Lab 5 Comparative Proteomics

Proteomics is primarily concerned with:
A) The study of genes and their sequences
B) The study of proteins, including their structures and functions
C) The study of RNA transcription mechanisms
D) The study of DNA replication

B) The study of proteins, including their structures and functions

The proteome differs from the genome because:
A) The proteome is constant while the genome changes frequently
B) The genome varies between cell types, but the proteome does not
C) The proteome changes depending on cell type, life stage, and environmental conditions
D) Both the genome and proteome remain constant throughout life

C) The proteome changes depending on cell type, life stage, and environmental conditions

Which of the following contributes most to protein diversity beyond the number of genes?
A) DNA replication errors
B) Alternative splicing and posttranslational modifications
C) The size of chromosomes
D) RNA degradation

B) Alternative splicing and posttranslational modifications

The Human Proteome Organization (HUPO) primarily aims to:
A) Sequence the human genome
B) Catalog all human proteins and study their functions and interactions
C) Develop gene-editing technologies
D) Study evolution through fossil records

B) Catalog all human proteins and study their functions and interactions

The central dogma of molecular biology states that information flows from:
A) Protein → RNA → DNA
B) DNA → RNA → Protein
C) RNA → DNA → Protein
D) DNA → Protein → RNA

B) DNA → RNA → Protein

One reason humans have only slightly more genes than C. elegans but are more complex is:
A) Humans have more chromosomes
B) Humans have a larger genome and more regulatory DNA controlling protein production
C) Worms do not have alternative splicing
D) Worms have fewer proteins overall

B) Humans have a larger genome and more regulatory DNA controlling protein production

Which of the following is NOT a mechanism that allows one gene to code for multiple proteins?
A) Alternative splicing
B) Posttranslational modification
C) Translational frameshifting
D) DNA methylation

D) DNA methylation

True or False Proteomics is simpler than genomics because the genome is constant while the proteome changes.

False

True or False The proteome of a cell is identical in all cells of an organism.

False

True or False Posttranslational modification of proteins contributes to protein diversity.

True

True or False According to Darwin, natural selection occurs because organisms produce more offspring than the environment can support.

True

True or False The central dogma implies that all information in DNA is directly translated into proteins without exception.

False

True or False Alternative splicing allows a single gene to produce multiple protein variants.

True

True or False The Human Genome Project confirmed that humans have over 100,000 genes.

False

RNA editing can alter proteins by:
A) Substituting, inserting, or deleting bases in mRNA
B) Changing the DNA sequence
C) Directly degrading proteins
D) Preventing transcription entirely

A) Substituting, inserting, or deleting bases in mRNA

Alternative splicing allows a single gene to produce:
A) Only one protein per gene
B) Different mature mRNAs that generate distinct proteins
C) DNA sequences with introns only
D) Proteins without amino acids

B) Different mature mRNAs that generate distinct proteins

Which of the following increases mRNA stability and thus protein expression?
A) Ubiquitination
B) Capping with 7-methyl guanosine and polyadenylation
C) Phosphorylation
D) Glycosylation

B) Capping with 7-methyl guanosine and polyadenylatio

Proteolytic cleavage can:
A) Only degrade proteins entirely
B) Activate or inactivate proteins by removing specific domains
C) Edit RNA codons
D) Modify DNA promoters

B) Activate or inactivate proteins by removing specific domains

Protein degradation is often regulated by:
A) RNA splicing
B) Polyadenylation
C) Ubiquitin tagging and proteasomes
D) Glycosylation

C) Ubiquitin tagging and proteasomes

The activity of many proteins depends on:
A) Their concentration only
B) The presence or absence of binding partners in protein complexes
C) The number of introns in their genes
D) DNA methylation

B) The presence or absence of binding partners in protein complexes

Carbohydrate modifications (glycosylation) of proteins are important for:
A) Protein degradation
B) Protein targeting and interactions with other proteins or structures
C) RNA splicing
D) Transcription initiation

B) Protein targeting and interactions with other proteins or structures

Phosphorylation regulates protein activity primarily by:
A) Changing the protein’s DNA sequence
B) Causing conformational changes in the protein
C) Removing carbohydrates
D) Altering mRNA stability

B) Causing conformational changes in the protein

RNA editing provides an evolutionary advantage because:
A) DNA mutations are reversible and low-risk
B) RNA edits are optional and reversible, allowing flexible adaptation
C) It eliminates the need for protein translation
D) It prevents mRNA degradation

B) RNA edits are optional and reversible, allowing flexible adaptation

True/False RNA editing only occurs in messenger RNA and never in transfer RNA.

False

True/False Alternative splicing allows exons to be differentially included or excluded in mRNA

True

True/False The stability of mRNA can affect protein expression levels in cells.

True

True/False Proteolytic cleavage can result in proteins of different sizes derived from the same gene.

True

True/False Ubiquitin tagging targets proteins for degradation in proteasomes.

True

True/False Protein-protein interactions have no effect on protein function.

False

True/False Glycosylation can alter a protein’s molecular weight and physiochemical properties.

True

True/False Phosphorylation always activates proteins.

False

True/False RNA editing is a rare, non-regulated process with no role in adaptation.

False

The basic contractile units of a muscle fiber are called:
A) Myofibrils
B) Sarcomeres
C) Actin filaments
D) Myosin filaments

B) Sarcomeres

Myofibrils are:
A) Bundles of sarcomeres within muscle fibers
B) Thick filaments only
C) Another name for muscle fibers
D) Thin filaments only

A) Bundles of sarcomeres within muscle fibers

Muscle contraction occurs when:
A) Actin filaments shorten independently
B) Myosin hydrolyzes ATP to slide along actin filaments, shortening the sarcomere
C) Sarcomeres elongate due to ATP consumption
D) Muscle fibers synthesize more actin

B) Myosin hydrolyzes ATP to slide along actin filaments, shortening the sarcomere

Which of the following statements is TRUE about actin and myosin?
A) They are highly variable across animal species
B) They are highly conserved across animal species
C) Only myosin is conserved, actin varies widely
D) Both are only found in human muscle

B) They are highly conserved across animal species

Variability in other muscle proteins besides actin and myosin is thought to:
A) Reduce muscle performance
B) Reflect adaptations to specific environments or physiological stresses
C) Occur randomly without function
D) Only affect non-contractile tissues

B) Reflect adaptations to specific environments or physiological stresses

The combined contraction of many sarcomeres along a muscle fiber:
A) Causes elongation of the muscle
B) Causes contraction of the entire muscle
C) Has no effect on the muscle fiber
D) Only occurs during passive stretching

B) Causes contraction of the entire muscle

Which muscle proteins are most likely to be highly conserved across all fish species?
A) Actin and myosin
B) Troponin and tropomyosin
C) Titin and nebulin
D) Myoglobin and creatine kinase

A) Actin and myosin

The primary function of sarcomeres in muscle fibers is to:
A) Store calcium ions
B) Facilitate ATP production
C) Contract and generate force
D) Maintain the shape of the muscle fiber

C) Contract and generate force

Which of the following fish groups is considered the most evolutionarily ancient among jawed vertebrates?
A) Actinopterygian (ray-finned)
B) Chondrichthyes (cartilaginous fish)
C) Sarcopterygian (lobe-finned fish)
D) Teleosts

B) Chondrichthyes (cartilaginous fish)

SDS-PAGE is useful in comparative proteomics because it can:
A) Measure the exact amino acid sequence of proteins
B) Show the presence or absence of specific proteins based on molecular weight
C) Determine the DNA sequence that encodes a protein
D) Replace phylogenetic analysis

B) Show the presence or absence of specific proteins based on molecular weight

Which statement best explains why actin and myosin are not sufficient alone to infer evolutionary relationships?
A) They are only found in mammals
B) They are highly conserved across all species
C) They degrade too quickly to be useful
D) They do not interact with ATP

B) They are highly conserved across all species

Comparing muscle proteins of a fast-swimming tuna and a slow-moving coelacanth could help scientists:
A) Determine the diet of each fish
B) Infer adaptive differences in muscle function related to swimming performance
C) Measure the intelligence of each species
D) Identify the presence of swim bladders

B) Infer adaptive differences in muscle function related to swimming performance

Which of the following is a correct method to construct phylogenetic trees using protein data?
A) Align amino acid sequences of homologous proteins across species
B) Compare only the presence or absence of actin
C) Measure the muscle contraction speed directly
D) Use SDS-PAGE to measure DNA content

A) Align amino acid sequences of homologous proteins across species

Which statement is true about using bioinformatic databases in evolutionary studies?
A) They only contain human protein sequences
B) They allow comparison of protein sequences across multiple species to infer evolutionary relationships
C) They can measure ATP hydrolysis rates in muscle
D) They replace the need for experimental data entirely

B) They allow comparison of protein sequences across multiple species to infer evolutionary relationships

Which muscle proteins might vary most between species due to environmental adaptation?
A) Actin and myosin
B) Regulatory proteins such as troponin, tropomyosin, and myosin light chains
C) Collagen in connective tissue
D) Ribosomal proteins

B) Regulatory proteins such as troponin, tropomyosin, and myosin light chains

Observing similar muscle proteins in distantly related fish species living in fast-flowing water is an example of:
A) Divergent evolution
B) Convergent evolution
C) Genetic drift
D) Random mutation

B) Convergent evolution

What is the main purpose of SDS in SDS-PAGE?
A) To maintain the protein's native 3D structure
B) To give proteins a uniform negative charge and denature them
C) To act as a molecular weight marker
D) To stain the proteins for visualization

B) To give proteins a uniform negative charge and denature them

Why are polyacrylamide gels used for proteins instead of agarose gels?
A) Proteins are larger than DNA fragments
B) Polyacrylamide gels have pore sizes suitable for proteins
C) Agarose gels can only be used with RNA
D) Proteins are negatively charged, so agarose cannot separate them

B) Polyacrylamide gels have pore sizes suitable for proteins

What is the role of the stacking gel in SDS-PAGE?
A) To separate proteins strictly by size
B) To concentrate proteins into a narrow band before entering the resolving gel
C) To provide a pH gradient for protein denaturation
D) To act as a buffer for SDS

B) To concentrate proteins into a narrow band before entering the resolving gel

Which of the following is NOT disrupted during SDS-PAGE sample preparation?
A) Primary structure
B) Secondary structure
C) Tertiary structure
D) Quaternary structure

A) Primary structure

Why might a reducing agent like DTT or BME be added to the sample buffer?
A) To help proteins migrate faster
B) To break disulfide bonds and ensure full denaturation
C) To stain the proteins for visualization
D) To increase the negative charge of the proteins

B) To break disulfide bonds and ensure full denaturation

What does a prestained molecular weight marker allow you to do?
A) Identify unknown proteins by sequence
B) Track protein migration and estimate molecular weights
C) Denature proteins completely
D) Quantify protein concentration

B) Track protein migration and estimate molecular weights

The major muscle proteins actin and myosin are visible in SDS-PAGE because:
A) They are unique to fish muscle
B) They are highly conserved and abundant in all muscle tissues
C) They migrate faster than other proteins
D) They are stained preferentially by SDS

B) They are highly conserved and abundant in all muscle tissues

Which factor primarily determines the migration rate of proteins in SDS-PAGE?
A) Net protein charge
B) Protein shape in native state
C) Molecular weight
D) Presence of cofactors

C) Molecular weight

Why is it difficult to definitively identify proteins using SDS-PAGE alone?
A) SDS alters the molecular weight of proteins
B) Proteins of similar size may be different, and post-translational modifications affect migration
C) Gels cannot separate proteins smaller than 220 kD
D) SDS-PAGE destroys all protein staining ability

B) Proteins of similar size may be different, and post-translational modifications affect migration

What is the purpose of heating protein samples to 95°C before SDS-PAGE?
A) To activate SDS
B) To denature proteins and ensure linear chains
C) To improve the binding of Coomassie stain
D) To polymerize the gel

B) To denature proteins and ensure linear chains

What is the primary goal of comparing protein banding patterns in different fish species?

A) To determine which fish are the largest in size
B) To infer evolutionary relationships among fish species
C) To identify the fastest-swimming fish
D) To measure protein concentration

B) To infer evolutionary relationships among fish species

In cladistic analysis of SDS-PAGE results, what does a shared protein band between two fish species indicate?

A) That the fish live in the same habitat
B) That the fish share a common ancestor
C) That the fish have identical DNA sequences
D) That the fish are the same species

B) That the fish share a common ancestor

Why might salmon and trout have very similar protein banding patterns?

A) Because they share a recent evolutionary ancestor
B) Because they eat the same food
C) Because they are the same species
D) Because the gel was run incorrectly

A) Because they share a recent evolutionary ancestor

Why is it not strictly necessary to determine the exact molecular weights of proteins when constructing a cladogram from SDS-PAGE?

A) Because protein bands are irrelevant for evolutionary analysis
B) Because the migration distance of bands alone can indicate shared characteristics
C) Because molecular weight measurements are inaccurate
D) Because all fish proteins have the same weight

B) Because the migration distance of bands alone can indicate shared characteristics

What is the purpose of creating a standard curve in SDS-PAGE analysis?

A) To separate large proteins from small proteins
B) To convert protein migration distance into molecular weight
C) To stain the proteins for visibility
D) To measure fish body size

B) To convert protein migration distance into molecular weight

Which proteins would a 15% polyacrylamide gel best separate?

A) Very large proteins (>200 kD)
B) Medium-sized proteins (40–100 kD)
C) Small proteins (<40 kD)
D) DNA fragments

C) Small proteins (<40 kD)

In a character matrix for cladogram construction, what do the entries typically represent?

A) The presence or absence of specific protein bands in each species
B) The total number of proteins in each species
C) The swimming speed of each species
D) The geographic distribution of each species

A) The presence or absence of specific protein bands in each species

If two fish share only one protein band out of several, what does this suggest?

A) They are closely related
B) They are distantly related
C) They are the same species
D) They have identical protein profiles

B) They are distantly related

In constructing a cladogram from SDS-PAGE results, which fish is placed as the outlier?

A) The fish with the most bands in common with others
B) The fish with the least bands in common with others
C) The fish with an intermediate number of shared bands
D) The fish with the heaviest proteins

B) The fish with the least bands in common with others

In a cladogram, what does a node represent?

A) A single protein band
B) A common ancestor of the descendant species at that branch
C) The heaviest fish in the analysis
D) The first fish to appear in evolutionary history

B) A common ancestor of the descendant species at that branch

If two fish share 10 protein bands, what can be inferred?

A) They are distantly related
B) They are likely closely related
C) They have identical DNA
D) They are the outliers in the cladogram

B) They are likely closely related

Why might a fish like sturgeon be tricky to place on a cladogram?

A) It shares more proteins with the outlier fish than with other fish
B) It shares an intermediate number of proteins with multiple groups
C) It has no proteins in common with any other fish
D) Its proteins are too large for SDS-PAGE analysis

B) It shares an intermediate number of proteins with multiple groups

What is the function of SDS in SDS-PAGE?

A) To preserve the protein’s 3D structure
B) To denature proteins and give them a uniform negative charge
C) To increase protein size
D) To visualize the proteins directly

B) To denature proteins and give them a uniform negative charge

In SDS-PAGE, why do smaller proteins migrate faster through the gel?

A) They are less negatively charged than larger proteins
B) They are more compact and experience less resistance in the gel matrix
C) They are lighter and therefore pulled faster by the cathode
D) They react with the tracking dye to increase speed

B) They are more compact and experience less resistance in the gel matrix

Which structural level of protein is destroyed by SDS and heat during sample preparation?

A) Primary structure only
B) Secondary and tertiary structure only
C) Tertiary and quaternary structure
D) Quaternary structure only

C) Tertiary and quaternary structure

What does the intensity of a protein band in SDS-PAGE indicate?

A) The size of the protein
B) The number of protein molecules at that position
C) The charge of the protein
D) The rate of migration

B) The number of protein molecules at that position

How is the molecular weight of a protein estimated in SDS-PAGE?

A) By comparing the color of the band to a standard
B) By comparing the distance migrated to a standard curve of known protein sizes
C) By measuring the thickness of the band
D) By calculating the number of amino acids directly from the sequence

B) By comparing the distance migrated to a standard curve of known protein sizes

What does a polyacrylamide gel do in SDS-PAGE?

A) Denatures proteins
B) Acts as a molecular sieve to separate proteins by size
C) Stains proteins for visualization
D) Generates an electric field

B) Acts as a molecular sieve to separate proteins by size

Why will you add Laemmli sample buffer to your fish samples? (Select all that apply)

A. Laemmli sample buffer contains SDS to coat and denature the proteins.

B. Laemmli sample buffer contains glycerol to help the sample sink into the well.

C. Laemmli sample buffer contains β-mercaptoethanol to reduce disulfide bonds.

D. Laemmli sample buffer contains Tris buffer to specifically bind to the fish proteins.

A. Laemmli sample buffer contains SDS to coat and denature the proteins.

B. Laemmli sample buffer contains glycerol to help the sample sink into the well.

C. Laemmli sample buffer contains β-mercaptoethanol to reduce disulfide bonds.

What is the purpose of heating the samples?

A. To ensure the proteins are fully denatured.

B. To sterilize the sample from any bacterial contamination.

C. To help the proteins refold into their native conformation.

D. To activate enzymes that will digest the proteins.

A. To ensure the proteins are fully denatured.

How are the proteins extracted from the fish samples?

A. Freezing

B. Centrifugation

C. Sonication

D. Heating in sample buffer

E. Agitation

D. Heating in sample buffer

E. Agitation

SDS-coated proteins carry a ___ that is proportional to the ___ of the protein. In an electric field, they will move towards the ___?

A) Positive charge / molecular weight / cathode (negative electrode)
B) Negative charge / molecular weight / anode (positive electrode)
C) Negative charge / length of polypeptide chain / cathode (negative electrode)
D) Positive charge / length of polypeptide chain / anode (positive electrode)

B) Negative charge / molecular weight / anode (positive electrode)

What is the purpose of the actin and myosin standards and the Precision Plus Protein Kaleidoscope pre-stained standard?

A) To act as a negative control, showing where no proteins should appear on the gel.
B) To stain the unknown proteins in the fish muscle samples, making them visible during electrophoresis.
C) To create the standard curve for quantifying the concentration of total protein in the samples.
D) To serve as references for known muscle proteins. These proteins should be observed in all muscle tissue samples.

D) To serve as references for known muscle proteins. These proteins should be observed in all muscle tissue samples.

Which proteins will migrate farthest? Why?

A) The smallest proteins will migrate the farthest because they will be most easily able to move through the gel matrix.
B) The most negatively charged proteins will migrate the farthest because they are more strongly attracted to the positive electrode.
C) The most compact, globular proteins will migrate the farthest because they experience less friction with the gel.
D) The largest proteins will migrate the farthest because they are heavier and are pulled through the gel with more force.

A) The smallest proteins will migrate the farthest because they will be most easily able to move through the gel matrix.

What is the purpose of the stain?

A) To denature the proteins, causing them to unfold into a linear shape.
B) To separate proteins based on their molecular weight.
C) To give all proteins a uniform negative charge for migration.
D) To visualize the proteins by giving them a blue color.

D) To visualize the proteins by giving them a blue color.