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118 Cards in this Set
- Front
- Back
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From the list of DNA, RNA and Proteins, which molecule reads information and translates it into a different molecule?
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RNA
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From the list of DNA, RNA and Proteins, which molecule is made to do things in or out of the cell
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Proteins |
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From the list of DNA, RNA and Proteins, which molecule stores the information |
DNA |
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What is the name of the process where you start with DNA and end with RNA? |
transcription |
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What is the name of the process where you start with RNA and end with Protein? |
translation |
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Who isolated nuclein; now known as nucleic acid?
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Miescher |
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What does DNA stand for?
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deoxyribonucleic acid |
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What is the shape of DNA molecule
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double helix
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What bonds the two strands of DNA together? |
H bonds between base pairs |
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What is the name of either end of a strand of DNA |
5' and 3' |
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What makes up the DNA backbone
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phosphates |
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On which atom does the deoxyribose and the phoshpdiester units bond? |
by the oxygen atom on the 5' and 3' carbons of the deoxyribose
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What are the "building blocks" of DNA |
deoxynuclotides |
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What is formed if you "chopped up" DNA into monomers
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deoxynucleotide monophosphate |
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What are the precursors used by DNA polymerase to make DNA? |
deoxynucleotide triphosphates |
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What are the 4 bases of DNA |
cytosine guanine thymine |
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What 2 categories can bases be grouped into |
purines |
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What are purines |
Adenine and Guanine |
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What are pyrimidines |
Cytosine and Thymine |
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Which atom in all bases does the deoxyribose ring bind to? |
Nitrogen |
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What are the differences between DNA and RNA
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Deoxyribose vs Ribose Thymine vs Uracil |
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How do ribose and deoxyribose differ?
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Ribose contains an extra hydroxyl group |
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What is the difference between Thymine and Uracil |
Uracil doesn't have a C5 methyl group |
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Two strands of DNA are held together by Hydrogen bonds and base pairing, but what other non-covalent interaction?
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Stacking
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How many H bonds between A & T
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2 |
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How many H bonds between C and G
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3 |
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Why is each base pair between a pyramidine and a purine |
to keep the distance between the two strands the same along the entire molecule |
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Which base pair is flatter and stronger than the other? |
due to 3 H bonds |
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What is base pair stacking
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because hydrophobic exclude water energetically stable |
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Why is DNA a helix?
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Don't sit directly on each other (each one slightly rotated) Phosphate charge repulsion |
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How many grooves are there on a DNA molecule? |
2 |
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What are the names of the grooves? |
Major and Minor |
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HOw many Bp for each turn of a helix? |
10 |
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What is the distance between bp?
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3.4 angstroms or .34 nm |
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Are the two strands making up the DNA molecule parallel or antiparallel? Explain |
one 5' - 3' other 3' - 5' |
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Is the DNA helix left handed or right handed? What is meant by this term?
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Right handed Look at spiral from one end and the strands are going away from you clockwise` |
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What is the difference between DNA and A-DNA
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Minor and major grooves more equal |
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What type of DNA exists in telomeres
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quadruplex DNA |
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What types of DNA structure is important for intermediates in recombination?
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4 way junction |
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What is the name for the 2 strands of DNA coming apart?
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melting or denaturation |
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What are ways to denature DNA
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denaturants such as urea |
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How are strands of usually separated in the cell?
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Helicases (enzymes) |
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Are helicases a passive or active way to denature DNA?
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active - they hydrolyse ATP |
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What enzyme makes new strands of DNA and from what does it make it?
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DNA polymerase from deoxynucleotide triphosphates |
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What does dNTP stand for
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deoxynucleotide triphosphates |
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What is the name of fragments of replicated DNA formed on the lagging strand of the DNA molecule? |
Okazaki fragments |
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What direction is new DNA synthesized?
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5' to 3' |
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What transcribes DNA into RNA?
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RNA polymerase |
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How does the enzyme know where to start transcription?
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Promoter regions |
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What are enhancers
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regions of DNA that regulate transcription |
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What are telomeres?
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regions of DNA that protect the ends of chromosomes
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Sequences for pulling chromosomes apart during mitosis and meiosis are also encoded in the DNA. True or False? |
True |
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How do proteins recognise particular DNA sequences? |
contact edges of base pairs stick into major or minor grooves use H bonds + hydrophobic interactions OR shape of DNA |
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What is the name sometimes given to the way that proteins recognize DNA sequences through the contact edges of bp?
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Direct Readout |
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What is the name sometimes given to the way that proteins recognize DNA sequences through detecting the shape of the molecule?
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Indirect Readout |
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How do cells rearrange their DNA sequences
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DNA Recombination |
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What is DNA topology
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the larger/secondary shape or form that the DNA molecule takes |
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What is the name for when DNA is twisted too much or too little
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supercoiling |
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What enzymes are used to change DNA topology - untangle or make it supercoiled?
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topoisomerases |
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How many chromosomes in a diploid human cell?
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23 pairs |
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How long is the human genome in base pairs? |
3 x 10^8 |
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What is the name for the basic storage unit in EuK? |
Nucleosome - 200bp of DNA in 2 turn spiral |
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What is the name of the protein that DNA in nucleosomes are wrapped around? |
histone proteins |
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How do DNA and histones come together?
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Histone - lots of positive charged amino acid side chains DNA - negatively charged phosphates Attract each other |
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What is the structure of the histones inside of a nucleosome
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Octamer 2 sub units each of H2A H2B H3 and H4 146 bp of DNA wrap around |
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If 146 bp of DNA wraps around the octamer core of nucleosomes, and 200 bp is used in the entire nucleosome, what happens to the remaining 50(approx bp) |
bound to H1 and other proteins |
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What is meant by the phrase "nucleosomes assemble into higher order structures"
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The nucleosome coils are further coiled, and then coiled again to eventually become chromosomes
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What is RNA
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Ribonucleic acid |
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For what organisms can RNA be a genetic material?
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viruses or phages |
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What is the consequence of the 2' hydroxyl group on the RNA molecule?
(this is in comparrison to a molecule of DNA) |
it makes the molecule chemically much less stable than DNA - easier to hydrolyse the 3' ribose-phosphate linkage |
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Is RNA double or single stranded?
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Can be both |
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Give an example of when ssRNA can fold into useful or complex structures |
ribozymes ribosomes |
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What is mRNA
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messenger RNA used in translation made by transcription of protein coding genes |
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What is tRNA
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needed to translate mRNA in ribosome 100 nucleotides long |
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What is rRNA |
used to make ribosomes |
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what are snRNAs |
small nucleolar RNAs |
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What are piRNA |
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what are siRNA |
small interferring RNA |
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What is the name for RNA molecules that catalyse reactions?
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ribozymes |
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Who discovered catalytic RNA
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Cech |
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Do ribozymes catalyse complicated or straight forward reactions?
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easy ones! |
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Give and example of ribozymes
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OR ribonuclease P which makes mature tRNA from precursors |
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Intron splicing is used when?
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For the production of mature mRNA in EuK |
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Ribozymes do not have active sites, unlike enzymes. T or F? |
False - they do have active sites! |
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How do Ribozymes recognize their substrate?
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base pairing and stacking interactions |
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Is the ribosome a ribozyme?
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Yes |
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What is the substrate for translation? |
amino acyl tRNAs |
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Why is there general excitment about ribozymes in the biological world? |
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What is DNA sequenceing
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finding the sequence of the bases in DNA |
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What is the process to sequence RNA?
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DNA sequenced |
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What are the 4 generations of DNA sequencing methods?
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Chemical degradation methods/Maxam-Gilber sequncing Dideoxynucleotide chain termination or Sanger sequencing Next generation sequencing |
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Assess Thin Layer Chromatography as a method for DNA sequencing
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very slow few base pairs sequenced |
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Assess Maxam-Gilbert Sequencing as a method for DNA sequencing
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faster than TLC sequences up to a few hundreds or thousands of bp |
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Assess Sanger sequencing as a method for DNA sequencing
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much easier and faster than TLC and M-G methods used for human genome project millions of bp |
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Assess Next generation sequencing as a method for DNA sequencing
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billions of bp from a single experiment
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What are 2 other names for Sanger sequencing
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chain termination |
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For sanger DNA sequencing, what must be true about all of the DNA that you start with? How can this be achieved?
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all the same PCR |
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Once you have your DNA sample, what must you do to it if using Sanger sequencing technique
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other methods fine |
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What is meant, in the context of DNA sequencing, by a molecule that anneals? |
it makes base pairs |
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Once the template DNA is single stranded, what is the next step in Sanger sequencing?
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add a short ssDNA primer that anneals with a known sequence at one end of the template ssDNA when the same is cooled |
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How can you get a sequence of DNA that has a known sequence at one end?
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Once a primer is added to a template in Sanger sequencing and the mixture is cooled, what do you add and why?
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this extends the primer |
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How can you detect the growing ssDNA chain in the sanger method for DNA sequencing
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use radioactively labelled nucleotides
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After the DNA polymerase and nucleotides have been added to the template strand in the Sanger sequencing method, what is added and to what effect? |
stops growth of DNA chain |
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What is an important feature of ddNTP which stops DNA polymerase
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no further nucleotides can be added to it |
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Once the ddNTP has been added, what are you left with in the mixture
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chain growth stopped at one of the positions of the template base which is complementary to the ddNTP base |
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What is important about the presence of dNTPs and ddNTPs in the sanger sequencing mixture? |
All dNTPs must be present - ensure DNA polymerase doesn't stop due to lack of bases ddNTP must be low level, otherwise all chains would stop at the first complementary base |
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Why is the sanger sequencing method repeated at least 4 times?
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1 time per base find positions for all different bases |
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Once the ddNTP has been added in the Sanger sequencing method, what is the next step?
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denature strands again |
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How do you separate the products of the sanger sequencing method
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high voltage to increase gel tempr |
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Why during the separation process of the sanger sequencing method should urea be present and the gel be kept hot.
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get accurate gel electrophoresis readings |
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In the results of the gel electrophoresis of the sanger sequencing experiment how can one read the results |
the beginning of the sequence is furthest end of the sequence nearest compare results of all 4 each size molecule should = 1 distance travelled |
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How does modern sanger sequencing differ from the traditional approach |
different colour in electrophoresis = different base means experiment only has to run 1 time |
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What electrode is needed for DNA separation in gel electrophoresis and why?
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DNA negative due to phosphates |
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Why is gel electrophoresis not as good for determining size of proteins?
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also variable shapes which may slow them |
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How can you get around the issue of proteins in gel electrophoresis
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polypeptide chain denatured coated with negatively charged detergent |
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What does SDS PAGE stand for
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SDS polyacrylamide gel electrophoresis
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What is blotting
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biomolecule in a gel transferred onto sheet of material that the molecule sticks to used to detect if molecule present |
