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78 Cards in this Set
- Front
- Back
The three key processes of macromolecular synthesis
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1) DNA replication
2) transcription 3) translation |
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Transcription
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synthesis of RNA from a DNA template
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Translation
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synthesis of proteins using messenger RNA as a template
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The three types of RNA
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1) Messenger RNA (mRNA)
2) Transfer RNA (tRNA) 3) Ribosomal RNA (rRNA) |
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Role of mRNA
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used to encode polypeptides (proteins)
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Role of tRNA and rRNA
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paly part in protein synthesis but do not themselves encode genetic information for making proteins
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Three characteristics of Prokaryotic Genetics
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1) circular DNA
2) no membrane separating the chromosome and cytoplasm 3) vast majority have no introns |
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Three characteristics of Eukaryotic Genetics
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1) linear DNA
2) chromosomes inside nucleus and ribosomes in the cytoplasm 3) all have introns between exons |
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Borrelia burgdorferi
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rare instance of prokaryotes with linear DNA
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Eukaryotic Coding/Non-coding regions
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most eukaryotic genes have both coding regions(exons) and noncoding regions (introns)
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Primary Transcript
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both introns and exons transcribed into this
an unprocessed RNA molecule that is the direct product of transcription |
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Three characteristics of DNA structure
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1) DNA is a double-stranded molecule
2) forms a helical configuration 3) measured in terms of numbers of base pairs |
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Nucleotide pairs (with number of hydrogen bonds)
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Adenine (A) pair with Thymines (T) [2 hydrogen bonds]
Guanines (G) pair with Cytosines (C) [3 hydrogen bonds] |
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How do the complementary strands of DNA run in respect to one another?
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They run in an "antiparallel" fashion, where the sense strand (5' to 3') runs antiparallel to the antisense strand (3' to 5')
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What is meant by DNA being a right handed molecule?
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This means that it is twisted in a right to left direction
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Kilobases (kb)
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The way DNA size is measured(1kb= 1000 bases)
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Megabases (mb)
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The way DNA size is measured in respect to genome sizes (1 mb= 1 million bases)
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Inverted Repeats
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Short repeated sequences in DNA molecules
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Stem-loop structures
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result from formation of inverted repeats
more common in RNA molecules than in DNA creat a type of secondary structure that can be critical to the function |
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Melting/Denaturation
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breaks apart hydrogen bonds
when two strands of a DNA molecule are separated by heat |
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Annealing
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when denatured strands are cooled
double stranded DNA molecule will reform |
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Hybridization
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invovles putting together two DNA strands from different sources
annealing can be used to do this |
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Supercoiling
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very long DNA molecule can be packaged into the cell because it is further twisted
can occur in a positive or negative direction |
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Negatively supercoiled
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Most DNA is supercoiled this way
twisted in the oppposite direction from the right handed double helix |
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DNA gyrase
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produces negative supercoiling in bacteria and Archae
belongs to group of enzymes caled "topoisomerases" classified as topoisomerase II |
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Topoisomerase
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a group of enzymes
DNA gyrase classified as type II of this |
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Three facts about viruses
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1) Consist of either RNA or DNA
2) control their own replication 3) viral chromosome may be linear or circular |
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Three facts about plasmids
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1) replicate separately from chromosomes
2) Double Stranded DNA that is usually circular but can be linear 3) Do not cause dammage and do not have extracellular forms |
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Three facts about organellar genomes
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1) Examples are chloroplasts and mitochondria
2) DNA is separate from nuclear DNA 3) DNA replicated independently of nuclear DNA |
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Transposable Elements
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Molecules of DNA
can move from one site on a chromosome to another paly an important role in genetic variation |
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DNA Polymerase
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Catalyzes the addition of nucleotides to the 3'-OH group
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Primer
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short (<15 bases) single stranded pieces of RNA
primer strand synthesized by "primase" has an available free 3' OH |
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Bidirectional replication in circular chromosomes
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1) replication is bidirectional from the point of origin of replication
2) two replication forks on chromosome replicating in opposite directions |
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Exonucleases
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DNA Polymerase I and III
have a proofreading function they can remove mismatched bases and replace them with the correct bases mutation rate 10^-8 to 10^-11 errors per base insertion |
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Restriction Enzymes/Endonucleases (Three facts)
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1) Found in both Archae and Bacteria (rarely found in Eukaryotes)
2) recognize specific DNA sequences and cut the DNA at those sites 3) Essential for in vitro DNA manipulation 4) in prokaryotes protect them from invading foreign DNA |
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How do prokaryotes protect their own DNA
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they do so by modifying through methylation
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methylation
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specific bases within the recognition sequence have methyl groups attached to them
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How does the Restriction Enzyme Digest work?
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DNA frament can undergo this
Restriction enzyme will cut DNA at each site it recognizes eletrophoresis gel contains digested fragments and yields a restriction map |
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What is nucleic acid hybridization and the southern blot used for and how do they work?
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used to check for the presence of DNA sequence in a DNA sampe
Double stranded DNA fragments from a gel are transferred to a membrane and denatured Single stranded denatured DNA fragments are annealed to complementary strands probe containing a label or are probed using a labeled single stranded oligonucleotide |
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What does DNA sequencing require? (5)
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1) DNA template
2) Primer 3) Deoxy nucleotides 4) Dideoxy nucleotides 5) A polymerase enzyme |
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What method is preferred for DNA sequencing and what does this method entail?
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The sanger method is used
DNA is sequenced by making a copy of a single stranded DNA template strand polymerase adds nucleotides dideoxy analog acts as the specific chain termination reagent |
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Difference between normal deoxynucleotide and dideoxy analog
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dideoxy analog is missing an OH at the 3' end
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Automated Sequencing
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based on sanger dideoxy method
fluorescent labeled primers or nucleotides are used |
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Synthetic DNA
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automated procedure used to synthesize short oligonucleotides (<100 bp)
can be used as primers or probes (may contain a label) |
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Polymerase Chain Reaction
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amplifys DNA
multiplies DNA sequence by a billioni fold DNA template is dantured by heat (requires Taq polymerase, a thero-stable enzyme) |
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Uses for the polymerase chain reaction (3)
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1) DNA sequencing
2) Cloning 3) DNA footprinting |
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Transcription Terminators (3)
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1) Intrinsic terminators that involve sequence patterns only
2) inverted repeats that lead to stem loop formation 3) GC rich followed by AT rich sequences |
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Specific Protein factors
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other termination factors require this
example is a Rho protein |
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Rho protein
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binds directly to RNA
causes both the RNA polymerase and newly synthesized RNA strand to be released from the DNA |
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Rho dependent termination site
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site where newly synthesized RNA is released from teh DNA
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RNA Longevity
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1) in prokaryotes, mRNA's have short "half lives" (usually only minutes)
2) rRNAs and t RNAs are more stable because of their highly folded structures 3) RNAs are degraded by cellular ribonucleases |
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Polycistronic mRNA
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genes encoding related proteins are clustered together in prokaryotes
mRNA encoding a group of "cotranscribed" genes |
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Operon
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Genes that are transcribed from a single promoter consitute this
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Codon
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triplet of bases that encode a specific amino acid
64 possible codons (4 bases taken three at a time 4^3) |
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Whats so special about the 3rd base position in the codon?
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1) changing this may not always change the amino acid
2) irregular base pairing may be tolerated at the 3rd base position |
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Start codon
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AUG (begins the reading frame)
establishes the open reading frame |
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Stop codons (3)
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UAA, UAG, UGA (transcription terminates)
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organisms where nonsense codons encode amino acids (3)
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Paramecium (Eukarya)
Mycoplasm (Bacteria) Some animal mitochondria |
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What is meant by the term "codon usage bias"?
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for multiple encoded amino acids, not all codons will be used equally
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Transfer RNA
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contain an anit-codon portion that base pairs with teh codon portion of the mRNA
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aminoacyl-tRNA synthetases
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enzyme that helps tRNAs bind a specific amino acid
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Structure of tRNAs (4 facts)
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1) short single stranded molecules with extensive secondary structure
2) have lengths of 73-93 nucleotides 3) have conserved and variable regions 4) have cloverleaf structure |
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How many different types of tRNAs are in bacteria cells and mammalian cells respectively?
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60 in bacteria
100-110 in mammalian cells |
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Anti-Codon
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one of the variable regions
consists of three nucleotides found on teh anti-codon loop |
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acceptor end
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where the amino acid is attached
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Ribosomes
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Site of protein synthesis
consist of two sub units meausured in Svedberg units consist of ribosomal RNA and ribosomal proteins |
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How long are prokaryotic subunits
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30S and 50S subunits
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composition of 30S subunit
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consists of 16S rRNA and ~21 proteins
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composition of 50S subunit
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consists of 5S and 23S rRNA and ~34 proteins
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how do antibiotics inhibit protein synthesis
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do so by inhibiting the activity of bacterial ribosomes
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the four steps of protein synthesis
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1) Initiation
2) Elongation 3) Termination 4) Release |
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Initiation in protein synthesis
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involves Shine Delgarno sequence on the mRNA (3-9 bp long)
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Shine Delgarno Sequence
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located at the 5' end of mRNA
binds by complementary base paring to regions in the 3' end of the 16S RNA portion of the ribosome sets up teh correct "reading frame" |
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3 Key sites on the ribosome
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1) Acceptor Site
2) Peptide Site 3) Exit Site |
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Acceptor Site
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where the charged amino acid first arrives
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Peptide Site
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where the growing polypeptide chain is held
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Exit Site
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where the tRNA is released from the ribosome
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Polysome
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several ribosomes can simultaneously translate a single mRNA
increases the speed of translation |