Chapter 12

Question 1

Pathway from Gene to Polypeptide

Answer 1

Central dogma: DNA → RNA → protein
Transcription: The process of making an RNA copy of DNA information.
Translation: The process of using RNA to assemble amino acids into a polypeptide chain.

Question 2

Transcription and Translation

Answer 2

Transcription:
- RNA polymerase copies the DNA sequence into a complementary RNA sequence.
-The resulting RNA is transcribed into messenger RNA (mRNA).

Translation:
- mRNA is translated into a polypeptide chain (protein) by ribosomes, using the genetic code to assemble amino acids.

Question 3

Genetic code

Answer 3

• The genetic code is the nucleotide information that specifies the amino acid sequence of a polypeptide.
• Information:
  
  • Nucleotide bases:
    
    • DNA: A, T, G, C
    • RNA: A, U, G, C
  • Amino acids: 20 different amino acids make up polypeptides.

Question 4

Features of the Genetic Code

Answer 4

• Commaless: There are no commas or spaces between codons.
• Universal: The genetic code is nearly the same in all organisms, from bacteria to humans.
• Degenerate: Multiple codons can code for the same amino acid.
• Start and stop signals: There are specific codons that signal the start (AUG) and stop (UAA, UAG, UGA) of translation.

Question 5

Genetic Code: Commaless and Universal

Answer 5

• Commaless:
  
  • Nucleic acid codes are read sequentially, with no spaces or commas between codons.
• Universal:
  
  • Each codon specifies the same amino acid in all living organisms, including viruses.
  • This suggests the genetic code was established early in the evolution of life and has remained almost unchanged throughout evolution.

Question 6

Genetic Code: Degenerate

Answer 6

• Degenerate:
  
  • Most amino acids are specified by multiple codons (degeneracy or redundancy).
  • Only two amino acids, methionine and tryptophan, are specified by a single codon.

Question 7

Genetic Code: Start and Stop Signals

Answer 7

• Sense codons:
  
  • 61 codons specify amino acids.
• Start codon (AUG):
  
  • Recognized as the first amino acid during translation (methionine in eukaryotes, formylmethionine in prokaryotes).
• Stop codons:
  
  • Three codons (UAA, UAG, UGA) that do not specify amino acids and act as “periods,” signaling the end of translation.

Question 8

Three Stages of Transcription

Answer 8

1. Initiation:
   
   • Molecules assemble at the promoter.
   • Synthesis of an RNA copy of the gene begins.
2. Elongation:
   
   • RNA polymerase moves along the gene.
   • RNA chain is extended.
3. Termination:
   
   • Transcription ends.
   • RNA transcript and RNA polymerase are released.

Question 9

DNA-Directed RNA Synthesis

Answer 9

• RNA is synthesized in the 5′→3′ direction.
• The 3′→5′ DNA strand serves as the template for RNA synthesis.

Question 10

Differences between DNA Replication and Transcription

Answer 10

Transcription:
Makes RNA from a gene.
Uses one DNA strand as a template.
Only a small part of DNA is copied.
RNA polymerase builds RNA.
RNA is single-stranded.
Uracil (U) pairs with adenine (A).

Question 11

Two Main Parts of the Gene

Answer 11

Promoter - Control sequence for transcription.
Transcription Unit - Section of the gene copied into RNA.

Question 12

Differences in Transcription: Eukaryotes vs. Bacteria

Answer 12

• Promoter sequences vary for transcription assembly.
• In eukaryotes, RNA polymerase II needs transcription factors to bind first; in bacteria, RNA polymerase binds directly.
• In bacteria, terminator sequences stop transcription; no equivalent in eukaryotic DNA.

Question 13

Transcription of Non–Protein-Coding Genes

Answer 13

• Eukaryotes:
  
  • RNA polymerase III transcribes tRNA genes and one rRNA gene.
  • RNA polymerase I transcribes the other three rRNA genes.
  • Each RNA polymerase type has specialized promoters.
• Bacteria:
  
  • Only one RNA polymerase type transcribes all genes, including non-protein-coding ones.

Question 14

Pre-mRNA Processing

Answer 14

• Precursor-mRNA (pre-mRNA): Needs processing in the nucleus to become translatable mRNA.
• 5′ Cap: A guanine cap is added to the 5′ end of mRNA. It helps the ribosome attach for translation.
• Poly(A) Tail: A poly-A tail (50-250 adenines) added to the 3′ end protects mRNA from degradation.
• Introns: Non-coding sequences in pre-mRNA that are removed before translation.

-Exons: Exons are coding sequences retained in mRNA and expressed as proteins.

Question 15

mRNA Splicing

Answer 15

• Introns are removed from pre-mRNAs.
• Spliceosome: A complex made of pre-mRNA, small ribonucleoprotein particles (snRNPs), and small nuclear RNA (snRNA) with proteins.
• snRNPs:
  • Bind to introns.
  • Loop out the introns.
  • Cut the intron at the exon boundaries.
  • Join the exons together.

Question 16

Why Are Introns Present?

Answer 16

Alternative splicing
* Different versions of mRNA can be produced
Exon shuffling
* Generates new proteins

Question 17

Alternative Splicing

Answer 17

• Exons rearrange to create multiple mRNAs from one gene.
• Each mRNA translates into a unique protein with specific functions.
• Increases protein diversity and maximizes DNA’s information storage.

Question 18

Exon Shuffling

Answer 18

• Intron-exon junctions lie between key protein regions.
• Exon shuffling creates novel protein domain combinations.
• Speeds up protein evolution compared to random mutations.

Question 19

Translation Overview

Answer 19

• Translation is the process where a ribosome reads mRNA to assemble amino acids into a polypeptide.

Question 20

3 Stages of Translation

Answer 20

1. Initiation: Translation begins when tRNA and mRNA bind to a ribosome.
2. Elongation: Amino acids are added one by one to the growing protein chain.
3. Termination: Translation ends when a STOP codon signals the completion of the protein.

Question 21

tRNA’s

Answer 21

• Carry specific amino acids to the ribosome.
  
  • Have a cloverleaf shape.
  • The bottom end of tRNA has an anticodon that pairs with the codon in mRNA.

Question 22

Wobble Hypothesis

Answer 22

• 61 sense codons don’t need 61 distinct tRNAs.
  
  • The first two nucleotides of the anticodon and codon must match exactly.
  • The third nucleotide can “wobble,” allowing more flexibility in pairing.

Examples:
- Phenylalanine tRNA: Can match codons UUU and UUC.
- Glutamine tRNA: Can match codons CAA and CAG.

Question 23

Aminoacylation

Answer 23

Aminoacylation adds an amino acid to a tRNA, forming aminoacyl–tRNA.
The process is catalyzed by aminoacyl–tRNA synthetases.

Question 24

Ribosomes

Answer 24

• Ribosomes are ribonucleoprotein particles that translate mRNA into polypeptides (chains of amino acids).
• In eukaryotes, ribosomes can either be free in the cytoplasm or attached to the endoplasmic reticulum.
  Ribosomes are made of two subunits:
• Large ribosomal subunit
• Small ribosomal subunit
• Both subunits are composed of rRNA and ribosomal proteins.

Question 25

Ribosome Binding Sites

Answer 25

- A site (aminoacyl site): tRNA carrying the next amino acid binds here. - P site (peptidyl site): tRNA with the growing polypeptide chain is bound here. - E site (exit site): tRNA without an amino acid binds here before exiting the ribosome.

Question 26

Polysomes

Answer 26

- A **polysome** is a complex where **multiple ribosomes** translate a single mRNA molecule simultaneously. - This process allows for the efficient production of multiple copies of a protein from one mRNA strand.

Question 27

Simultaneous Transcription and Translation

Answer 27

- In prokaryotes, transcription and translation can occur simultaneously because there is no nuclear envelope separating the two processes. - As soon as an mRNA strand is being transcribed, ribosomes can start translating it into a protein, allowing for quick protein production.

Question 28

Polypeptide Processing

Answer 28

Amino acid removal: Some amino acids are removed. Group addition: Organic groups may be added. Folding: Chaperones help fold the protein. Alternative pathways: Different protein forms can be produced.

Question 29

Sorting Signals

Answer 29

- Proteins are directed to specific locations within the cell using sorting signals. - These signals ensure proteins are sent to the correct location (e.g., cytoplasm, mitochondria, nucleus).

Question 30

Sorting Signals in the Endomembrane System

Answer 30

- The endomembrane system is responsible for protein transport. - **Signal sequence**: A short peptide at the start of the polypeptide chain. - **Signal recognition particle (SRP)**: Binds to the signal sequence. - **SRP receptor**: The SRP binds to a receptor on the ER membrane, guiding the polypeptide into the ER lumen. - **Signal peptidase**: Removes the signal sequence, and translation continues until the polypeptide is complete.

Question 31

Genetic Changes Affecting Protein Function

Answer 31

- **Mutations**: Changes in DNA sequence. - **Types of mutations**: 1. **Missense**: Changes one amino acid. 2. **Nonsense**: Creates a stop codon, shortening the protein. 3. **Silent**: No change in amino acid. 4. **Frameshift**: Insertion/deletion shifts the reading frame.

Question 32

Missense Mutation

Answer 32

- A sense codon is changed to another codon that codes for a different amino acid. - The effect on the polypeptide's function depends on the specific amino acid change. - **Diseases caused by missense mutations**: Sickle cell disease, albinism, hemophilia, and achondroplasia.

Question 33

Silent Mutation

Answer 33

- A sense codon is changed to a different codon, but it still codes for the same amino acid. - The function of the polypeptide remains unchanged.

Question 34

Frameshift Mutation

Answer 34

- A single base-pair insertion or deletion in a gene shifts the reading frame of the mRNA. - This changes the codons read by the ribosome, producing a different amino acid sequence. - The resulting polypeptide is typically nonfunctional due to the altered amino acid sequence.