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53 Cards in this Set
- Front
- Back
What is is the main role of DNA |
To store information, info to make and maintain a new organism |
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What is a nucleotide? |
Building block of DNA/RNA, and made up of either ATCG. And it is linked to a sugar, which is linked to a phosphate group |
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Which base in DNA is methylated |
Cytosine, methylation had the effect of inactivating a gen. |
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What is the error rate of DNA replication and why is it so low |
One in every 10^9 bases replicated. It is so low because the mechanisms of DNA fix errors in the base pairing of the new DNA strand.
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What part of dna determines whether a gene is active or inactive? |
Determined by the non coding regions that surround the coding sequence in the gene. |
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What does it mean when genetic code is degenerate? |
Most amino acids can be specified by more than one codon; we can deduce the protein sequence from DNA, but we cannot unambiguously deduce a nucleic acid sequence from a protein sequence. |
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What amino acid is usually removed from newly synthesized protein? |
Methionine, the first amino acid of most proteins. |
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RNA main role |
Transfer if data from DNA and use thus information to manufacture proteins. |
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What is the connection between the mrna and protein chain? |
The trna, it binds to the ribosome. |
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Is it possible for a rns polymerase molecule and a ribosome to be attached to a eukaryotic mRNA simultaneously? |
False |
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At no time during protein synthesis does an amino acid make direct contact with the mRNA being translated. T or F |
True |
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What are promoters? |
Promoters are control regions in dna at which RNA polymerase binds to initiate transcription. |
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Where do bacterial promoters usually start before what site? |
Transcription start site |
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What are the main problems finding promoters in DNA sequence? |
Because the sequence outside of the conserved motif varies alot, and motifs also vary from gene to gene. |
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Is the prokaryote terminator sequence more variable than the promoter sequence? |
Yes |
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Is the prokaryote terminator sequence usually included in genome annotations? |
No |
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What are activators? |
They are proteins that enhance the binding g of RNA polymerase leading to increase gene expression. |
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What are repressors? |
They inhibit the expressions of the gene by blocking the promoter sites. |
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Why are activators and repressors important ? |
They are an additional controls for regulating and translating genes. Have a say on when or whether transcription actually occur. |
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What us the major difference between eukaryotes and prokaryotes in terms of their transcription? |
Eukaryotes mRNA transcripts are super modified before translation. (Splicing) |
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What is the shine dalgarno sequence? |
Sequence ths indicates the ribosome binding site in bacterial dna. Typically AGGAGGU. It is located a few beds up stteam from start codon AUG. |
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How do viruses replicate? |
Utilize cell machinery to replicate and produce proteins. They must hijack a living cell of another organism |
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What are plasmids? |
Plasmids are small circular extra chromosomal DNA molecules that carry extra Gene's. Gene's from drug resistance are what a plasmid can carry. |
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Two groups for classifying proteins |
Polar and hydrophobic |
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What are homologous proteins? |
Proteins with a common ancestor. |
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What would be attached to the 5' carbon of the ribose(sugar) of the first nucleotide in a polymer? |
A phosphate group, |
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What are the differences in the monomer in dna versus rna. |
Thymadine is found in DNA but not in RNA. There is a 2' hydroxilc on the RNA monomer but not th4 dna. |
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Pairwise alignment |
Infer biological relationships from sequence similarity |
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Multiple sequence alignment |
Infer sequence similarity from biological relationships |
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Why do we align sequences? |
Similar dna sequences produce similar proteins, which can show what functions and structures those proteins may have if they are similar. Also to check whether to or more genes/proteins are evolutionarily related. |
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Why would a Dot matrix SA be good? |
Can see all the possible marches of residues |
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Pam and blossom differences |
Pam is used to track evolutionary origins of proteins where blossom is designed to find their conserved domains. |
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What is this image of |
Genback database results |
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Just study it |
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Remember that noncoding and template are the same |
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What are the stop codons? |
UAA, UAG, UGA |
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What tool is this |
Blast Tool |
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What Tool is this? |
Genome Browser |
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On genome browser tool, what does red indicate? |
Non synonymous mutations, red, synonymous for green |
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How do you create a odds table from frequency? |
Take the frequency of the amino acid in the column and divide it by the frequency of the amino acid in the organism |
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How do you get a value of the PWM |
take log 2 of the odds |
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What can you say about the box? |
There are TANDEM REPEATS |
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Paired-end sequencing, bowtie? |
This creates 2 FASTQ files that respond to the forward orientation of fragments, and the other the opposite |
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What is a Phred Quality Score? |
A Phred quality score is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing. |
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What is a reference Genome? |
A set of nucleic acid sequences assembled as a representative example of a species’ genetic material. Do not represent a SINGLE organism more like a mosaic of different nucleic acid sequences from each individual. |
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NGS, types from back then to now |
Gel based, Sanger Sequencing, NextGen |
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Why is NGS MASSIVE PARALLEL SEQUENCING |
because you are sequencing all these different parts of the genome all at the same time! |
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NGS DNA Prep Steps |
- Fragment DNA - Repair ends of the DNA - A-tailing, adapters are ligated - Bridge formation and amplification - Finished flow cell - sequence by synthesis note: Flow cell has adapters at each end |
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NGS Libraries |
creates a library of DNA fragments for sequencing |
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NGS Lanes |
flow cell has several independent lanes during single sequencing |
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NGS Flowcells |
NGS machine processes a single one |
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Clean C/T heterozygote |
half of them are going to have one base to another one |
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What is the lowest Phred Score for good quality? |
20 |