MCAT Biochemistry Review

Chapter 7: RNA and the Genetic Code

Conclusion

To carry out the functions of life, we must produce around 100,000 different proteins using our 20,000–25,000 available genes. Every protein in the biosphere is produced through the central dogma of molecular biology, as genes in DNA are transcribed into mRNA and then translated into a functional protein. This is a complex, highly regulated process in both prokaryotes and eukaryotes, and questions on transcription and translation, and their regulation, are frequent on the MCAT.

The last two chapters focused on the important roles played by many organelles in the cell, including the nucleus, nucleolus, ribosome, rough endoplasmic reticulum, and Golgi apparatus. After secreted proteins such as hormones and digestive enzymes are produced, they make their way to the plasma membrane for exocytosis. It is this last stop that we'll examine in the next chapter: the structure, function, and biochemistry of the biological membranes.

Concept Summary

The Genetic Code

·        Central Dogma: DNA → RNA → proteins.

·        A degenerate code allows multiple codons to encode for the same amino acid.

o   Initiation (start) codon: AUG

o   Termination (stop) codons: UGA, UAA, UAG

·        Redundancy and wobble (third base in the codon) allows mutations to occur without effects in the protein.

·        Point mutations can cause:

o   Silent mutations with no effect on protein synthesis.

o   Nonsense (truncation) mutations that produce a premature stop codon.

o   Missense mutations that produce a codon that codes for a different amino acid.

·        Frameshift mutations result from nucleotide addition or deletion, and change the reading frame of subsequent codons.

·        RNA is structurally similar to DNA except:

o   Substitution of a ribose sugar for deoxyribose.

o   Substitution of uracil for thymine.

o   It is single-stranded instead of double-stranded.

·        There are three types of RNA with separate jobs in transcription:

o   Messenger RNA (mRNA): carries the message from DNA in the nucleus via transcription of the gene; travels into the cytoplasm to be translated.

o   Transfer RNA (tRNA): brings in amino acids, recognizes the codon on the mRNA using its anticodon.

o   Ribosomal RNA (rRNA): makes up the ribosome; enzymatically active.

Transcription

·         

o   Helicase and topoisomerase unwind the DNA double helix.

o   RNA polymerase II binds to the TATA box within the promoter region of the gene (25 base pairs upstream from first transcribed base).

o   hnRNA is synthesized from the DNA template (antisense) strand.

·        Posttranscriptional modifications include:

o   A 7-methylguanylate triphosphate cap is added to the 5′ end.

o   A polyadenosyl (poly-A) tail is added to the 3′ end.

o   Splicing is done by snRNA and snRNPs in the spliceosome; introns are removed in a lariat structure, and exons are ligated together.

o   Prokaryotic cells can increase the variability of gene products from one transcript through polycistronic genes (starting transcription in different sites within the gene leads to different gene products).

o   Eukaryotic cells can increase variability of gene products through alternative splicing (combining different exons in a modular fashion to acquire different gene products).

Translation

·        tRNA translates the codon into the correct amino acid.

·        Ribosomes are the factories where translation (protein synthesis) occurs.

·        There are three stages of translation.

o   Initiation in prokaryotes occurs when the 30S ribosome attaches to the Shine–Dalgarno sequence and scans for a start codon; it lays down N-formylmethionine in the P site of the ribosome.

o   Initiation in eukaryotes occurs when the 40S ribosome attaches to the 5′ cap and scans for a start codon; it lays down methionine in the P site of the ribosome.

o   Elongation involves the addition of a new aminoacyl-tRNA into the A site of the ribosome and transfer of the growing polypeptide chain from the tRNA in the P site to the tRNA in the A site. The now uncharged tRNA pauses in the E site before exiting the ribosome.

o   Termination occurs when the codon in the A site is a stop codon; release factor places a water molecule on the polypeptide chain and thus releases the protein.

o   Initiation, elongation, and release factors help with each step in recruitment and assembly/disassembly of the ribosome.

·        Posttranslational modifications include:

o   Folding by chaperones

o   Formation of quaternary structure

o   Cleavage of proteins or signal sequences

o   Covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)

Control of Gene Expression in Prokaryotes

·        The Jacob–Monod model of repressors and activators explains how operons work.

o   Operons are inducible or repressible clusters of genes transcribed as a single mRNA.

·        Inducible systems (such as the lac operon) are bound by a repressor under normal conditions; they can be turned on by an inducer pulling the repressor from the operator site.

·        Repressible systems (such as the trp operon) are transcribed under normal conditions; they can be turned off by a corepressor coupling with the repressor and the binding of this complex to the operator site.

Control of Gene Expression in Eukaryotes

·        Transcription factors search for promoter and enhancer regions in the DNA.

o   Promoters are within 25 base pairs of the transcription start site.

o   Enhancers are more than 25 base pairs away from the transcription start site.

o   Modification of chromatin structure affects the ability of transcriptional enzymes to access the DNA through histone acetylation (increases accessibility) or DNA methylation (decreases accessibility).

Answers to Concept Checks

·        7.1

1.    mRNA carries information from DNA by traveling from the nucleus (where it is transcribed) to the cytoplasm (where it is translated). tRNA translates nucleic acids to amino acids by pairing its anticodon with mRNA codons; it is charged with an amino acid, which can be added to the growing peptide chain. rRNA forms much of the structural and catalytic component of the ribosome, and acts as a ribozyme to create peptide bonds between amino acids.

2.     

·        GAT: mRNA codon = AUC; Isoleucine (Ile)

·        ATT: mRNA codon = AAU; Asparagine (Asn)

·        CGC: mRNA codon = GCG; Alanine (Ala)

·        CCA: mRNA codon = UGG; Tryptophan (Trp)

3.    The start codon is AUG, which codes for methionine; the stop codons are UAA, UGA, and UAG.

4.    Wobble refers to the fact that the third base in a codon often plays no role in determining which amino acid is translated from that codon. For example, any codon starting with “CC” codes for proline, regardless of which base is in the third (wobble) position. This is protective because mutations in the wobble position will not have any effect on the protein translated from that gene.

5.     

Type of Mutation

Change in DNA Sequence

Effect on Encoded Protein

Silent (degenerate)

Substitution of bases in the wobble position, introns, or noncoding DNA

No change observed

Missense

Substitution of one base, creating an mRNA codon that matches a different amino acid

One amino acid is changed in the protein; variable effects on function depending on specific change

Nonsense

Substitution of one base, creating a stop codon

Early truncation of protein; variable effects on function, but usually more severe than missense mutations

Frameshift

Insertion or deletion of bases, creating a shift in the reading frame of the mRNA

Change in most amino acids after the site of insertion or deletion; usually the most severe of the types listed here

·        7.2

1.    RNA polymerase I synthesizes most rRNA. RNA polymerase II synthesizes mRNA (hnRNA) and snRNA. RNA polymerase III synthesizes tRNA and some rRNA.

2.    RNA polymerase II binds to the TATA box, which is located within the promoter region of a relevant gene, at about –25.

3.    The major posttranscriptional modifications are:

·        Splicing: removal of introns, joining of exons. Uses snRNA and snRNPs in the spliceosome to create a lariat, which is then degraded. Exons are ligated together

·        5′ cap: addition of a 7-methylguanylate triphosphate cap to the 5′ end of the transcript

·        3′ poly-A tail: addition of adenosine bases to the 3′ end to protect against degradation

4.    Alternative splicing is the ability of some genes to use various combinations of exons to create multiple proteins from one hnRNA transcript. This increases protein diversity and allows a species to maximize the number of proteins it can create from a limited number of genes.

·        7.3

1.    Initiation, elongation, and termination

2.     

·        A site: binds incoming aminoacyl-tRNA using codon–anticodon pairing

·        P site: holds growing polypeptide until peptidyl transferase forms peptide bond and polypeptide is handed to A site

·        E site: transiently holds uncharged tRNA as it exits the ribosome

3.    Posttranslational modifications include proper folding by chaperones, formation of quaternary structure, cleavage of proteins or signal sequences, and addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation).

·        7.4

1.    The trp operon is a repressible system; the lac operon is an inducible system.

2.     

Component

Role

Regulator gene

Transcribed to form repressor protein

Promoter site

Site of RNA polymerase binding (similar to promoters in eukaryotes)

Operator site

Binding site for repressor protein

Structural gene

The gene of interest; its transcription is dependent on the repressor being unbound from the operator site

3.    Positive control systems (inducible systems) require an inducer to pull the repressor from the operator site. Negative control systems (repressible systems) require a corepressor to couple with the repressor and allow binding of the repressor–corepressor complex to the operator site.

·        7.5

1.    Signal molecules include steroid hormones and second messengers, which bind to their receptors in the nucleus. These receptors are transcription factors that use their DNA-binding domain to attach to a particular sequence in DNA called a response element. Once bound to the response element, these transcription factors can then promote increased expression of the relevant gene.

2.    Histone deacetylation and DNA methylation will both downregulate the transcription of a gene. These processes allow the relevant DNA to be clumped more tightly, increasing the proportion of heterochromatin.

Shared Concepts

·        Biochemistry Chapter 1

o   Amino Acids, Peptides, and Proteins

·        Biochemistry Chapter 2

o   Enzymes

·        Biochemistry Chapter 6

o   DNA and Biotechnology

·        Biology Chapter 1

o   The Cell

·        Biology Chapter 3

o   Embryogenesis and Development

·        Biology Chapter 12

o   Genetics and Evolution