D1.2  Protein Synthesis

Theme:  Continuity and Change

There is continuity in the transfer of genetic information (from DNA, to RNA, to protein) and in the universality of the genetic code across all forms of life.

• The same three-letter codons code for the same amino acids in almost every organism. This suggests that the genetic code of life has remained largely unchanged for billions of years. 
• ​During transcription, RNA Polymerase uses complementary base pairing to ensure the message from DNA is preserved in the mRNA transcript. This ensures the cell builds exactly what the genome specifies.
• The ribosome is where the mRNA codon and the tRNA anticodon meet. By holding these molecules in the precise orientation required for H-bonding, the ribosome ensures that the correct amino acid is added to the polypeptide chain. 
  
  

The same genetic information can lead to different outcomes through the regulation of expression and the impact of mutations.

• While every cell in an organism contains the same DNA, the proteins they synthesize differ. By "turning on" or "off" specific transcription factors, a cell can specialize in form and function.
• A change in a single DNA base can lead to a change in the mRNA codon, which may result in a different amino acid. 
• By rearranging which exons are kept, the cell can change the final mRNA sequence.  As a result, a single gene can produce functionally different proteins from the same DNA code.
• Post-translational modification of proteins allow a cell to change a proteins properties rapidly without needing to go back to the DNA or RNA level.

Guiding Questions:  
Guiding questions help students view the content of the syllabus through the conceptual lenses of both the themes and the levels of biological organization.

• How does a cell produce a sequence of amino acids from a sequence of DNA bases?
• How is the reliability of protein synthesis ensured?

​
​Linking Questions:  
Linking questions strengthen students’ understanding by making connections between topics.  The ideal outcome of the linking questions is networked knowledge.

• What biological processes depend on hydrogen bonding? 
• How does the diversity of proteins produced contribute to the functioning of the cell?

Key Terms to Know: * higher level only

3' PolyA Tail*
5' Cap*
5' Terminal*
5' to 3' Transcription*
5' to 3' Translation*
A Site (of Ribosome)*
Adenine
Alternative Splicing*
Amino Acid
Anticodon
Base Sequence
Codon
Complementary Base Pair
Conserved Sequence
Degeneracy (of Genetic Code)
Deoxyribonucleic Acid (DNA)
E Site (of Ribosome)*
Elongation (of Translation)
Eukaryote*
Exon*

Gene Expression
Genetic Code
Hydrogen Bond
Initiation (of Transcription)*
Initiation (of Translation)*
Initiator tRNA*
Insulin*
Intron*
Large Subunit (of Ribosome)
mRNA
Mutation
Non-Coding DNA*
P Site (of Ribosome)*
Peptide Bond
Point Mutation
Polypeptide
Post-Transcriptional* Modification*
Pre-Proinsulin*
Proinsulin*
Promoter*

Proteome*
Proteosome*
Ribonucleic Acid (RNA)
Ribosome
RNA Polymerase
rRNA*
Small Subunit (of Ribosome)
Somatic Cell
Splicing*
Start Codon*
Telomere*
Template
Transcription
Transcription Factors*
Translation
Triplet Code
tRNA
Universality (of Genetic Code)
Uracil

D1.2.1—  Transcription as the synthesis of RNA using a DNA template.

• Define transcription.
• List the roles of RNA polymerases in the process of transcription. ​​

D1.2.2— Role of hydrogen bonding and complementary base pairing in transcription.​

• State the complementary base pairing utilized in transcription. 
• Distinguish between the sense and antisense strands of DNA.

D1.2.3— Stability of DNA templates.

• Outline how stability of the information stored in DNA is maintained.

D1.2.4-- Transcription as a process required for the expression of genes.

• Define gene expression.
• Outline the major steps of gene expression.
• State that the pattern of gene expression is how cells differentiate for specific functions.
• Outline the role of transcription in regulating gene expression.​

D1.2.5— Translation as the synthesis of polypeptides from mRNA.

• Define translation.
• State the location of translation in cells.​

​​​​D1.2.6- Roles of mRNA, ribosomes and tRNA in translation.

• Outline the roles of mRNA, ribosomes and tRNA in translation. 
• Describe the structures of mRNA and tRNA.
• Describe the structure of the ribosomes, including the small and large subunits and the names and roles of the tRNA binding sites.

 ​​​​D1.2.7- Complementary base pairing between tRNA and mRNA.

• State the complementary base pairing utilized in translation. 
• Define codon and anticodon. 
  
• Describe the formation of hydrogen bonds between codon and anticodon.

D1.2.8- Features of the genetic code.

• Explain the reason that a sequence of three nucleotides is required to code for the 20 amino acids commonly utilized by organisms.
• Define codon, degenerate and universal as related to the genetic code.

D1.2.9-  Using the genetic code expressed as a table of mRNA codons.

• Use a genetic code table to determine the amino acid sequence coded for by a given DNA or RNA sequence.

D1.2.10- Stepwise movement of the ribosome along mRNA and linkage of amino acids by peptide bonding to the growing polypeptide chain.

• Outline the process of translation elongation, including codon recognition, bond formation and translocation.

D1.2.11- Mutations that change protein structure.

• Define gene mutation.
• State the cause of sickle cell anemia, including the differences in the HbA and HbS alleles.
• State the difference in RNA sequences in the transcription of the HbA and HbS alleles.
• State the difference in amino acid sequences in the translation of the HbA and HbS alleles.
• Outline the consequences of the HbS mutation on the  structure and function of the hemoglobin protein. 
• Discuss the symptoms of sickle cell disease.

AHL ​​​​D1.2.12- Directionality of transcription and translation.

• Identify the 5’ ends and 3’ ends of a strand of RNA.
• Describe the formation of the covalent bond between adjacent nucleotides during transcription. 
• State that RNA polymerases can only add the 5’ phosphate of a free nucleotide to the 3’ deoxyribose of the elongating strand.​
• State the direction of movement of the ribosome along the mRNA molecule.
  

AHL ​​​​D1.2.13- Initiation of transcription at the promoter.

• Outline the structure and function of the promoter regions of DNA.
• Describe the initiation of transcription, including the role of the promoter sequence, transcription factors and RNA polymerase.
• Compare the function of activator and repressor sequences within the promoter.
• State that transcription factors are proteins that bind to the promoter.
• State that some transcription factors activate transcription while others inhibit transcription. 

AHL ​​​​D1.2.14- Non-coding sequences in DNA do not code for polypeptides.

• Define “coding” and “non-coding” sequences of DNA.
• Outline five functions of noncoding DNA sequences found in genomes.

AHL ​​​​D1.2.15- Post-transcriptional modification in eukaryotic cells.

• Outline the location and timing of post-transcriptional modification of RNA.
• Describe the function of the 5’ cap and poly-A tail.
• Compare intron and exon sequences of genes. 
• Outline the process of RNA splicing. ​

AHL ​​​​D1.2.16- Alternative splicing of exons to produce variants of a protein from a single gene.

• Describe the process of alternative RNA splicing.
• Outline the benefit of alternative RNA splicing.​

AHL ​​​​D1.2.17-  Initiation of translation.

• Outline the process of translation initiation.​

AHL ​​​​D1.2.18- Modification of polypeptides into their functional state.

• List types of modifications of polypeptides that may be required to form a functional protein.
• Outline the stages of modification of preproinsulin to form functional insulin.​

AHL ​​​​D1.2.19- Recycling of amino acids by proteasomes.

• List reasons when proteins typically exist for a relatively short time within a cell. 
• Outline the function of proteasomes in the recycling of amino acids.