Protein Structure & Translation

Change the first base in the simulation back to adenine by clicking on the letter three more times. Click on other bases in the sequence and run the simulation to see what peptide is created. How many codons in this sequence can be altered at a single position to result in a prematurely terminated peptide?

1

Referring to the figure, what is the codon (5'>3') that specifies the addition of Arg (amino acid argenine) to the polypeptide?

AGA

Which step occurs in the A site of the ribosome during translation?

An incoming charged tRNA binds to this site.

Which of the answer choices occurs in the E site of the ribosome during translation?

An uncharged tRNA is ejected from this site as the ribosome slides to the next codon.

tRNA genes are transcribed by:

RNA polymerase.

This image represents _____________ and _______________ is attached at the outlined region labeled ______.

a tRNA; an amino acid; A

The protein shown being synthesized during the animation is:

actin

Endomembrane System. Consider a protein that is targeted to be excreted to the outside of the plasma membrane. Where would this protein be located in the endoplasmic reticulum?

in the lumen (inside) of the E.R.

In which eukaryotic organelle are various macromolecules broken down and destroyed?

lysosome

Which components make up the ribosome?

protein, RNA

Ribosomes in prokaryotes and eukaryotes are:

similar in structure and translate using the same genetic codes.

Which of the following types of RNA molecule delivers amino acids to the ribosomes?

transfer RNA

How many aminoacyl-tRNA synthetase enzymes must be present in cells to properly synthesize proteins?

20, one for each amino acid

Which tRNA anticodon sequence is the correct match to the mRNA codon listed below? Note: codon-anticodon base-pairing is antiparallel. 5'-CGA-3'

3'-GCU-5' The tRNA anticodon always binds antiparallel to the mRNA codon. The 5'end of the tRNA anticodon is therefore complementary to the 3'end of the mRNA codon. Since the answer choices for the mRNA codon sequence are written 3'to 5', start with the 5'end of the tRNA anticodon and determine the complementary base of the mRNA codon written from the 3'end. Also, since we are looking for the mRNA codon sequence, it will include uracils and not thymines. This is why 3'-GCU-5' is correct and 3'-GCT-5' is incorrect.

Referring to the figure, what is the anticodon of the next tRNA to enter the A site?

3'CUU5'

For the numbered steps below, select the option that places them in the correct order. 1) The ribosome binds to the mRNA and uses tRNAs to translate mRNA into the corresponding amino acid polypeptide sequence. 2) The spliceosome removes introns. 3) The primary structure of the polypeptide chain undergoes hierarchical foldings to form the tertiary structure. 4) RNA polymerase binds to the promoter region of a gene and initiates transcription.

4 > 2 > 1 > 3 A gene must first be transcribed from DNA into RNA. This is carried out by RNA polymerase, which binds to the promoter region of a gene to initiate transcription. After the gene has been transcribed, the spliceosome removes the non-protein-coding regions (introns). The mature mRNA transcript is then exported from the nucleus to the cytoplasm where the ribosome can bind and use tRNAs to translate the mRNA into the corresponding amino acid polypeptide sequence. Once the polypeptide chain has been translated, the chain then undergoes hierarchical foldings from primary structure (linear sequence of amino acids) to tertiary structure (3-dimensional, fully-folded protein).

The nonmutant version of the simulated stretch of DNA (the sequence shown when the simulation first loads) depicts synthesis of a peptide that is how many amino acids in length?

5

Consider the events that describe the progress of a protein that will be secreted from the cell. 1. SRP binds to the growing polypeptide chain and to the ribosome. 2. Translation resumes. 3. SRP binds to its receptor. 4. The signal sequence is cleaved. 5. Protein synthesis begins in the cytosol. 6. Translation pauses. Which of the sequences of events correctly describes the progress of a protein that will be secreted from the cell?

5 → 1 → 6 → 3 → 2 → 4

Which of the following mRNA processing events occurs in the nucleus of human cells? (Select all that apply.) 5' cap addition splicing of exons excision of introns poly-A tail addition

5' cap addition splicing of exons excision of introns poly-A tail addition

Shown here is a portion of the final mRNA sequence. Which sequence is from the corresponding DNA template strand? mRNA 5'-CCAUGUUCGAAUGGCUUG-3'

5'-CAAGCCATTCGAACATGG-3' The mRNA strand is always complementary (antiparallel) to the template DNA strand. The 5' end of the template DNA is complementary to the 3' end of the mRNA strand. To determine the sequence of a DNA template strand, work backwards from the 3' end of the mRNA. Note that when we are looking for the DNA sequence, there are thymines instead of uracils in the sequence. For this reason 5'-CAAGCCATTCGAACATGG-3' is correct and 5'-CAAGCCAUUCGAACAUGG-3' is incorrect.

Assuming A-U and G-C pairing between the anticodon and the codon, what anticodon in tRNAMet would pair with the codon 5′-AUG-3′?

5′-CAU-3′

In the evolution of resistance in the malaria parasite to pyrimethamine, what do you think happened to the mutations that decreased survival or reproduction of the parasites?

A mutation that decreases survival or reproduction will likely decrease in number in each generation because mutant forms leave fewer offspring than nonmutant forms. Eventually, the harmful mutation may disappear from the population because its final carriers failed to survive or reproduce. In the extreme case when the harmful mutation causes death or sterility, it can disappear in just one generation.

Enzymatic catalysis of the peptide bond between the growing polypeptide and the next incoming amino acid takes place in which binding site?

A site

Which base pairing is incorrect? A-G A-T U-A G-C

A-G

Several sets of percentage of DNA bases that make up the genome are listed below. Which set is correct?

A: 30%, T: 30%, G: 20%, C: 20% Since all the adenine bases pair with the thymine bases, the percentage of these two bases must equal each other. The same is true for guanine and cytosine bases. The total percentage of all the bases in the genome must add up to 100%.

The interactions between amino acids are major factors in determining the shape of a protein. These interactions can be affected by the environment surrounding a protein. Which factor would have an effect on the shape of a protein? the concentrations of ions present in the environment All of these choices are correct. whether the other molecules in the environment are predominantly hydrophilic or hydrophobic the temperature of the environment. the pH of the environment

All of these choices are correct.

What are the three major groups of amino acids as categorized by the properties of their R groups? How do the chemical properties of each group affect protein shape?

Amino acids can be categorized into three major groups based on the properties of their side chains. The first group consists of the hydrophobic ("water-fearing") amino acids, whose side chains are nonpolar, usually found buried in the interior of the folded proteins, and typically form bonds with other hydrophobic amino acids (for example, valine) or solvents. The second group consists of the hydrophilic ("water-loving") amino acids. Hydrophilic amino acids include ones with polar side chains, usually found on the outside surface of folded proteins, and typically form bonds with other hydrophilic amino acids or water. Hydrophilic amino acids also include basic amino acids with side chains that are positively charged at intracellular pH (for example, lysine), and acidic amino acids with side chains that are negatively charged (for example, aspartic acid). The third group includes "special" amino acids, whose unique structures and chemical properties have significant effects on higher levels of protein structure because they allow more or less flexibility around the peptide bond (glycine and praline), or allow covalent interactions between side chains (cysteine). The way in which amino acids interact and bond in a polypeptide chain is important for the structure and function of the protein. Peptide bonds are important in maintaining the primary structure of a polypeptide chain. These bonds form between the carboxyl group of one amino acid and the amino group of the next amino acid in the chain. Note that these bonds are typically found between amino acid residues in the polypeptide. Hydrogen bonds are important in maintaining the secondary structure of the polypeptide chain. These bonds form between the oxygen in the carbonyl group (C=O) of one peptide bond and the hydrogen in the amide group (NH) of another. This allows regions of the polypeptide to interact with each other and enables the polypeptide to fold. Two common types of secondary structure formed by hydrogen bonding are a helices and ~ sheets. In terms of secondary structure, these bonds are found between groups in the polypeptide backbone (see Figs. 4.5 and 4.6).

In the figure, which box encloses the codon currently at the P site of the ribosome?

Box B

In the figure, which box encloses the anticodon currently at the A site of the ribosome?

Box C

Which statements about the simulation are TRUE? Select all that apply. Changing the uracil in the first codon of the original sequence to a cytosine will not change the outcome of the simulation. Every amino acid in a synthesized polypeptide enters the ribosome at the A site. By changing zero, one, or two bases from each of the labeled codons, it is possible to create a tetrapeptide (four amino acids) of all methionines. Changing the guanine in the sixth codon of the original sequence to an adenine will not change the outcome of the simulation. Changing the adenines at the 3' end of the mRNA will result in a nonfunctional protein because it is critical that every protein possesses a tail of lysine amino acids at the C-terminus.

By changing zero, one, or two bases from each of the labeled codons, it is possible to create a tetrapeptide (four amino acids) of all methionines. Changing the guanine in the sixth codon of the original sequence to an adenine will not change the outcome of the simulation.

Where is the anticodon located?

C

Once the molecule shown here is "charged," the outlined region labeled ______ will form complementary base pairs with the codon in the ________ in the A site of the ribosome.

C; mRNA

Proteins that prevent inappropriate folding of newly synthesized proteins are called:

Chaperones

What does RNA polymerase bind to in order to initiate transcription?

DNA promoter region

The unfolding of a protein by heat or chemical treatment is referred to as:

Denaturation

In which ribosome site would you find the uncharged tRNA?

E site

T/F: In a protein-coding region of DNA, any mutation that replaces a single nucleotide for another will replace any amino acid with any other amino acid.

False

T/F: Most proteins retain metabolic activity when denatured.

False

T/F:Protein families contain proteins with identical primary, secondary, and tertiary structures.

False

How do peptide bonds, hydrogen bonds, ionic bonds, disulfide bridges, and noncovalent interactions (van der Waals forces and the hydrophobic effect) define a protein's four levels of structure?

Four groups of bonds or interactions are important in creating tertiary and quaternary structure. The first group is the ionic bonds that form between a negative charge and a positive charge. For example, an ionic bond would form between a basic amino acid and an acidic amino acid because they have oppositely charged side chains. These bonds can occur between amino acids that are located far apart in the polypeptide chain, thus creating loops and bends in the overall structure. The second group comprises the hydrogen bonds that form between the oxygen of one amino acid's side chain and the hydrogen of another amino acid's side chain. The third group consists of the disulfide bridges. These covalent bonds form between two cysteine residues in the same polypeptide chain, or between two cysteines in two different chains. Note that when discussing tertiary structure, these bonds are found between different side chains. The fourth group important to maintaining tertiary and quaternary structure is noncovalent interactions, which include van der Waals forces and hydrophobic interactions that maintain interactions with different domains of the protein and result in a protein's specific shape.

The number of hydrogen bonds between two molecules affects how much energy is needed to break those two molecules apart. The more hydrogen bonds there are, the more energy that is required. Which of the following base pairs requires the most energy to break apart?

G-C Any pairing between A-T or between A-U only involves two hydrogen bonds while the pairing between G and C involves three hydrogen bonds. Because of this, of the answer options, the G-C base-pairing requires the most energy to break apart.

Endomembrane System. Consider a protein that is targeted to be an integral membrane protein on the surface of a cell. It has a specific functional domain (domain X) facing the external environment of the cell. How will this protein be oriented in the E.R.?

It will be embedded in the E.R. membrane with domain X facing the lumen of the E.R.

Endomembrane System. Consider a protein that is targeted to be an integral membrane protein on the surface of a cell. It has a specific functional domain (domain Y) facing the cytoplasm of the cell. How will this protein be oriented in the Golgi?

It will be embedded in the Golgi membrane with domain Y facing the cytoplasm of the cell.

Endomembrane System. Many cell functions involve communication between cells via molecular signals that must be sent from one cell to be received by a target cell. Suppose the signal to be sent is a small protein. Where would you expect to find the protein in the Golgi?

It would be in the lumen of the Golgi.

he ribosome ______ subunit has _______ binding sites for tRNA molecules

Large; three

Which proteins would be synthesized on the rough endoplasmic reticulum and processed in Golgi apparatus?

Lysosomal enzymes that break down proteins in the lumen of the lysosome.

How does a protein end up free in the cytosol, embedded in the plasma membrane, or secreted from the cell?

Proteins produced on free ribosomes in the cytosol are directed to their final destination through particular amino acid sequences called signal sequences. These proteins are sorted after they have been translated. Proteins destined for the nucleus, mitochondria, and chloroplasts have specific signal sequences (e.g., nuclear localization signals will direct the protein to the nucleus). Proteins with no signal sequence remain in the cytosol. Proteins produced by ribosomes on the rough endoplasmic reticulum end up in the lumen of the endomembrane system or embedded in its membrane. They may also be secreted out of the cell. These proteins are sorted as they are translated. They are initially translated by a ribosome in the cytosol, but a signal sequence in the growing protein directs the ribosome to a channel on the rough ER. As the protein is translated, it is threaded through the channel. These proteins are destined for the ER lumen, Golgi apparatus, lysosomes, or for secretion outside the cell. If the protein contains an additional signal sequence called a signal anchor sequence, it remains in the ER membrane as it is synthesized, rather than passing entirely into the ER lumen.

Which of the following reads the nucleotide sequence of a gene and synthesizes the corresponding primary transcript?

RNA polymerase.

The fully folded structure of a functional protein composed of a single polypeptide chain is referred to as:

Tertiary

Draw one of the 20 amino acids and label the amino group, the carboxyl group, the R group (side chain), and the α carbon.

The carboxyl group and the a carbon are the same for all amino acids. The amino group is the same for almost all the amino acids, with praline being the exception. The variety of functions and forms among the amino acids is mainly due to their different side chains (R groups). See Fig. 4.2.

What are the relationships among the template strand of DNA, the codons in mRNA, anticodons in tRNA, and amino acids?

The codons of mRNA are groups of three nucleotides that code for a particular amino acid. Each is transcribed from the template strand of DNA according to the normal rules of base pairing (but in RNA, U replaces T). The sequence of the codons in the mRNA gives rise to the order of the resulting amino acid polypeptide chain. The codons are translated by tRNAs. The sequence of each tRNA includes a group of three nucleotides called an anticodon that is complementary in sequence and, therefore, can recognize and bind to a specific codon in the mRNA. Because of the complementary and antiparallel nature of nucleic acid structures, an anticodon in a tRNA has the same 3' to 5' sequence as the template DNA, except with U's instead of T's. Each tRNA is also bound to a specific amino acid, affiliated with a particular anticodon/codon pair, on the 3' end of the molecule. When the mRNA is being "read" through the ribosome, the order of the amino acids in the polypeptide chain is dependent upon the sequential interaction of the mRNA codon with the correct tRNA anticodon/amino acid pair. See Fig. 4.15.

What are the names and functions of the major organelles of the endomembrane system in eukaryotic cells?

The nucleus stores the cell's genetic information and is the site of transcription. The endoplasmic reticulum (ER) is the organelle in which proteins and lipids are synthesized. The Golgi apparatus modifies proteins and lipids produced by the ER and acts as a sorting station as those molecules move to their final destinations. Lysosomes contain enzymes that break down macromolecules such as proteins, nucleic acids, lipids, and complex carbohydrates.

What ultimately determines the three-dimensional shape of a protein?

The order of amino acids in the polypeptide chain determines the way in which proteins fold because of the various interactions and bonds formed between the amino acids. These interactions, depending on the type and location, will give rise to specific secondary and tertiary structures.

A mutation leads to a change in one amino acid in a protein. The result is that the protein no longer functions properly. How is this possible?

The sequence of amino acids in a protein determines how a protein folds, so a change in even a single amino acid can affect the way the protein folds and can disrupt its function. For example, if the hydrophobic R groups of two amino acids must aggregate for proper structure and function, then a mutation that changes one of the hydrophobic amino acids to an acidic or a basic amino acid will prevent this aggregation and disrupt structure and function. Similarly, if proper folding requires interaction between the R groups of an acidic and a basic amino acid, then changing either one of them to a hydrophobic amino acid means that proper folding will not take place.

What feature or structure in the simulation indicates that this is eukaryotic translation?

The small ribosomal subunit binds to the 5' end of the mRNA and scans to the nearest AUG codon.

Which step occurs in the P site of the ribosome during translation?

The tRNA carrying the growing polypeptide moves to this site as the ribosome slides to the next codon.

Which polypeptide sequences would you expect to result from a synthetic mRNA with the repeating sequence 5′-UUUGGGUUUGGGUUUGGG-3′?

The three reading frames are as follows: • UUU GGG UUU GGG ... , which codes for repeating Phe-Gly-PheGly... • UUG GGU UUG GGU ... , which codes for repeating Leu-Gly-LeuGly... • UGG GUU UGG GUU ... , which codes for repeating Trp-Val-Trp-Val...

What are the steps of translation? Name and describe each one.

Translation of mRNA by ribosomes can be divided into three steps. • Initiation: Initiation factors bind to the 5' cap of the mRNA (in eukaryotic cells) or at the Shine-Dalgarno sequence (for prokaryotes) and recruit the small subunit of the ribosome and a tRNA charged with methionine. This complex then moves along the mRNA until it finds a start codon (AUG, coding for methionine). The large ribosomal subunit then joins the complex and causes the initiation factors to be released. The tRNAMet is then bound in the P site of the ribosome. The next tRNA, determined by the codon of the mRNA, binds in the A site of the ribosome. This elicits a coupled reaction in which the bond between the Met and its tRNA is broken and a new bond is formed between the carboxyl group of the Met and the amino group of the next amino acid (a peptide bond). The ribosome complex then slides to the next codon on the mRNA, shifting the now-uncharged tRNAMet to the E site, where it is released from the ribosome complex, and moving the peptidebearing tRNA to the P site. The A site is now free for the next charged tRNA. • Elongation: The ribosome continues in this fashion, shifting down the mRNA one codon at a time, adding amino acids to the growing peptide chain. Elongation factors provide the energy needed for these reactions to happen. • Termination: When the ribosome complex comes across a stop codon (UAA, UAG, or UGA), a protein release factor binds in the A site of the ribosome and causes the bond between the polypeptide chain and the last tRNA to break. Once the polypeptide chain is released, the ribosomal subunits disassociate from the mRNA and each other, and translation is complete. See Figs. 4.17 and 4.18.

What are two ways that proteins can acquire new functions in the course of evolution? Explain each one.

Two ways in which proteins can acquire new functions through the course of evolution are (1) mutation and selection and (2) combining different folding domains. • Mutation and selection: The sequence of the amino acids in the polypeptide chain is important for the proper folding, and ultimately the function, of the protein. If the sequence is altered by a mutation that changes a codon to specify for a different amino acid, this could affect the function of the protein and whether it is selected for in the population. A mutation that leads to a nonfunctioning protein will most likely lead to the impaired survival and reproductive ability of that organism and, therefore, will be eventually eliminated from the population. A neutral mutation that does not impair or improve protein function will likely remain in the population because those organisms will survive and reproduce at normal levels. A mutation that improves the function of the protein, altho1ugh rare, would give a selective advantage to that organism if it could survive and reproduce more successfully. • Combining different folding domains: Form leads to function. If a gene gains a new folding domain by joining with a folding domain from another gene, for example, its product now has the additional function provided by that folding domain. If this function is beneficial or benign to the protein, and ultimately has a positive or neutral effect on the survival and reproductive ability of the organism, the new gene, and therefore the protein will be maintained in the population.

Bacterial DNA containing an operon encoding three enzymes is introduced into chromosomal DNA in yeast (a eukaryote) in such a way that it is properly flanked by a promoter and a transcriptional terminator. The bacterial DNA is transcribed and the RNA correctly processed, but only the protein nearest the promoter is produced. Why?

With proper eukaryotic processing, the RNA transcript from the bacterial DNA will be capped at the 5' end. The initiation complex will form at the 5' cap and move along the mRNA until the first AUG codon is encountered. At that point, then translation begins. When one of the termination codons is encountered, the polypeptide is released. Translation of the downstream polypeptides cannot take place because the Shine-Dalgarno sequences preceding them are not recognized by the eukaryotic translational machinery.

The sequence for a portion of the DNA template strand and the corresponding mRNA that is being transcribed is shown here. mRNA 5'-GCAGCC-3'DNA template 3'-GCGCGTCGGTACA-5' Which base will the RNA polymerase add next to the growing mRNA molecule?

adenine The RNA polymerase synthesizes the growing mRNA strand in the 5' to the 3' direction and reads the corresponding DNA template strand from 3' to 5'. The DNA template strand indicates that the next base will be a thymine. The ribonucleotide that base pairs with thymine is adenine

Where does transcription of mRNA begin?

at the 3' end of the gene on the DNA template strand

Where are the ribosomes that translate proteins to be secreted from the cell?

attached to the rough endoplasmic reticulum

Which of the following is the actual event that translates the language of nucleic acids (the sequence of bases, A, T (U), C, and G) to the language of proteins (determining which amino acid will be added to the polypeptide)?

attachment of the appropriate amino acid to the tRNA by aminoacyl tRNA synthetase

Which portion of DNA contains the genetic information "read" by the RNA polymerase and transmitted into mRNA?

base

The genetic information carried by DNA is in the ___________ and their __________.

bases; sequence

The primary transcript is _________ to the DNA template strand

complementary antiparallel

How is the amino acid held on the charged tRNA?

covalent bond

Which sequence accurately describes the path traveled by a new protein from when it first starts to be translated to its release from the cell?

cytosol → ER → Golgi → vesicle → plasma membrane → external environment

An area of a polypeptide that bends in a particular way, relatively independent of the rest of the molecule, is a folding:

domain

The simulation demonstrates translation in:

eukaryotes

The controlled release of cellular material stored in membrane-bound vesicles to the outside of the cell is an example of:

exocytosis

T/F All genes in DNA code for proteins.

false

When a charged tRNA is about to bind to the vacant A site of a ribosome, where is the growing polypeptide?

in the P site

Endomembrane System. Consider a protein that is targeted to be excreted to the outside of the plasma membrane. Where would this protein be located in the Golgi?

in the lumen (inside) of the Golgi

Where does the expression of a protein begin?

in the nucleus

Which process is carried out by the spliceosome?

intron removal

Which of the answer choices is not considered to be a part of the endomembrane system? Golgi mitochondria lysosome plasma membrane endoplasmic reticulum

mitochondria

Change the first base in the simulation from an adenine to a uracil (change bases by clicking on them in the simulation), then re-run the simulation. This change results in:

no peptide being synthesized.

Which protein level best matches the description "blocks on a string"?

primary Amino acids are linked together via covalent peptide bonds to make a polypeptide chain or a protein. The primary structure of a protein is the linear sequence of all the linked amino acids while the secondary, tertiary, and quaternary structures of a protein involve some level of three-dimensional protein folding. For this reason, the primary structure of a protein best matches the description "blocks on a string."

Which enzyme is made up of both RNA and protein?

ribosome

In a population of organisms, beneficial and harmful random mutations are retained or eliminated through the process of:

selection

Disorders of which organelle are often associated with defects in transport from compartment to compartment, resulting in poor sorting of protein components within the cell?

the Golgi apparatus

Binding sites for tRNA are located in:

the large ribosomal subunit.

Non-protein coding genes are typically found in:

the nucleolus.

or each of the following organelles or structures, check the corresponding box if the organelle or structure is named or discussed in the animation. (Select all that apply.) the Golgi apparatus lysosomes the nucleus mitochondria ribosomes

the nucleus mitochondria ribosomes

A protein with an internal signal sequence is most likely to be located in:

the nucleus.

Does protein expression begin with transcription or translation?

transcription

Which base is not found in DNA? adenine guanine cytosine uracil thymine

uracil

Endomembrane System. Most elements of the endomembrane system are connected by:

vesicular trafficking.