P r e v i e w T e s t : T a ke - h om e E x a m 1 , 2 0 2 1

9/26/21, 7:35 PM Preview Test: Take-home Exam 1, 2021 – MCB-3421-...

https://huskyct.uconn.edu/webapps/assessment/take/launch.jsp?course_assessment_id=_230435_1&course_id=_97685_1&content_id=_5971334_1&step=null 1/11

Preview Test: Take-home Exam 1, 2021

Test Information

Description

Instructions

MultipleAttempts

This test allows multiple attempts.

ForceCompletion

This test can be saved and resumed later.

Your answers are saved automatically.

Please follow the honors code and work on this on your own. This is an open book exam,but if you use sources in your short written answers, you need to provide a citation of thesource.

Please note that there are different types of questions. Multiplechoice questions where youare asked to select the single most correct answer; and multiple answer questions, whereyou are asked to select all correct answers (i.e. there may be more than on correct answer).

QUESTION 1

Which of the following is the currently most often used delineation of thefield of Bioinformatics?

Bioinformatics applies the tools of informatics to biological data

bioinformatics applies the tools of informatics to -omics (proteo-,transcript-, metabol-, gen-, metagenom-, etc) data

bioinformatics applies the tools of informatics to genomic data

bioinformatics applies biological solutions such as the DNA computerto problems in computer sciences

5 points Saved

For the toolbar, press ALT+F10 (PC) or ALT+FN+F10 (Mac).

QUESTION 2

What are the names of the scientists that first used ribosomal RNAs to study the relationshipbetween organisms and discovered the the third domain (aka Ur-kingdom) of life?

5 points Saved

Question Completion Status:

Paragraph Arial

10pt

Click Save and Submit to save and submit. Click Save All Answers to save all answers.

Save All Answers Close Window



Carl Woese and George FoP 5 WORDS POWERED BY TINY


QUESTION 3

What were the names of the scientists who first proposed the Gaia hypothesis?

James Lo elock and L nn Marg lisP 5 WORDS POWERED BY TINY

5 points Saved

QUESTION 4

For most, but certainly not all, scientists, the field of bioinformatics doesNOT include which of the following activities? (Note this is a multipleanswer questions)

Analyzing genome sequence data using computers

Figuring out the structure of a single protein using X-raycrystallography

Use of gene calling software to determine regions in a genome that areencode proteins

Creating a database of morphological characteristics of beetles

Detecting homology using similarity in the secondary ortertiary structure of proteins

Detecting homology using similarity in the amino acid sequence ofproteins

5 points Saved


10pt

Paragraph Arial

10pt



https://www.tiny.cloud/?utm_campaign=editor_referral&utm_medium=poweredby&utm_source=tinymce&utm_content=v5





QUESTION 5

Are viruses alive? Please include 2-4 points of evidence to back up your answer (simply a yesor no will not suffice). Answers that argue that this questioned cannot be answered will also beconsidered, provided you give a reasonable justification. You also could give a split answer,"Yes" because ..., "No" because ... . Be bold! (you might get extra credit, not for bold font, but for bold content).

Viruses are part of the biosphere. Dividing living systems into smaller and smaller units ends up with units which fail most definitions of life. Some have argued that viruses are not alive because they do not have metabolism; however, the virus factories set up in host cells do ha e metabolism Vir ses are certainl dependent on other li ing entities b t so are mostP 65 WORDS POWERED BY TINY

10 points Saved


QUESTION 6

The Levinthal's paradox argues that if a protein would fold randomly in an undirected fashion itwould take longer than the age of the universe for a protein to explore the possibleconformation space. How did Levinthal arrive at the number of possible conformations of the PHI and PSI angles ateach alpha carbon along the peptide backbone? Why did he only consider a limited number of conformations? What was the number he assumed?

10 points Saved


Paragraph Arial

10pt

Paragraph Arial

10pt






The staggered conformations are most stable, thus for each angle, he only considered the three staggered conformations, For each alpa carbon that is part of the peptide backbone, he considered 2 x 3 possible confomations. From slide 12, class 1: "100 amino acids has 99 peptide bonds, each with a phi and psi angles, resulting in a total of 198 angles around which the peptide backbone can rotate. If each of these can exist in three possible energetic minima (the sidechains are staggered), one arrives at 3198 = 3•1094 possible

f tiP 92 WORDS POWERED BY TINY


QUESTION 7

How many peptides (short proteins) of 75 amino acids in length are possible, giventhat there are 20 possible amino acids? For your answer only consider the principles ofcombinatorics and ignore possible incompatibilities between neighboring amino acids.How does this number compare to the estimated number of elementary particles* orprotons* in the universe? * your choice, pick one or both for comparison

2075 = 3.8 x 1097

This is much more than the number of protons in the known universe, and about the same order of magnitude as the estimated number of elementary particles (mostly photons) in theP » SUP 38 WORDS POWERED BY TINY

10 points Saved

QUESTION 8

How many types of subunits form F1-ATPase? Note: this asks forthe different types of subunits, encoded by separate genes, not the number ofsubunits in the hexamer. What are the names given to the subunit types? What is the function of the different subunit types? Which of these types are homologous? Try to be concise in your answer (if your answer contains everything and thekitchen sink we will substract points)

10 points Saved


Paragraph Arial

10pt








kitchen sink, we will substract points).

The F1 ATPase we looked at in the 3rd computer lab had 3 alpha, 3 beta and 1 gamma subunit, i.e. three types of subunits

beta: binds and hydrolyses ATP and rotates the gamma subunit. (or synthesizes ATP from ADP and Pi using the mechanical energy transmitted to F1 through the rotation of the gamma subunit.

alpha: binds ATP but does not hydrolyze it. Often described as regulatory subunit. Also was reported to be a chaperone for the beta subunit.

gamma subunit: communicates the mechanical energy to the Fo part of the ATPase.

Alpha and beta subunits are homologs (ancient paralogs), P 127 WORDS POWERED BY TINY

A.

B.

C.

D.

E.

QUESTION 9

Which elements make up the secondary structure of proteins?

Beta barrels, alpha corkscrews, and delta turns.

Van der Waals interactions, hydrogen bonds, and disulfide bridges.

Hydrophobic domains, nucleotide binding motifs, and proteinchannels.

Multiple protein chains interacting to form one macromolecule.

Beta sheets, alpha helices, beta turns, and omega loops.

5 points Saved

A.

B.

C.

QUESTION 10

What does the Gaia hypothesis postulate?

Earth’s plants control the planet’s temperature by selection forflower color

All life on Earth descended from ONE common ancestor

The unit of life is Earth's entire biosphere, because no singlespecies can exist in complete isolation. The ecosystems on the

5 points Saved


Paragraph Arial

10pt






D.

E.

F.

p p yEarth are protected by negative feedback loops that help maintainhomeostasis.

Mars cooled faster than the Earth and therefore was a morehabitable place for life earlier. Life arose first on Mars and traveledto Earth on meteorites

Large glaciers and ice ages result from a runaway cold-house,where the Earth gets colder because glaciers reflect more light fromthe surface

Zircon crystals in 3.8 billion year old rocks were produced byancient life over 4 billion years ago. The zircon crystals are formedby running water and the bias in carbon isotope ratios indicates thepresents of life.

A.

B.

C.

D.

E.

QUESTION 11

What is homology?

The creation of artificial life by any means.

A difference found because of diverging evolutionary paths sincethe last common ancestor.

Similarity due to shared ancestry, i.e. both got it from a commonancestor.

When two proteins share a function, such as nucleotide binding,they also share sequence similarities, because of the limited size ofprotein space.

Shared sequence similarity based on convergent evolution, i.e. theancestor did not have it.

5 points Saved


QUESTION 12

A friend of yours is writing a report for a biochemistry lab. In describing a sequence alignmentshe concludes that the sequences are 55% identical and 65% homologous. What would youtell her to consider in improving the description of the alignmnet?

5 points Saved


Paragraph Arial

10pt





Your friend is likely confusing similarity and homology, a frequent occurence among molecular biologists. You should suggest to use similarity instead of homology. (Similarity P 30 WORDS POWERED BY TINY

A.

B.

C.

D.

E.

QUESTION 13

Proteins that evolved from the same ancestral protein

ALWAYS have significant similarity in their primary sequence.

Cannot have different functions

Can diverge so that they have only limited homology.

Do not necessarily retain detectable similarity in their primarysequence.

Will ALWAYS have detectable levels of primary sequence similarity

5 points Saved

QUESTION 14

How does Lysozyme destroy the stability of the bacterial cell wall?

Lysozyme prevents crosslinks made out of short peptides to beformed between the NAG-N-acetylmuramic acid polymers.

Lysozyme cleaves the crosslinks made out of short peptides thatconnect the NAG-N-acetylmuramic acid polymers.

Lysozyme cleaves the beta 1-4 glycosidic bond between NAG and N-acetylmuramic acid.

Lysozyme prevents the final transpeptidation step in the synthesisof the peptidoglycan.

5 points Saved

QUESTION 15

In the lysozyme structure 1HEW, the enzyme is crystallized together withan NAG trimer. This trimer

is a substrate of lysozyme

is an inhibitor of lysozyme

is the naturally occurring substrate of lysozyme

binds to the substrate binding site of lysozyme

binds to a subunit of lysozyme that regulates the catalytic activity

10 points Saved







QUESTION 16

Which of the following are NOT part of the explanation for how complexfunctional molecules were assembled despite the vastness of proteinspace.

There are multiple unrelated solutions for the same functionality,exemplified by the fact that there are non-homologous enzymesinhabiting completely different regions of protein space with the samefunction.

An exact function does not need to be hit upon, because naturalselection can take a protein with limited function and make it better.

Gaia directs protein evolution, through negative feedback loops, to thecorrect region of protein space.

Similar structures have similar function, so there are entire regions ofprotein space occupied by homologs that all function equally well, ornearly so.

Protein space is made slightly smaller by removing all of thepossibilities that cannot be synthesized or they will clog up theribosome

10 points Saved

True

False

QUESTION 17

In the catalytic cycle of the ATPase, all of the catalytic subunits work indifferent phases of the catalytic cycle at any one point in time.

5 points Saved

QUESTION 18

If the murein sacculus of a bacterial cell is weakened, the cells may die

because the cells blow up, because the osmotically driven water influxis no longer balanced by the turgor pressure.

because the osmotically driven influx of water changes theintracellular ion concentration leading to an inhibition of proteinbiosynthesis

because without a turgor pressure the cells can nolonger importsugars and other substrates

5 points Saved


QUESTION 19

Give a very brief description of the conditions under which evolutions by natural selectionoccurs.

5 points Saved






p

Offspring similar, but not identical to parents. This variation is inherited. More offspring than needed for replacement of the parent generation.* Competition for resources.

* It seems possible to replace fitness measured by number of offspring through differential persistence E g a geochemical cycle might be selected for because it persists whereasP 52 WORDS POWERED BY TINY

QUESTION 20

Transcription denotes the process

the inverse DNA strand is transcribed from a DNA strand

by which mRNA is synthesized on a DNA template

a protein sequenced is transcribed from an mRNA at the ribosome.

the processing of a pre-mRNA to the final mRNA that can betranslated into a protein at the ribosome.

5 points Saved

QUESTION 21

Translation denotes the process by which

mRNA is synthesized on a DNA template

the inverse DNA strand is transcribed from the complementary DNAstrand

a protein is synthesized from an mRNA at the ribosome.

a pre-mRNA is processed into the final mRNA that can be translatedinto a protein at the ribosome.

5 points Saved

QUESTION 22

Moritz Traube discovered that cells begin to grow when Copper sulfate crystals are thrown intoa potassioum hex a cyano fer rate (II) solution. What characteristics do these cells share with life and why today do we not consider them

10 points Saved

Question Completion Status: Paragraph Arial

10pt







What characteristics do these cells share with life, and why today do we not consider themalive ?

they grow

they respond to the environment (different osmotic values in the solution lead to different morphologies), but their main response is falling apart if the solution is agitated

the have a semipermeable membrane separating inside from outside.

BUT

they do not have inheritanceP 44 WORDS POWERED BY TINY


QUESTION 23

The RNA World hypothesis says that before a biology that depended on different biopolymers(DNA, RNA, Protein), a single biopolymer world existed in which RNA was the only biopolymerused for information storage and as catalyst. Briefly summarize the arguments for the existence of an RNA world.

RNA can be both catalyst and genetic material

It is central in todays biology. Proteins are made by ribosomes, and the ribosomes catalytic activity resides in the ribosomal RNA

Man cofactors are deri ed from n cleotides and this can be considered a remnant of theP 46 WORDS POWERED BY TINY

10 points Saved


Paragraph Arial

10pt

Paragraph Arial

10pt










Documents

P r e v i e w T e s t : T a ke - h om e E x a m 1 , 2 0 2 1