The bio chemistry of modern living cells was discussed in Chapter 2 evolution.
Chapter 7 contains information about what relationships can be seen between genes and organisms.
There are related genes that are called homologous.
Paralogous and orthologous are the two main types of related proteins used for different tasks.
There are shared sequences and visible similarities in three-dimensional structure that can be shown to be related.
Sequence shuffling and substitution matrices are some of the tests described.
Even if there isn't a lot of similarity in the sequence, truly related proteins will still have the same three-dimensional structures.
It is not possible to be related simply because they have similar functions.
Different proteins can be produced by convergent evolution.
Sequence information can be used to build trees.
Sequence analysis is an easy way to detect repeated domains.
Recovering sequence information from fossils can be done with modern methods.
You should be able to complete the objectives once you have mastered this chapter.
Sequence shuffling is different from sequence sliding.
Evaluate the significance of a high score in the Blosum-62 matrix for a given pair of amino acids.
When the score is low, contrast the situation with N-W.
The correspondence is not the result of chance if 25% sequence identity is used.
The relationship has not been demonstrated if the identity is less than 15%.
Large amounts of sequence data are available online, and new sequence data is compared to existing data on the internet.
If this were to happen, the genes would be considered to be related.
Function and form are closely related.
There are not many parallel functions in the cell for proteins with similar shapes.
Even though the active sites of two enzymes have the same key catalytic residues, they don't need to be related.
convergent evolution is the explanation.
Understand why analysis of self-pairing is important.
Explain how dates can be calculated.
Dinosaurs lived 65 million years ago.
It is unlikely that dinosaurs' genes can be found.
Human myoglobin and human hemoglobin are paralogs.
Human myoglobin and Chimpanzees are orthologs.
You should know how to use the codon chart by the end of this chapter.
A single "H" in one sequence is replaced with "Q" in the other.
Look at the codon chart.
In the introduction to this chapter, angiogenin and ribonuclease were described as 35% identical.
The two malate dehydrogenases have the same reaction, but their sequence and three-dimensional structures don't match.
The location of hairpin folds is analyzed with the help of RNA.
An evolutionary tree is shown using various, mostly paralogous, globin genes.
Many animals use globin to carry oxygen.
A tooth from a 9000-year-old skeleton was found in England.
These are paralogs because they originally differed from one another.
The ancestors of myoglobin and hemoglobin would have existed hundreds of millions of years ago.
About 10 million years ago, the ancestors of humans and Chimpanzees existed.
The cause of the separation is not because of the two different species of the proteins.
The text is not clear on this point.
Histidine has the codons CAU and CAC.
Q, or glutamine, has the codons.
There are only four kinds of "letters" or "nucleotides" in DNA.
This would make the shuffled score artificially high.
Yes, there are two proteins with 35% identity that would definitely be considered homologous.
The example in the chapter is myoglobin, which is related to the alpha chain of hemoglobin.
It's easy to understand this if you remember that most of the proteins are the same shape.
There are three very vivid repeats of the CH domain and a sketchier repeat of the VH domain in the heavy chain of IgG.
Oxidation of malate is a problem that evolution had to solve.
convergent evolution was caused by two different solutions.
The structure at the active site of enzymes that do similar jobs is often the same as the rest of the molecule.
The tree that would be drawn from orthologous gene data would show the relationships between different species rather than the differences between them.
Taxonomy is the relationship between species.
The shark and lemur have the same type of blood.
The horseshoe crab's blood is blue rather than red because of the copper it uses to carry oxygen.
An approximate date is needed for the divergence of var ious species.
Consider diseases such as Escherichia coli andSalmonella.
The organisms are similar, but the one that lives in the gut of birds and reptiles is called E.
To answer this, we have to look for the divergence of mammals and reptiles in the fossil record.
Our species from thousands of years ago have the same genes as members of the human species.
A local teacher lived a few miles from where the fossil was found.
Scientists have found that the relationships between species can be very different if a common gene is being studied.
It is possible to make the same eucaryote appear closer to the archaea by comparing its genes.
The Blosum-62 matrix has high- scoring pairs of the amino acids.
The codon chart has the highest scoring pairs.
On the codon chart and the Blosum-62 matrix, look up the names of the three people.
There are two sequences here.
Pyrococcus furiosus is an Archaeal organisms that lives in very hot water.
The other is from the fruit fly.
Actin and Hsp 70 are shown to be similar on the basis of their three-dimensional structures.
Actin is often found in the contractile apparatus with myosin.
Hsp 70 is found in the eucaryotes, procaryotes, and archaea.
The Archaea were a separate kingdom from the Procaryotes, according to an article published in 1977.
Microbiologists assumed that all single-celled organisms were related.
No matter how exotic the organisms are, Woese had to pick something that would be in them.
Several years ago, there were reports in the literature that dinosaur fossils had their genomes amplified.
The genes obtained appeared to be human.
In the last section of the chapter, you can compare and contrast the evolution experiment described in Chapter 2.
It is obvious that horizontal gene transfer is very common in nature now that several complete genomes have been mapped.
Even if the species are very different, a gene can move from one species to another.
We have some "bacterial" genes as well as "archaeal" genes, and using one of those to construct a tree of relationships would have very strange results.
Other "easy" replacements have lower scores.
Even though the codon structures are close, T, H, and L have negative scores.
There is a similarity in the structure of the acids.
It's very similar to the functions of valine/isoleucine and phenylalanine/tyrosine.
Very similar amino acids will have high Blosum-62 replacement scores.
Of the 16 amino acids shown, seven are the same.
The two proteins seem to be related despite being very distantly related.
The shapes of other members can be inferred if a single member of a "COG" is crystallised so that the three-di mensional structure can be solved.
It isn't always the case, but orthologous proteins can have the same or very similar functions.
There are many uses for the data sets.
The earliest use of this fold was as a chaperone for folding, according to the universal distribution of Hsp 70.
The theory is that the earliest cells lived in a hot environment.
HSP stands for "heat shock" and can be difficult to fold in high heat.
Actin is found in all of the eucaryotes, but it is not found in the other kingdoms.
Even though its use is different, the hexokinase-I is a member of this family.
The actin-like filaments in somebacteria are called MreB.
The structure is close to actin and has the same fold.
Many of the Archaea live in environments that are high in salt, strong acid, and water, and they might need different enzymes.
All organisms have ribosomes.
The 16S rRNA is found in the smaller ribosomal subunit.
Back in the early 1970s, a way to sequence the small fragments of the 16S rRNA was found by Woese.
The methanogens he was studying, and later most of the "funny bugs" that live in extreme environments, turned out to be quite different from the "regular"bacteria that live in easier locations.
The new kingdom is called the Archaea.
Modern methods are so powerful that they can amplify the smallest trace of DNA to an amount 888-282-0465 888-282-0465 888-282-0465 888-282-0465 888-282-0465 888-282-0465 888-282-0465 888-282-0465.
This technology can be used to sequence some of the DNA from fossils, which are usually a few thousand years old.
Errors can be made.
It appears that something containing the researchers' DNA got into the fossil sample.
Since all of the actual dinosaur DNA had degraded over millions of years since the animal died, this was the only DNA available as a starting material.
The Qb experiment started with a single naturally occurringRNA.
The experiment in this chapter started with a lot of artificially constructed RNA.
AnRNA replicase was used to replicate Qb.
The process of replicating the RNA in this chapter involved a number of different processes, including reverse transcriptase, a DNA polymerase, and an RNA polymerase.
The available time for reproduction was shortened in the Qb experiment.
The experiment in this chapter was more contrived, testing for binding to ATP on an affinity column.
The complicated process in this chapter is modeled after real cellular processes.
The reproduction of retroviruses involves reverse transcription into DNA.
There are 27 identities and 2 gaps in the sequence shown.
A score of ;10 for an identity and :25 for a gap would be used to calculate the score.
The percentage can be calculated using 27/98 and 27.6%.
The % identity is higher over the first 75 residues.
The first sequence has one gap and no identities, hence a score of :25, while the second sequence has one gap and four identities, hence a score of 40-25.
The scores would be ;7 for the first sequence and ;12 for the second, using the Blosum-62 substitution matrix.
Sometimes U and G are in the same sequence.
G7 and U19 are in the same sequence.
The answer is obtained by considering the number of mole cules and the number of positions.
The number is equal to something.
One mole of the RNA will weigh around 40 grams and contain Avogadro's number of molecules.
One has 26,400 grams of combining all data.
It is more important to conserve particular three-dimensional structures than one-dimensional sequences because biomolecules function at the level of three-dimensional structure.
The effects of mutations are felt at the level of function.
Sequence changes can be made because they preserve a common three-dimensional structure.
The score for the initial alignment would be 60 with six identities and no gaps.
A lot of shuffled versions of sequence 2 can be generated.
At the other end of the scale, sequences that are less than 15% identical are not likely to have significant sequence similarity.
Further analysis is needed to determine the significance of the alignment for pairs that show between 15% and 25% identity.
These are the answers to the guidelines.
The three-dimensional structure is more closely related to the amino acid sequence.
Sequence B is likely to have a three-dimensional structure similar to A and C.
If you want to check for possible alignments between the inverted first half and the non-inverted second half of the sequence, invert the first half and check for possible alignments between the inverted first half and the non-inverted second half of the sequence.
The original sequence begins at the 5 and ends at the 3.
Enzymes are involved in the transformation of one form of energy into another in a cell.
The most important reactions are also the ones that arecatalyzed byRNA.
The authors begin the chapter with an overview of the power and specificity of the enzymes.
They point out that small molecule partners are needed to effect catalysis.
They explain how the concepts of free energy change and free energy of activation are used to determine whether or not chemical reactions can occur and the rate at which they will occur.
They show how the transition state of a reaction provides the basis for catalysis.
They describe the analysis of the speed of the reactions.
The chapter ends with a discussion of vitamins.
This chapter is based on your knowledge of the interactions between biomolecules.
The majority of the text deals with biochemical reactions.