction Enzymes, Hybridization, Gene cloning, & PCR
Hybridization DNA strands base pair with each other, DNA probes hybridize onto DNA fragments containing a target sequence (Southern Blotting). Sticky ends from a restriction fragment of a gene base pair with the same sticky ends on a plasmid (gene cloning).
Gene cloningA method that involves the replication of recombinant DNA molecules in a host organism. Single DNA ➙ large population of replicated DNA. Requires a source of DNA and a host organism in which to replicate
Gene cloning processIsolate DNA, Treat plasmid and foreign DNA with the restriction enzyme, Mix foreign DNA with plasmid fragments, Add DNA ligase, Introduce recombinant plasmid into bacterial cells, Multiplication/transformation of gene copies, Screening
Isolate DNAObtain a bacterial plasmid and foreign DNA with gene of interest. That way, there is a recognition sequence for a restriction enzyme
Treat plasmid and foreign DNA with the restriction enzymePlasmid DNA is cut at the restriction site by the restriction enzyme. Foreign DNA is also cut
Mix foreign DNA with plasmid fragmentsWhen cut by the restriction enzyme, there are sticky ends that allow for complementary sticky ends to pair
Introduce recombinant plasmid into bacterial cellsSome recombinant plasmid will be taken up by the bacteria by transformation
Multiplication/transformation of gene copiesRecombinant plasmids are replicated and Can be identified by growth in different environment (e.g. ampicillin)
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Polymerase Chain ReactionThe purpose is to take a small piece of DNA and amplify (multiply) it. The process mass produces a sample of DNA. also used to identify small segments of DNA within a larger DNA strand. e.g If we wanted to detect whether a DNA contained a viral sequence, we can use this to detect that viral sequence
PCR generally has three stepsInitialization, Annealing, Elongation
InitializationThe sample containing the DNA is heated up so the hydrogen bonds holding the double-stranded DNA breaks apart. The DNA are now single stranded.
ElongationThe sample is slightly heated. Polymerase goes to the site of the primers. Since the DNA polymerase is heat-sensitive, they start up and begin to polymerize the single strands of DNA
Denaturationdouble stranded of DNA comes apart due to heating (increase in temperature in the environment) or a change in pH
Annealingif the temperature decreases to normal (or the environment changes back to normal), two single strands form double stranded DNA again due to the complementary nucleotide sequences and random molecular motion. Much slower process. Requires salt to neutralize the repulsion of sugar phosphate backbones from each strand
DNA hybridizationA molecular biology technique that compares and analyzes the degree of genetic similarity between identical or related DNA sequences. Measures the genetic distance between two species. Denatures two different DNA sequences then uses single stranded DNA from each to anneal to double-stranded DNA
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Replication only occursin the 5’ to 3’ direction
Helicaseunwinds the double helix of DNA
Elongation/terminationDNA polymerase III, Primase, Okazaki fragments, DNA Polymerase I, DNA ligase
DNA polymerase IIIbinds to one strand of DNA from the RNA primer and moves from the 3’ to 5’ direction, producing a leading strand of nucleotides
Primaseproduces RNA primers at the 5’ end, allowing for the synthesis of Okazaki fragments
Okazaki fragmentsshort, discontinued fragments of replication products on the lagging strand
DNA Polymerase Iremoves RNA primers by the 5’ end to 3’ end
DNA ligaseseals the spaces in the strand (between the Okazaki fragments)
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Section 5

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Protein synthesis involves RNA. DNA can control protein synthesis by controlling the RNA, but DNA has to be converted to RNA (switching out thymine with uracil and deoxiribose with ribose) in order to make protein
Genetic CodeCentral Dogma: DNA -> RNA -> protein
TranscriptionInside the nucleus, the DNA genes get transcribed into RNA
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RNAThe mRNAs get transported out of the nucleus into the cytoplasm. mRNAs are working copies of the gene.
Translationribosomes read off the mRNAs to make proteins.
Proteinsynthesized by ribosomes. They are the end product of what's encoded in the genes and they perform all the functions in the cell.
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Codonare continuous, non-overlapping and degenerate. There're no nucleotides in between.
Proofreading/repairExonuclease scans behind DNA polymerase III to proofread the sequences being replicated. If there is an error, it removes the incorrect sequences and inserts the correct bases
Anticodon3 bases (one single anticodon) at the end of tRNA (transfer anticodon) that correspond to the nucleotide triplet (codon) in mRNA during translation by ribosomes
Wobble pairingWhen two RNA nucleotides couple together. Guanine—uracil (G—U), Hypoxanthine—uracil (I—U), adenine (I—A), cytosine (I—C)
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Section 6

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codon-anticodon relationshipDuring translation, codons pair with anticodons so that the correct amino acids can be linked to a given codon.
Missense codonmutated codon that results in a different amino acid.
Nonsense codonmutated codon that results in something other than an amino acid. For example, a stop codon.
Initiation codon (AUG) signals the start of translation.
Termination codon (UAG,UGA,UAA)signals the end of translation.
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TranscriptionMaking RNA copies of pieces of DNA in the nucleus.
Initiationthe RNA Polymerase sees a bookmark (promoter) that lets it know where to start copying (promoter recognition). The Book (double stranded DNA) is opened.
Elongationcopies are made of the book pages, but they are black and white (RNA) not color (DNA), they are still readable.
Terminationwhen the end of the needed chapter is reached copying is done.
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mRNA composition messenger RNA is made of neucleotides (uracil, cytosine, adenine and guanine) during transcription (in the nucleus) and used for translation (in the cytoplasm)
mRNA structure The 5' cap and poly-A tail prevent exonuclease degradation at the 5' and 3' end respectively (only in Eukaryotes).
tRNA and rRNA compositiontransfer RNA and ribosomal RNA are made during transcription (brothers of mRNA), but they don't get translated into protein like mRNA does.
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Section 7

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tRNAis made of nucleotides, many of which is modified for structural and functional reasons. At the 3' end of the tRNA, the amino acid is attached to the 3'OH via an ester linkage.
tRNA structureclover leaf structure with anticodon at the tip, and the amino acid at the 3' tail.
rRNAis made of nucleotides, many of which is modified for structural and functional reasons.
rRNA is highly structured it contains the active site for catalysis. The rRNA of the large ribosomal subunit is responsible for catalyzing peptide bond formation, and can do this even without ribosomal proteins.
Mechanism of transcriptionChain Initiation, Chain elongation, Chain termination
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Chain Initiation.RNA polymerase latches onto the promoter (TATA box) of the double stranded DNA opening up the complex
Chain elongation. Nucleoside Triphosphates (AUGCs) add correspondingly to the present DNA. No primer is used (RNA polymerase is like 2 in one paint and primer). RNA is made in the 5' to 3' direction (like DNA).
Chain TerminationSequences cause a stem-loop structure that causes the RNA to slip off (intrinsic termination) or Rho (ρ) dependent termination occurs due to a protein called the ρ factor that bumps off the polymerase
TranslationmRNA, tRNA, rRNA
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mRNA (messenger RNA) contains codons that code for the peptide sequence.
tRNA (transfer RNA) contains the anticodon on the "tip" and the corresponding amino acid on the "tail".
rRNA (ribosomal RNA) forms the ribosome. Catalyzes the formation of the peptide bond.
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Section 8

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Ribosomeis the enzyme that catalyzes protein synthesis. has 2 subunits - the large and the small.
The large subunitis responsible for the peptidyl transfer reaction.
The small subunitis responsible for the recognizing mRNA and binds to the Shine-Dalgarno sequence on the mRNA
Chain Initiation An initiation complex including mRNA, initiator tRNA (fmet) and a ribosome is formed by initiation factors and GTP around an initiation codon (AUG) following a Shine-Dalgarno or Kozak sequence
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Chain Elongation protein is made from the N terminus to C terminus. mRNA are read 5' to 3' (opposite of DNA). Binding occurs between the chain of amino acids and tRNA's amino acid at the A site of the tRNA
Peptidyl transfer occurs at the P site by the whole chain moving onto the A site of the tRNA. The tRNA in the P site gets kicked of the E site. The codon that was in the A site is now in the P site (translocation) and the A site is open for binding to a new aminoacyl-tRNA to a new codon
Chain Termination a stop codon (UAG, UGA, UAA) causes release factors bound to GTP to block the A site. The chain gets cut off at the P site, falls off and the translation complex falls apart.
Amino acid activation enzymes called aminoacyl-tRNA synthetases attach the correct amino acids to their corresponding tRNAs. ATP required.
Role and structure of ribosomesRibosomes catalyze protein synthesis by using tRNA to bring amino acids and mRNA to give the proper sequence.
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Section 9