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molecular evolution?

the study of how proteins, nucleic acids, and other molecules have changed through time


what does it mean if two molecules are said to be homologous?

they are derivied from a common ancestor and later diverggd from this ancestral sequence


what are the 2 types of homology?

paralogs: homologs that are present within on speciies

2. orthologs: homologs that are present within different species and have very similar functions


how can homlogy be detected?

significant sequence similarity resulting in a common 3d structure


example of orthologs?

bovine and human ribonucleaase


example of paralogs?

human ribonuclease and angiogenin


why is knowing homology useful?

it can be used to infer function. large scale genome seq has resulted in discovery of many new genes whos functionscan be compared with genes of known function


how is sequence similarity determined?

sequence allignment


how are sequence allignments performed?

aligned in regions of siliarity either in the specific amino acid squence or in the physical character of the amino acid

squences are slid past eachother to find windows of greatest similarity


why are gaps sometimes added while performing sequence alignments/

allows all regions of similarity to be included in the allignment. it is needed because one protein has evolved to either gane or lose an amino acid(S)


how are sequence alignments scored to see how likely it is that the similarities occured due to chance

each sequence identity is given +10 points whereas each gap is given a penalty of -25 points.


what does shuffling do?

the amino acid in one of the proteinsfrom the alignemnt is shuffled (bar graph showing likeliness of each shuffle) compared to the alignment score of the 2 proteins


what are conservative subsitutions?

substitutions that result in the replacement of an amino acid with one thath as similar physical or chemical properties / size


what does a substitution matrix tell you?

it shows you the frequency of a substitution: large positive score means the substiution occurs frequently while large negative score indicates a rare substitution


why is substitution matrix a better scoring system for homology?

because it takes into account protein structure


what does blast stand for

basic local alignment search tool


what should the expected value be from blast to be considered significant? what does the expected value mean?

less than 10^-5. expected value is the number of sequences with this level of similarity expected to be in the data base by chance


is 3d structure more closely associated with function or primary sequence?



the globins have very similar structures, are they sequentially similar?

no human mioglobin and lupin leghemoglobin is only about 15.6% similar which is not statistically significant


can structural hology be found for proteins having unrelated biochemical function?

yes. an example of actin (component of cytoskeleton) and heat shock protein (hsp) which assists in the folding of proteins inside cells.

suggests they are paralogs and that they descended fro ma common ancestor and adopted different roles


in a family of proteins, which residues are conserved?

residues critical for function


if sequence alignments are not statistically significant does this mean proteins are not related at all?

no, conservation of residues critical for function can be used as a signal in the detection of similar proteins despite not statistically significant alignment..


what is it called if 2 unrelated proteins from a different ancestor evolve to form the same structure or function?

convergent evolution. active sites are almost identical but overll 3d structures are very different


how do repeat motifs occur?

result of gene duplication event


how are repeat motifs detected?

by aligning protein with itself


what is a compensatory mutation in RNA?

mutations that alter sequence, but maintain base pairing within secondary structure


what is Mfold?

MFOLD is a web server for predicting RNA secondary structures. Input RNA sequence and MFOLD outputs multiple RNA secondary structures arranged in order from most likely to least liekly


why are phylogenetic trees created from the sequencing of large ribosomal RNA

protein synthesis by the ribosome is an ancient reaction carried out by all living things


what are the three basic requirements of evolution

1. generation of a diverse population
2. selection of the most fit members
3. reproduction of these fit members


why can evolution be done in a test tube using RNA as a model system?

RNA has both catalytic and binding affininties for other molecules which can be used as selectable traits


how do you do invitro evolution?

in vitro transcription of randomized dna pool to create library of mutant rnas

selection for binding to atp

elution of selected molecules using atp solution

can be repeated many more times to gradually improve binding efficiency
1. mutagenic PCR using manganese ions to generate mutant dna molcules
2. in vitro transcription using T7RNA polymerase to generate the pool of mutant RNAs
3. select for binding affinity or catalysis
4. reverse transcription of selected members back into DNA

10-30 rounds of selection done


ATP binding aptamer?

conserved secondary structure common to all varients that bound to ATP.