Comp. Bio Lab Phase 1 quizzes

Which biological process helps the virus get better at infecting a new host?

\
Natural selection

\
Metabolism

\
Homeostasis

\
Cell differentiation

Natural Selection

Which of the following E-values is likely due to chance and not biologically meaningful?

\
1e-100

\
1e-61

\
1

1

Coronavirus polyproteins pp1a and _____ contain the non-structural proteins that are involved in the replication.

\
pp1ab

\
pp1b

\
S

\
N

pp1ab

When a rare mutation by chance allows a protein to infect a new species, this is called a spill-over infection. Which of the following statements is not true about spill-overs

\
The mutation may alter how the virus infects its primary host.

\
Most are successful. Once a virus can infect a new species it does so very well.

\
The mutated virus is usually not very good at infecting the new host.

\
Most spill-overs are dead-ends.

Most are successful. Once a virus can infect a new species it does so very well.

What is an E-value of 0.0?

\
A really large E-value - a really good hit

\
A really large E-value - a really bad hit

\
A really small E-value - a really good hit

\
A really small E-value - a really bad hit

A really small E-value - a really good hit

Which of the following E-values means that the BLAST result is not due to chance and means that there might be a biologically meaningful relationship between the two sequences?

\
10

\
1

\
1e-50

1e-50

The protein on the surface of the coronavirus that sticks out, facilitating attachment to the host cell, is called

\
Spike

\
Nucleocapsid

\
Membrane

\
ACE-2

Spike

True or False: The lower the e-value, the more we can infer homology between a query sequence and a hit.

True

The previous figures are showing the polyprotein 1a and polyprotein 1ab of SARS-CoV-2. What is the name of the protein that is only found in pp1a?

\
Hel

\
NSP11

\
3CL

\
NSP12

NSP11

True or False: Viralzone is a database that can provide you with information about viruses.

True

Coronavirus genomes are approximately 29.9kb in length and are composed of

\
a negative-strand RNA genome

\
a positive-strand RNA genome

\
a DNA genome

\
no genome

a positive-strand RNA genome

BLAST is short for Basic Local Alignment Search Tool and is "roughly speaking" used to

\
find sequences that are related to your search words, e.g. virus proteins

\
find sequences that are related to the sequences that you input

find sequences that are related to the sequences that you input

The reference proteins database will limit the output so that there are no __1__ in the output. Had I used the nr database, there would be __*__1__*__ in my output because nr is __2__.

\
1: missing sequences, 2: small

\
1: duplicate sequences, 2: redundant

1: duplicate sequences, 2: redundant

What is a non-silent mutation?

\
A mutation that changes a nucleotide in a codon but not the amino acid in the protein sequence

\
A mutation that only changes the nucleotide sequence outside of the gene

\
A mutation with a large effect on the protein's function.

\
A mutation that changes a nucleotide in a codon so that the amino acid in the protein sequence will change

A mutation that changes a nucleotide in a codon so that the amino acid in the protein sequence will change

Other coronaviruses with recent spillovers that have caused severe human disease and high mortality are

\
SARS and MERS

\
HIV

\
Ebola

\
SARS

SARS and MERS

What is a likely natural explanation for the origin of SARS-CoV-2, the virus that causes COVID-19?

\
This new virus has just appeared "out of the blue"

\
It may have escaped a laboratory

\
It has evolved from an older animal infecting coronavirus

\
It has evolved from an older animal infecting the influenza virus

It has evolved from an older animal infecting coronavirus

There are other coronaviruses that infect humans and most of them result in a

\
severe rash

\
mild infection such as a cold

\
high mortality

\
severe upper respiratory infection

mild infection such as a cold

Compared to a bacterial cell, viruses are

\
tiny

\
huge

\
about the same size

tiny

Based on what you have read about SARS-CoV-2's genome/expression on ViralZone, subgenomic mRNAs are the result of ________________________ and can be translated into viral proteins.

\
discontinuous transcription

\
natural selection

\
replication

\
spill-over

discontinuous transcription

True or False: A virus reproduces by getting its genes into a living cell, where it uses the cell's machinery to make more copies of itself.

True

It can often be inferred that sequences with a very small Expect value (e-value) are __________________

\
related (homologous)

\
not related

related (homologous)

The Spike protein of SARS-CoV-2 attaches to the host cell using ............receptor?

  

Nicotinic receptors

 

CEACAM

   

ACE2

ACE2

What does BLAST stand for?

  

Biology Lookup and Alignment Search Tool

  

Basic Local Alignment Search Tool

  

Best Lookup Algorithm Search Tool

 

Biotechnology Language Algorithm Search Tool

Basic Local Alignment Search Tool

What is the name of the format of the following sequence:

>A_Spilosum CAE7333586.1 \n MAPMKAMKAAGASKSMKVMKMKAVRALPKSGIAAQVAENTGLKKSAVTQVLSSLADIGATEVKKAGKFVLPGLVMIKTRQ \n KPATKAGKRQMFGKEVLVKAQPAKTVVKAYPVKAVKAQF

\
Tabular

\
BLASTP

\
Genomic

\
FASTA

FASTA

Which biological process, involving mutation events, helps the virus get better at infecting a new host?

  

Homeostasis

  

Natural Selection

 

Metabolism

   

Digestion

Natural Selection

Fill in the one letter abbreviation

 

Phenylalanine

\
Proline

\
Alanine

\
Asparagine

\
Glutamine

\
Aspartate

\
Glutamate

\
Glycine

\
Arginine

\
Lysine

\
Leucine

\
Isoleucine

\
Serine

\
Threonine

\
Tyrosine

\
Tryptophan

\
Valine

\
Histidine

\
Cysteine

\
Methionine

F

P

A

N

Q

D

E

G

R

K

L

I

S

T

Y

W

V

H

C

M

A branch point in a tree suggests that

\
it is the point where different lineages split in two directions

\
convergent evolution

\
the last common ancestor is found in the upper clade

\
this part of the tree is not related to the rest of the tree

it is the point where different lineages split in two directions

Which of the following amino acids is the most hydrophobic?

\
A

\
P

\
S

\
Q

A

Phylogenetic trees can be constructed based on

(select all that apply).

\
RNA

\
protein

\
morphological data

\
DNA

All of the above (check all)

Which of the following amino acids have the most similar physiochemical properties as L?

\
V

\
K

\
R

\
D

V

Which amino acid is the least hydrophobic?

\
R

\
E

\
W

\
F

R

The goal of making a phylogenetic tree is to see how different organisms are related to each other. A phylogenetic tree often has several clades. Which is the best definition of a clade?

\
A clade can be formed by species in different parts of a phylogenetic tree, excluding several species in between as long as they don't have similar morphological characters

\
A clade is another name for a phylogenetic tree

\
A clade contains all decendents found under an ancient organism

\
A clade is an outgroup

A clade contains all decendents found under an ancient organism

Which set of amino acids contains only charged amino acids?

\
H, L, R, N

\
A, G, W, Y

\
I, L, V, M

\
D, E, K, R

D, E, K, R

A synapomorphy is

\
a method for building trees

\
another word for common descent

\
a characteristic shared by all species in a clade

\
a characteristic shared by all species in a tree

a characteristic shared by all species in a clade

Which set of amino acids are all hydrophobic?

\
A, L, V, S

\
H, E, Y, W

\
S, T, Y, R

\
I, V, L, M

I, V, L, M

Which of the following amino acids has **a Positive charge** at pH (\~7.4)?

\
K

\
D

\
E

\
S

K

Which of the following amino acids has **a negative charge** at pH (\~7.4)?

\
H

\
G

\
D

\
F

D

Which of the following is **Polar uncharged** amino acid?

\
G

\
N

\
V

\
E

N

Which of the following is an **extra large** amino acid?

\
Threonine

\
Glycine

\
Serine

\
Tryptophan

Tryptophan

Which of the following pairs of amino acids have the **most similar** properties?

  

Tryptophan & Serine

 

Glutamine & Glycine

  

Lysine & Leucine

  

Valine & Alanine

Valine & Alanine

Q is the one-letter abbreviation of 

  

Lysine

  

Tryptophan

 

Tyrosine

\
Glutamine

Glutamine

Which one of these amino acids **is small**?

  

R

   

W

  

G

   

H

G

All of these amino acids are considered small except

\
F

\
V

\
A

\
L

F

What is the one-letter code for Phenylalanine?

  

G

  

F

  

H

 

C

F

G is the one letter abbreviation for

\
Glycine

\
Serine

\
Alanine

\
Glutamic acid

Glycine

What is the Protein Data Bank, or PDB for short?

  

A publicly available database for predicted macromolecular structures

   

A publicly available database for experimentally determined macromolecular structures

 

A licensed database for experimentally determined macromolecular structures

   

An equivalent database to NCBI

A publicly available database for experimentally determined macromolecular structures

A nucleotide change in a gene will 

  

change the encoded amino acid and but it does not always mean a change in the structure or function of the protein

 

sometimes change the encoded amino acid and but even if the amino acid is changed, it does not always change the structure and function of the protein

 

sometimes change the encoded amino acid and thus the protein's structure

  

change the encoded amino acid and thus the protein's function

sometimes change the encoded amino acid and but even if the amino acid is changed, it does not always change the structure and function of the protein

Why is NMR not a good method for determining the structure of a virus? (check boxes)

\
It shows a dynamic structure

  

It only works for smaller biomolecules

   

It shows a static structure

   

It is in solution

it only works for smaller biomolecules

Which representation shows areas that are accessible to water molecules?

\
Surface diagram

 

Cartoon diagram

   

Ribbon diagram

 

Space-filling diagram

Cartoon diagram

If you want to view a protein's structure which of the following can help? (check boxes)

  

AliView

  

PYMOL

  

BLAST

  

PyMOL

PYMOL

Why are protein structures with higher resolution more desirable?

  

Higher resolution means that longer distances between atoms can be discerned

 

Higher resolution means that it is a newer structure

 

Higher resolution means a higher number of amino acids are included in the structure

 

Higher resolution means greater molecular detail

Higher resolution means greater molecular detail

To determine a structure of a protein using the X-ray method, which of the following is a problematic requirement?

  

The protein must be flexible, but some proteins are rigid

 

The protein must be small, but most proteins are not

   

The protein must be mostly hydrophobic, but most proteins are hydrophilic

 

The protein must be crystallized, but not all proteins form crystals 

The protein must be crystallized, but not all proteins form crystals

What information is found on one ATOM line in the PDB file?

  

The complete set of x, y, and z coordinates for an amino acid residue in the protein structure

 

The x, y, and z coordinates for an atom in the protein structure

The x, y, and z coordinates for an atom in the protein structure

The amino acids in a protein are linked through

  

hydrophobic peptide bonds

 

hydrogen bonds

 

electrostatic interactions

 

covalent peptide bonds

covalent peptide bonds

A protein's primary structure is….

\
* alpha helices and beta strands

\
* its linear amino acid sequence

\
* the most important function

\
* the 3D structure of the protein

its linear amino acid sequence

Which file do you need to view a protein in PyMOL?

  

the PDB file

 

the Phylip file

  

the FASTA file

 

the Newick file

the PDB file

Which coloring option do you think was used to make the following figure?

\
Color by chain

   

Color by atom

   

Color by secondary structure

  

Color by function

color by chain

Which statement is true?

  

Alpha helices and beta sheets are formed by hydrogen bonds between amino acids that are far apart in the linear amino acid sequence

  

An alpha helix is formed by hydrogen bonds between amino acids that are nearby in the linear amino acid sequence, while beta sheets are formed by hydrogen bonds between amino acids further away from each other in the linear amino acid sequence

 

A beta-sheet is formed by hydrogen bonds between amino acids that are nearby in the linear amino acid sequence, while an alpha helix is formed by hydrogen bonds between amino acids further away from each other in the linear amino acid sequence

 

Alpha helices and beta sheets are formed by hydrogen bonds between amino acids that are nearby in the linear amino acid sequence

An alpha helix is formed by hydrogen bonds between amino acids that are nearby in the linear amino acid sequence, while beta sheets are formed by hydrogen bonds between amino acids further away from each other in the linear amino acid sequence

What color are the alpha helices in the picture?

\
magenta

 

light pink

 

dark blue

  

light blue

light blue

Which of the following was recently awarded a Nobel prize for being an up-and-coming technique that allows protein structures of different shapes and sizes to be readily determined at high resolution?

  

NMR

   

X-ray

   

Next-gen sequencing

  

Cryo-EM

Cryo-EM

When a protein folds (or forms its 3D shape) amino acids with side chains that are  ____________ end up buried inside the protein unless it is a membrane protein.

\
small

   

large

  

hydrophilic

   

hydrophobic

hydrophobic

Which amino acid of these can be glycosylated by glycosylation enzymes? (Select all that apply).

\
Y

\
T

\
S

\
N

T, S, N

Which test compares the mean between two populations?

  

Shapiro-Wilk

 

Wilcoxon Rank Sum test

 

Mann-Whitney

  

t-test 

t-test

What is the Null hypothesis (H0) when testing for normality? Select all that apply.

  

If the data is normal, we can be certain that the data in different samples are similar. This means that there is no statistical difference.

  

H0 states that the values are sampled from a population that does not follow a normal distribution.

 

H0 states that there is not statistically significant difference between two samples.

  

H0 states that the values are sampled from a population that follows a normal distribution.

H0 states that the values are sampled from a population that follows a normal distribution.

If your data is normal you can run a parametric test to test if two samples are different from each other. Which of the following tests is suitable? Select all that apply. 

\
a Mann-Whitney test

\
a t-test

\
a Shapiro-Wilk test

\
a Wilcoxon Rank Sum test

a t-test

If your data is not normal you can run a nonparametric test to test if two samples are different from each other. Which test is suitable? Select all that apply.

  

a Wilcoxon Rank Sum test

 

a t-test

\
a Shapiro-Wilk test

  

a Mann-Whitney test

a Mann-Whitney test and a Wilcoxon Rank Sum test

The median is commonly shown as a line in a boxplot. In the boxplots below, the "star" or "dot" shows the mean. Which sample has the smallest mean?

\
Clade 4

   

Clade 1

 

Clade 3

 

Clade 2

Clade 3

True or False: In hypothesis testing of two samples, Are the following definitions of H0 and HA true or false?

H0: Two populations are the not same

HA: Two populations are the same

False

Using a 5% error rate or a p-value of 0.05 to determine if the difference between two samples are statistically significant, what does it mean if the a test is found to have a p-value of 0.1. 

  

H0 is supported. There is no difference between samples.

 

H0 is rejected. There is a difference between samples.

  

H0 is rejected. There is no difference between samples.

   

H0 is supported. There is a difference between samples

H0 is supported. There is no difference between samples.

How does the power of a statistical test depend on sample size? 

\
Large sample can mean too much power.

 

Sample size does not matter.

  

Small sample can mean too much power.

 

Large sample can mean not enough power.

Large sample can mean too much power.

Which amino acid of these can be phosphorylated by kinase enzymes? Select all that apply

\
N

\
T

\
S

\
Y

T, S, Y

What is the Null hypothesis (H0) when testing for normality? Select all that apply.

  

H0 states that the values are sampled from a population that follows a normal distribution.

  

H0 states that the values are sampled from a population that does not follow a normal distribution.

  

If the data is normal, we can be certain that the data in different samples are similar. This means that there is no statistical difference.

  

H0 states that there is not statistically significant difference between two samples.

H0 states that the values are sampled from a population that follows a normal distribution.

How does the power of a statistical test depend on sample size? 

\
Small sample can mean too much power.

  

Large sample can mean too much power.

  

Large sample can mean not enough power.

  

Sample size does not matter.

Large sample can mean too much power.

This picture shows alignment sequences that is mapped to its midpoint rooted tree. According to this picture, Which position of the following is totally conserved?

\
Position 1

 

Position 4

   

Position 2

  

Position 3 

Position 2

This picture shows alignment sequences that is mapped to its midpoint rooted tree. According to this picture, Which position of the following has the lowest evolutionary rate?

\
Position 10

\
Position 8

\
Position 11

\
Position 9

Position 10

This picture shows alignment sequences that is mapped to its midpoint rooted tree. The active site of this family of proteins will bind to a positively charged ligand. According to the picture, which position of the following is the active site?

\
Position 8

\
Position 10

\
Position 2

\
Position 4

Position 8

This figure shows the SARS-CoV-2 nucleocapsid protein colored based on conservation of amino acids in multiple sequence alignment and phylogenetic tree using Consurf webserver. Choose the correct answer based on the previous picture.

\
The site that is evolving fast (Higher evolutionary rate) → ?

\
Possible Active site (low evolutionary rate) → ?

\
More mutations/change are occurring at this site → ?

\
? = A or B

B, A, B

Which of the following is not a post-translational modification?

\
Methylation

\
Phosphorylation

\
Glycosylation

\
Recyclination

Recyclination

True or False: Protein structure is more conserved than the sequence.

True

What would be an appropriate label for the blue box in the boxplot image above? (HINT: It is the same thing as the gray line.)

\
Halftile

  

Median

   

Range

   

Mean

Median

Phosphorylation is the addition of a phosphate group to which of the following amino acids? (select all that apply)

  

Serine (S)

\
Threonine (T)

  

Cytosine (C)

  

Tyrosine (Y)

Serine (S), Threonine (T), Tyrrosine (Y)

BLASTp search was done using the protein data bank (PDB) database to search for structure representatives for NS1 protein from Influenza Virus.  Which of the following results is the best structure representative to use?

   

5YQ4_A

 

6N3H_A

   

5YY8_A

\
More information is needed to determine which one is the best

More information is needed to determine which one is the best