BioConc ept Question s

Programming a computer to model manipulation of DNA requires that the programmer first have a solid understanding of
how real DNA is manipulated within the cell. If you understand how DNA is transcribed ~nd ?ecoded, you should be able
to answer these questions; use the BioBackground section to fill gaps in your understanding if needed.

1• How can Mary be sure she is a carrier of CF (one functional allele, one CF allele} without genetic
testing? If Tom is also a carrier, what is the probability that their child would be born with CF?
2. One strand of a segment of a DNA molecule has the nucleotide sequence 5' ACGTAGCAGATCAT.
Show the double-stranded DNA molecule; don't forget to label the ends~
3. The template strand of a short DNA molecule has the nucleotide sequence 5' GATGAGACTCCCATG.
What would be the sequence of an mRNA molecule produced using this template? Write your
mRNA sequence starting with the 5' end, which is conventional whenever nucleotide sequences are
.
written out.
' .

4. The nontemplate strand of a short DNA molecule has the nucleotide sequence 5' CGACCTATGCAGACT.
What would be the sequence of an mRNA molecule produced from this DNA segment?
s. If your mRNA sequence for question 4 represented the first part of an mRNA encoding a protein,
where could the coding sequence possibly start? Underline this start point and list the first two
amino acids that would be found in the protein, using the three-letter code.
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 Bi oC on ce pt Q ue st io ns
. h• for gene alignment depend on understanding of the biologic
computat,ona 1tee rnques al basis for gene comparison
and the meaning of similarity and variation among the genes of . . .
different organism~. Use t~ese question s to test your
biological understan ding; read the BioBackground box at the
end of the chapter if you find that you need a better
foundation.

1. How is similarity between genes related to the biol

ogic al concept of descent from a common ancestor?

2 . Given the sequ ence s ACGAT and CGA TC, why is ACG AT
the sim ples t alig nm ent CGA TC not a ver y
satisfactory one? What do we hav e to allo w for in ord er
to gen era te an alig nm ent tha t app ear s mor e
biologically relevant?
 Discuss why"brute-force"
3. List all the poss ible ways to align the very short sequences ACC and ACT.
is not a practical meth od of
align men t (tryin g all the possible combinations to ident ify the best one)
align ing real genes.
align them optimally. How -
4. Often, it is necessary to intro duce gaps into one or both sequences to
um. Why are gaps poten tially
ever, mos t align men t prog rams penalize gaps to keep them to a minim
prob lema tic, parti cular ly for sequences that represent codin g regions?
ify at least a couple of
s. The influe nza virus muta tes so rapid ly that you woul d likely be able to ident
enced two viruses from two
muta tions over the leng th of the comp lete virus genome even if you sequ
some considerations in deciding
diffe rent patie nts ·w ithin the same influenza outbreak. What migh t be
two differ ent strains?
whet her two viruses with diffe rent geno me sequences actually represent
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 Bi oC on ce pt Qu es tio ns
t antib iotic resistance, HGT, and how
To successfully complete this chapter's projects, you need to understand a little abou
ions to test your biolog ical under-
similarity measurement can help us decide whether HGT has occurred. Use these quest
.
standing; read BioBackground at the end ~thechapter if you need a better foundation
' ~ ~
Why are the terms "vertical"
1. What is the difference between~ - i~avand horizontal gene transfer?
and "hor izon tal" used to describe tnese processes? ~v
~v ,_
- C' -
mut~tion. Why i~ ~ ~fonsidered ~o
2. Any bact erium could become a_ntibio~ic resista~t by ~eans of
tance? ~ --- ·
,nuch more of a threat, at least in terms of medically impo rtant resis
...
~ l'T"" ·
...,

descen~ed
~o w does the deg~ee of similarity between two genes help us und~rstand wheth~r they \ \\(n
they could ~ave m~ved_from one
\..: )~~r~i~ally from a comn:ion ancestor_(recent O( dist~~_t) or whether 1
s~ec1es to the othe r b y ~ \'a\-\ ~"'~,\o...-,~ ~~
0-1 ~~\W \\\u( ~-9e.ct e..~ b\l~~e~
species have a single, com-
4. Suppose you have evidence that two ge_nes in two different bacterial
occurred. ~ \~ ~l' :
mon origi n. Give two possible explanations for how this migh t have
. ·......... .................. ...................... ·;;1,;.· ..~U \~(:)-'\·\, .............
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 BioConcept Questions
· . d tand the basics of amino-acid structure and the chemical nat
This chapter's projects require you t? un erpsut together. use these questions to test your biological understaurde_of these
b u,·1d·mg bl ocks, as well as how proteins are . I n ing·
h t 1·t you need a better foundation. You may a so want to review the intr0d :rea~
BioBackground at the end of the c ap er . Uct1onto
the genetic code in Chapter 2.

. changes a codon in a gene from GTA (or GUA in mRNA) to GAA. What is the
1. Suppose a mu t at ,on ~ A l • II h
• ·· •

corresponding amino-acid change? What ~--'1(va~s in wh1c;h this s~a c ~nge in DNA could
produce a drastic change in the function of the protein encoded by this g~e.
2 . Even though this particular mutation (GTA to G~) changes ~nly a single nucleotide ~nd.in turn
only a single aming aci~, it ~hould be qu!te ~a~e__!9_91?~-~~"'.~...!h1s change w ~ comp~n~g genes that
are genuinelyrelat~ Why would this be an u~common change?
3 . A mutation that is even more rarefy observed within a coding region is a change from a TGG codon
- ·-·-- ., . -J• - ...- - .._.....

to a TGA codon. Explain why this mutation would be selected against so strongly. _
.~~ .

4 . The enzyme lactase is found in your small intestine and converts lactose from dairy products
into two simple sugars. Some people are lactose Jntolerant because they carry mutations in the
lactase gene that result in production of a less-active enzyme. As you would expect, some of
these mutations change amino acids that are found at the active site of the enzyme, the region
where the lactose actually binds and is split. However, some mutations that affect lactase activity
 change amino acids located far from the active site. What could explain the effect of these .
mutations?
s. suppose a gene's coding region begins with the sequence ATGCTCCGGCAAAGG. A gene in
another organism begins with the sequence ATGTTAAGAAACCGT, so there does not seem to be
much sequence similarity. Is it likely that these two genes encode proteins of similar functions?
(Hint: Translate the sequences before answering the question.)

6• The coding sequence for the Stx toxin in a particular strain of E.coli 0157:H7 begins with
ATGAAGTGTATATTATTTAAA. Suggest one possible single-nucleotide substitution mutation that
would change an amino acid (missense mutation) but would not have a drastic effect on protein
function. Then suggest one missense mutation that would have a drastic effect on protein function.
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 i3iocon cept Quest ions
r sequencing, why does a newly synthesized strand of DNA terminate when DNA
In sange I .d 7 H h po 1Y_
1. inserts a dideoxy nuc eot1 e. ow are t ese terminated DNA strands used to "read"th
rnerasetide sequence of the original DNA molecule? · e
nuc1eo ·..
Wh is shotgun sequencing so much faster ~han the directed approach originally taken by the
2• IHJ?Why
is it more dependent on comp~ter power and bioinformatics?
• If the entire huma_n genome were cleaved into ~ si~gle s_et of small, non-overlapp ing fragments, we
3
could not determine the genome sequence by sequencing the fragments. Explain why this is the case.

4, How do next-genera tion sequencing techniques extend and improve on the shotgun sequencing
technique? What are their disadvantag es?
s. Complex genomes often contain many repeated sequences. For example, there are many STR
(short tandem repeat) sites in the human genome, where a short sequenc~ such as GATA might
be repeated anywhere from a few to dozens of times. Why would an STR region potentially pose a
problem for sequencing? Are next-genera tion techniques more or less susceptible to errors result-
ing from repeated sequences than older technologie s?
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 Bi oC on ce pt Q ue st io ns
ORF s som etim es con side red to be the sam e ~ s gen es? In wha t ways is this definition
1. Why are long 1

-
insufficient? " I

mer ase find the tran scri ptio nal star t site of.a gen e in pro kary otes ? How can we
2 . How does RNA poly
.
use this information in a gene predict.ion algo rith m? .

How doe s RNA poly mer ase find the tran scri ptio nal star t site of a gen e in euk ary ote s? Wh y is it more
3 .
icul t to dev elop an algo rithm to find a euk ~ry otic pro mo ter t~n a pro kar yot ic pro mot er?
diff
doe s a prok aryo tic ribo som e find the corr ect star t cod on with in an mRNA? How can we use
5. How
es?
this info rma tion in distinguishing which ORFs are gen
ch ORFs are gen es in euk ary ote s?
6. Wh y can't we use a similar strategy to dist ingu ish whi
A sim ple ORF -find ing prog ram wou ld do a·ve ry poo r job of pre dict ing the am ino -ac id sequences of
7. · ·
gen ome ._Disc u~s why this is the case.
the pro tein s enc ode d in the hum an . .
.
RNA (tha t doe s not enc ode a pro tein )? How
8. How mig h! you identify a gene encoding a fun ctio nal .
th e discove ry of key func tion s for ver y sma ll RNA mo lecu les com plic ate the issue?
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 BioCo ncept Quest ions
. d d" tor of the point where an exon and intron are-joined? Why is th e
1. Why 1s co on usage a poor pre 1c
5' splice site consensus also a poor predictor?
2 . How much of a typical human gene is usually coding sequenc~, versus intron sequences that are
spliced out (you may wish to recall the gene displays you saw in the UCSC Genome Browser in
Chapter 1)? How does this pattern affect the difficulty of predicting introns and exons?
3 . Why are CpG islands considered valuable for gene prediction? Where would you expect to find one
with respect to a eukaryotic transcription unit? What other elements might you look for in connec-
tion with the CpG island to increase the strength of a gene prediction?
4. How could_alignment of a sequence with orthologous sequences contribute to the prediction of
exons and mtrons? How could expression data (e.g., cDNA sequences) contribute?
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