Biology Chapter 17: From Gene to Protein

Questions and Answers

List 5 types of post-translational modifications.

Amino acid removal from the end of the polypeptide chain 2. Chain enzymatically cleaved into pieces 3. Cut out central & reattach other parts (insulin) 4. Attach two or more separate polypeptides (hemoglobin) 5. Add sugars, phosphates, lipids, etc.

Define a mutation in terms of molecular genetics.

Changes to the genetic information of a cell or virus.

Define point mutations.

Chemical changes in a single base pair of a gene.

What are frameshift mutations?

Insertions or deletions of base pairs that cause the whole later sequence to be off, shifted by one or more. Signup and view all the answers

Explain how proteins are targeted for the ER (6 steps).

<ol> <li>Polypeptide synthesis begins on a free ribosome in the cytosol. 2. SRP binds to signal peptide, halting synthesis. 3. SRP binds to a receptor protein in the ER membrane. 4. SRP leaves and synthesis resumes, translocating across the ER membrane. 5. Signal-cleaving enzyme cuts off the signal peptide. 6. The completed polypeptide leaves the ribosome and is processed in the ER.</li> </ol> Signup and view all the answers

Where does polypeptide synthesis take place?

Always in the cytosol unless it has a signal peptide. Signup and view all the answers

What is the difference between a nonsense and missense mutation?

Nonsense mutations cause translation to be terminated too early, resulting in non-functional proteins, while missense mutations lead to the incorporation of the wrong amino acid. Signup and view all the answers

Identify two mechanisms by which frameshifts may occur.

Insertion and deletion. Signup and view all the answers

How can a base pair substitution result in a silent mutation?

If CCG mutated to CCA, the corresponding anticodon would change but still attach the same amino acid, leaving the organism unaffected. Signup and view all the answers

What are the two categories of mutagens?

Physical and chemical agents that interact with DNA. Signup and view all the answers

Describe 2 important ways in which bacterial and eukaryotic genes differ.

<ol> <li>Initiation & termination of translation is different. 2. Bacteria have no compartmental organization, enabling simultaneous transcription and translation.</li> </ol> Signup and view all the answers

What is a gene? Write a more accurate version of 'one gene codes for one polypeptide.'

A gene is a region of DNA that can be expressed to produce a final functional product that is either an RNA or a polypeptide. Signup and view all the answers

Summarize 'From Gene to Protein' (6 steps).

<ol> <li>RNA is transcribed from DNA. 2. Pre-mRNA is spliced to produce mRNA. 3. mRNA leaves the nucleus and attaches to a ribosome. 4. Each amino acid attaches to its tRNA with enzyme attachment. 5. tRNAs add their amino acids to the chain as the mRNA moves through the ribosome. 6. Polypeptide is released for modification or as a finished product.</li> </ol> Signup and view all the answers

What is gene expression?

The process by which DNA directs the synthesis of proteins (or sometimes just RNAs). Signup and view all the answers

What situation did Archibald Garrod suggest caused inborn errors of metabolism?

That some people are unable to make a particular enzyme to metabolize certain things. Signup and view all the answers

Describe one example Garrod used to illustrate his hypothesis.

Alkaptonuria: most people have an enzyme to metabolize alkapton, but people who have inherited an inability to do so have black urine because of the presence of alkapton. Signup and view all the answers

State the hypothesis formulated by George Beadle while studying eye color mutations in Drosophila.

Each of the various mutations affecting eye color blocks pigment synthesis at a specific step, by preventing the production of the enzyme that catalyzes that step. Signup and view all the answers

What strategy did Beadle and Tatum adopt to test George Beadle's hypothesis about eye color mutations in Drosophila?

They experimented on Neurospora, which only need a minimal food supply. After mutating some of them with X-rays, some couldn't survive on minimal since their enzymes couldn't synthesize needed molecules from that food. Signup and view all the answers

How did Beadle and Tatum figure out what mutant was defective in what area?

If several identical mutants were put in different solutions, and one of these was Arginine and that was the only one that survived, the mutant must have been defective in making arginine since that's the one that survived. Signup and view all the answers

Cite two significant findings that resulted from the research of Beadle and Tatum.

<ol> <li>The function of a gene is to dictate the production of a specific enzyme. 2. Not all proteins are enzymes.</li> </ol> Signup and view all the answers

What is the hypothesis of gene expression?

One gene -> one polypeptide. Many eukaryotic genes can code for a set of related proteins though, called alternative splicing. And many genes code for RNAs that don't become proteins. Signup and view all the answers

What are three ways that RNA differs from DNA?

<ol> <li>It contains ribose instead of deoxyribose. 2. It has uracil instead of thymine. 3. It's usually single-stranded instead of double-stranded.</li> </ol> Signup and view all the answers

What are the monomers of DNA, RNA, or proteins?

DNA + RNA = the 4 types of nucleotides (U or T). Proteins = amino acids. Signup and view all the answers

Define the process of transcription.

DNA is used as a template to make a complementary sequence of mRNA. Signup and view all the answers

Define the process of translation.

Synthesis of a polypeptide under the direction of mRNA. Translates codons to amino acids at ribosomes. Signup and view all the answers

Where does translation occur in a eukaryotic cell?

In the cytoplasm. Signup and view all the answers

In eukaryotes, what is the pre-mRNA called?

The primary transcript. It's only called this in the nucleus, before modification. Signup and view all the answers

Write the central dogma of molecular genetics, as proclaimed by Francis Crick.

DNA -> RNA -> Protein. Signup and view all the answers

How many nucleotide bases are there? How many amino acids?

4, 20. Signup and view all the answers

How many nucleotides are required to code for these 20 amino acids?

4, in triplet arrangements (4^3 = 64 unique triplets). Signup and view all the answers

How many codons are there?

4^3 = 64. 300 codons in an mRNA -> 100 polypeptides in the amino acid. Signup and view all the answers

DNA is double stranded, but for each protein, only one of these two strands is used to produce an mRNA transcript. What is the coding strand called?

The template strand, since it gives the pattern/template for the sequence of nucleotides in an RNA transcript. Signup and view all the answers

What are codons?

The mRNA base triplets. Signup and view all the answers

Describe Nirenberg's experiment in which he identified the first codon.

He synthesized an artificial mRNA by linking identical RNA nucleotides containing uracil at their base: one codon in repetition: UUU. Signup and view all the answers

What was the first codon-amino acid pair to be identified?

UUU -> Phe. Signup and view all the answers

Of the 64 possible codons, how many code for amino acids, and what are the rest?

<ol start="61"> <li>UAA, UAG, and UGA are stop signals.</li> </ol> Signup and view all the answers

What is the start codon?

AUG -> Met. Signup and view all the answers

Why is the genetic code said to be redundant but not ambiguous?

Both GAA and GAG specify glutamic acid (redundancy for less harmful mutations), neither specifies any other amino acid (no ambiguity for no mix-ups). Signup and view all the answers

Explain the concept of reading frame.

Reading symbols of a language in the correct groupings. Signup and view all the answers

Name the enzyme that uses the DNA template strand to transcribe a new mRNA strand.

RNA polymerase, assembles RNA in 5' -> 3'. Signup and view all the answers

Both DNA polymerase III and RNA polymerase can assemble a new polynucleotide only in the 5' -> 3' direction. Which enzyme, DNA pol III or RNA pol, doesn't need a primer to begin synthesis?

RNA polymerase doesn't need a primer. Signup and view all the answers

What is a transcription unit?

The stretch of DNA that's transcribed into an RNA (from promoter to terminator sequence). Signup and view all the answers

What are the 3 stages of transcription?

<ol> <li>Initiation: After RNA pol binds to the promoter, the DNA strands unwind, and the pol initiates RNA synthesis at the start point on the template strand. 2. Elongation: The polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5' -> 3'. In the wake of transcription, the DNA strands re-form a double helix. 3. Termination: Eventually, the RNA transcript is released, and the polymerase detaches from the DNA.</li> </ol> Signup and view all the answers

How many RNA polymerases do bacteria and eukaryotes have?

Bacteria = 1, Eukaryotes = 3. Signup and view all the answers

List 3 important facts about the promoter.

<ol> <li>The transcription start point (the nucleotide where RNA synthesis begins) is included in the promoter. 2. Determines which of the two strands are used as the template. 3. Needs transcription factors (in eukaryotes) to mediate the binding of RNA pol + initiation of transcription.</li> </ol> Signup and view all the answers

What are the 3 stages of initiation?

<ol> <li>The eukaryotic promoter includes a nucleotide sequence containing TATA about 25 nucleotides upstream from the start point. 2. One or a few transcription factors recognize the TATA box and bind to the DNA so that RNA polymerase II can do so. 3. Additional transcription factors bind to the DNA along with RNA polymerase II, forming the transcription initiation complex. The DNA double helix then unwinds, and RNA synthesis begins at the start point on the template strand.</li> </ol> Signup and view all the answers

What is the TATA box?

A crucial promoter DNA sequence. Signup and view all the answers

What comprises a transcription initiation complex?

The complex of transcription factors and RNA polymerase II bound to the promoter. Signup and view all the answers

RNA processing happens only in ______ cells. What is it in one sentence?

Eukaryotic cells. The primary transcript is altered at both ends and sections in the middle are removed. Signup and view all the answers

What happens at the 5' end of the primary transcript in RNA processing?

It receives a 5' cap, where a form of guanine modified to have 3 phosphates on it is added after the first 20-40 nucleotides. Signup and view all the answers

What happens at the 3' end of the primary transcript in RNA processing?

An enzyme adds 50-250 adenine nucleotides, forming a poly-A tail. Signup and view all the answers

What are 3 important functions of the 5' cap and the poly-A tail?

<ol> <li>They seem to help facilitate the export of the mature mRNA from the nucleus. 2. They protect the mRNA from degradation by hydrolytic enzymes. 3. They help ribosomes attach to the 5' end of the mRNA once it reaches the cytoplasm.</li> </ol> Signup and view all the answers

What are UTRs?

Untranslated regions: parts of mRNA that won't be translated to protein but have functions like ribosome binding, located at the 5' and 3' ends. Signup and view all the answers

Distinguish between introns and exons.

Introns are noncoding segments of nucleic acid between coding regions. Exons are expressed regions that exit the nucleus. Signup and view all the answers

Explain eukaryotic termination.

RNA polymerase II transcribes the polyadenylation (PD) signal sequence, which codes for a PD signal in the pre-mRNA. Then 10-35 nucleotides downstream, associated proteins with the growing RNA cut it free from the polymerase. The polymerase continues transcribing though for hundreds of nucleotides past termination. This extra RNA is then digested by an enzyme that moves along the pre-mRNA until it reaches the polymerase, then the polymerase falls off and transcription is terminated. Signup and view all the answers

What are snRNPs and what two types of molecules make up snRNPs?

Small nuclear ribonucleoproteins are proteins in the nucleus that recognize the splice sites at each end of an intron (short nucleotide sequences). Made up of RNA and protein molecules. Signup and view all the answers

What type of RNA is in a snRNP?

Small nuclear RNA about 150 nucleotides long. Signup and view all the answers

How do spliceosomes work?

Spliceosomes interact with certain sites along an intron, releasing it and joining the exons that were around it. Signup and view all the answers

List the 3 steps of modifying a pre-mRNA.

<ol> <li>snRNPs and other proteins together form a spliceosome on a pre-mRNA molecule containing introns and exons. 2. Within the spliceosome, snRNPs base pair with nucleotides at specific sites along the intron. 3. The spliceosome cuts out the intron and at the same time splices the exons together. The spliceosome then comes apart itself and releases the only-exon mRNA.</li> </ol> Signup and view all the answers

Explain how splice sites are recognized.

The RNA parts of snRNP base-pair to specific sites along an intron. Signup and view all the answers

What are ribozymes?

RNA molecules that function as enzymes. In some organisms, RNA splicing can occur without any other proteins or RNAs: the intron acts as its own excisor. Signup and view all the answers

What commonly held idea was rendered obsolete by the discovery of ribozymes?

That all biological enzymes were proteins. Actually, RNA can be enzymes/catalysts too. Signup and view all the answers

What are the 3 properties of RNA that allow it to function as an enzyme?

<ol> <li>Since RNA is single-stranded, a region of an RNA molecule may base-pair with a complementary region in the same molecule, giving it a 3D shape that's specific. 2. Like amino acids in an enzymatic protein, some of the bases in RNA contain functional groups that may participate in catalysis. 3. It's able to H bond with other nucleic acids (RNA/DNA), which adds specificity to its catalytic activity.</li> </ol> Signup and view all the answers

What is the consequence of alternative splicing of identical mRNA transcripts?

A single gene can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA processing. Signup and view all the answers

What is an anticodon?

A nucleotide triplet at the bottom of the tRNA that base pairs to the codon of the mRNA so the amino acid can detach. Signup and view all the answers

Describe the structure and function of mRNA.

Messenger RNA: modified single-strand chain of nucleotides that are complementary to DNA. Carries the message of genes, of what proteins to make. Signup and view all the answers

Describe the structure and function of tRNA.

A tRNA has an anticodon on one end and an amino acid on the other end. Functions to transfer amino acids from the cytoplasm to the mRNA, at the ribosome. Signup and view all the answers

Describe the structure and function of rRNA.

Ribosomal RNA: molecules that make up a ribosome, where mRNA's message is translated to amino acids. Signup and view all the answers

What is exon shuffling?

Introns increase the probability of beneficial cross-overs between the exons of alleles by not interrupting coding sequences. Either allelic or nonallelic shuffling can lead to new proteins with new functions. Signup and view all the answers

Where is tRNA made and what are the bonds it makes?

tRNA is made in the nucleus and forms hydrogen bonds between base pairs of itself (in the T) and hydrogen bonds from anticodon to codon. Signup and view all the answers

How many different aminoacyl-tRNA synthetases are there, and what are they?

20, one for each amino acid. They are a group of related enzymes that facilitate the correct matching up of tRNA and amino acids. Signup and view all the answers

What is wobble?

Wobble explains why the synonymous codons for a given amino acid can differ in their third base, but usually not in their other bases. Signup and view all the answers

Explain the process of a specific amino acid being joined to a tRNA.

<ol> <li>Active site of aminoacyl-tRNA synthetase binds the amino acid and ATP. 2. ATP loses two P groups and joins amino acid to AMP. 3. Appropriate tRNA covalently bonds to an amino acid, displacing AMP. 4. The tRNA charged with amino acid is released by the enzyme.</li> </ol> Signup and view all the answers

Describe the structure of a eukaryotic ribosome and how it's made.

In the nucleus, rRNA genes on the chromosomal DNA are transcribed, and the RNA is processed and assembled with proteins from the cytoplasm. The resulting ribosomal subunits are then exported to the cytoplasm. Signup and view all the answers

How does a prokaryotic ribosome differ from a eukaryotic ribosome? What is the medical significance of this difference?

Prokaryotic ribosomes are smaller and have 3 rRNA molecules. Eukaryotic ribosomes are larger and have 4 rRNA molecules. Certain antibiotic drugs can inactivate bacterial ribosomes without inhibiting the ability of eukaryotic ribosomes to make proteins. Signup and view all the answers

Explain the functions of the APE sites.

A site holds the tRNA carrying the next amino acid to be added to the chain. P site (start site) holds the tRNA carrying the growing polypeptide chain. E site is where discharged tRNAs exit the ribosome. Signup and view all the answers

What are the 3 stages of translation?

<ol> <li>Initiation: Initiation factors bring together mRNA and tRNA carrying the first amino acid met. 2. Elongation: Amino acids are added one by one to the preceding amino acid, stimulated by elongation factors. 3. Termination: UAG, UAA, or UGA codes for a stop signal and release factor binds.</li> </ol> Signup and view all the answers

Summary of initiation:

<ol> <li>Small ribosomal subunit binds to mRNA, and initiator tRNA with the anticodon UAC base pairs with the start codon AUG, carrying the amino acid met. 2. Large ribosomal subunit binds to complete the complex, using GTP. Initiation factor proteins bring all the components together.</li> </ol> Signup and view all the answers

Is a ribosome an enzyme?

True Signup and view all the answers

Summary of elongation:

<ol> <li>Codon recognition: The tRNA anticodon base-pairs with the mRNA codon in the A site. Hydrolysis of GTP here increases efficiency and accuracy. 2. Peptide bond formation: The large ribosomal subunit catalyzes the formation of a peptide bond between the new amino acid in the A site and the growing polypeptide in the P site. 3. Translocation: The ribosome moves the tRNA in the A site to the P site.</li> </ol> Signup and view all the answers

What is a release factor? By what mechanism is termination accomplished?

A protein that binds directly to the stop codon in the A site. It causes the addition of a molecule of H2O instead of an amino acid. This hydrolyzes the bond between the completed polypeptide and the tRNA on the P site, releasing the polypeptide through the E site of the ribosome. Signup and view all the answers

What is a polyribosome?

String of ribosomes all translating the same mRNA at the same time allowing many copies of the polypeptide to be made more quickly. Signup and view all the answers

What are some of the things that will result in a final-form functional protein?

Protein folding due to primary structure and amino acid interactions, which sometimes occur in chaperonins, determine shape and function. Post-translational modifications: attachments (sugars, phosphates) or removal (of 1 or more amino acids) have to occur sometimes for the protein to function in the cell. Signup and view all the answers

Study Notes

Gene Expression and Its Mechanisms

Gene expression refers to the process by which DNA instructs the synthesis of proteins and sometimes RNA.
Archibald Garrod proposed the concept of inborn errors of metabolism, indicating that some individuals cannot produce specific enzymes necessary for metabolism.
Alkaptonuria exemplifies Garrod's hypothesis; individuals with this condition cannot metabolize alkapton, resulting in black urine due to its accumulation.

Research by Beadle and Tatum

George Beadle hypothesized that mutations affecting eye color in Drosophila hinder pigment synthesis by blocking specific enzymatic production.
Beadle and Tatum utilized the fungus Neurospora to test their hypothesis, finding that mutants unable to survive on minimal media lacked necessary enzymes for specific nutrient synthesis.
Their research confirmed that genes dictate specific enzyme production and highlighted the fact that not all proteins are enzymes.

Transcription and Translation Processes

One gene corresponds to one polypeptide; however, eukaryotic genes can code for multiple related proteins through alternative splicing.
RNA differs from DNA in three ways: it contains ribose instead of deoxyribose, uses uracil instead of thymine, and is typically single-stranded.
Transcription involves using DNA as a template to produce a complementary mRNA strand, while translation is the synthesis of a polypeptide directed by mRNA.
In eukaryotic cells, translation takes place in the cytoplasm, with pre-mRNA referred to as a primary transcript before modifications occur.

Genetic Coding and Codons

The central dogma of molecular genetics presents the flow of genetic information as DNA → RNA → Protein.
There are 64 codons used to code for 20 amino acids, with UAA, UAG, and UGA serving as stop codons.
The start codon is AUG, coding for methionine.

RNA Processing and Splicing

Eukaryotic RNA processing involves modifications to the primary transcript, including the addition of a 5' cap and a poly-A tail, which protect mRNA and facilitate its export.
Introns are non-coding segments, while exons are the coding regions that exit the nucleus.
Spliceosomes, formed from small nuclear ribonucleoproteins (snRNPs), splice out introns and join exons together.

Ribosomes and Protein Synthesis

Ribosomes consist of rRNA and proteins, with distinct sites for aminoacyl-tRNA (A site), peptide chains (P site), and ejected tRNAs (E site).
The translation process includes three stages: initiation (bringing mRNA and tRNA together), elongation (adding amino acids to the growing chain), and termination (recognizing stop codons).
Release factors bind to stop codons during termination, releasing the completed polypeptide.

Post-Translational Modifications

Proteins may undergo post-translational modifications like amino acid removal, cleavage, or addition of functional groups to achieve their active forms.
Alternative splicing allows a single gene to code for multiple proteins by varying the exon combinations in mRNA.

Mutations and Genetic Variability

Mutations are alterations in genetic information, leading to genetic diversity among organisms.
Point mutations involve changes to individual base pairs, while frameshift mutations occur from insertions or deletions, shifting the reading frame and altering subsequent amino acids.

Targeting Proteins to the Endoplasmic Reticulum (ER)

Polypeptide synthesis is initiated on free ribosomes in the cytosol until a signal peptide is recognized by a signal recognition particle (SRP).
The SRP guides the ribosome to the ER, where synthesis resumes and the signal peptide is cleaved upon entry into the ER, allowing for further processing.### Mutations
Nonsense mutations lead to premature termination of protein translation, generally resulting in non-functional proteins.
Missense mutations modify a single amino acid in the protein sequence, potentially altering protein function.

Frameshift Mechanisms

Frameshifts occur through insertion or deletion of nucleotides that are not multiples of three, disrupting normal codon grouping.
The impact of frameshifts is that all downstream codons are misread, causing extensive sequence changes.

Silent Mutations

Base pair substitutions, like the change from CCG to CCA, can result in silent mutations where the same amino acid is still produced, leaving the organism unaffected.

Mutagens

Two categories of mutagens affecting DNA are physical and chemical agents.
- Physical mutagens, such as X-rays, induce mutations by damaging DNA.
- Chemical mutagens include:
  - Base analogs that mispair during DNA replication.
  - Insertions that physically distort the DNA double helix.
  - Agents causing chemical changes that alter base pairing properties.

Gene Differences in Bacteria and Eukaryotes

Bacterial and eukaryotic gene expression differs mainly in translation initiation and termination processes.
Bacteria, lacking compartmentalization, can simultaneously transcribe and translate mRNA.

Definition of a Gene

A gene is a DNA segment that encodes a functional product, which may be RNA or a polypeptide.

From Gene to Protein Overview

Transcription of RNA from DNA occurs first.
In eukaryotes, pre-mRNA is spliced and modified to form mRNA, which exits the nucleus to the cytoplasm.
mRNA attaches to ribosomes for translation.
tRNA brings appropriate amino acids to the ribosome with ATP assistance.
Amino acids are sequentially added to the growing polypeptide chain as mRNA codons are read.
The completed polypeptide is released for further modification or is finalized as a functional protein.

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Test your knowledge on Chapter 17 of Biology regarding gene expression and protein synthesis. This quiz covers key concepts and examples related to the process through which DNA influences metabolism and enzyme production. Perfect for reviewing flashcards and preparing for exams.