Protein Synthesis Flashcards

DNA, RNA, Transcription, and Translation

• DNA: Deoxyribonucleic acid, the genetic material containing the code for an organism's traits. It is a double-stranded helix composed of nucleotides, each containing a phosphate group, a deoxyribose sugar, and a nitrogenous base (Adenine, Thymine, Cytosine, or Guanine).

• Transcription: The process of copying the genetic code from DNA to mRNA in the nucleus. This involves RNA polymerase binding to DNA, unwinding the helix, and synthesizing an mRNA strand complementary to the DNA template.

• RNA: Ribonucleic acid, a molecule that carries genetic information from DNA to the ribosomes. RNA differs from DNA in that it is single-stranded, contains ribose sugar instead of deoxyribose, and uses Uracil instead of Thymine.

• Translation: The process of decoding the mRNA sequence to assemble amino acids into a polypeptide chain (protein) in the cytoplasm. This occurs on ribosomes, where tRNA molecules bring specific amino acids to match the mRNA codons.

• Codons: Sequences of three nitrogenous bases on mRNA that specify particular amino acids. Each codon corresponds to a specific amino acid or a stop signal during translation.

• Amino Acids: The building blocks (monomers) of proteins. There are 20 different types of amino acids, each with a unique structure and properties.

• Polypeptide: A chain of amino acids linked by peptide bonds, forming a protein. The sequence and types of amino acids in a polypeptide determine the protein's structure and function.

Summary of Protein Synthesis

• Protein synthesis involves two main stages:

  • Transcription (in the nucleus)

  • Translation (in the cytoplasm)

• The genetic code is crucial for determining the sequence of amino acids in a protein. It provides the instructions for how the mRNA codons are translated into amino acids.

Subject Assessment Guidelines (SAG)

• Strand: Life at the molecular, cellular, and tissue level.

• Focus on DNA, genetics, and genetic engineering.

• DNA contains the genetic code with information about an organism's characteristics and functions. This code is found in genes within DNA.

• Genes are carried in sex cells to offspring, contributing to their traits.

• Changes in the DNA code (naturally or through human interference) can alter an organism's structure or life processes.

• Aims of Life Sciences:

  • Knowing Life Sciences: Understanding DNA, RNA.

  • Investigating Phenomena: Hands-on activities like modeling nucleic acids or comparing DNA extraction methods.

  • Appreciating the History and Importance: Learning about Watson and Crick's discovery, DNA's role in everyday life, and the use of pharmacological drugs that interfere with protein synthesis (antibiotics).

• Candidate Knowledge:

  1. Understanding how scientists unraveled the genetic code and protein synthesis mechanisms.

  2. Knowing the structure and location of DNA and RNA (mRNA, tRNA) in a cell.

  3. Understanding the structure of nucleotides, including nitrogenous bases (Adenine, Thymine, Cytosine, Guanine) and the difference in RNA (Uracil replaces Thymine) and base pairing rules.

  4. Knowing about mitochondrial DNA and its maternal inheritance for determining relatedness.

  5. Understanding the process of transcription, including the role of RNA polymerase.

  6. Understanding the process of translation, including the roles of mRNA, tRNA, amino acids, and ribosomes. Familiarity with codons and anticodons is important.

  7. Understanding mutations (point and frameshift), their causes (mutagens and chance), and effects (insertion, deletion, substitution).

  8. Understanding the application of DNA technology, such as DNA fingerprinting and PCR.

Introduction to Proteins and Protein Synthesis

• Protein Synthesis: The process by which cells create proteins.

• Control: Controlled by DNA (containing genes) and involves RNA.

Proteins

• Complex molecules made of amino acid monomers.

• There are 20 different types of amino acids.

• Proteins are chains of amino acids linked by peptide bonds; they range in size from about 50 to 300+ amino acids.

• The sequence and type of amino acids determine a protein’s specific structure and function.

Location of Protein Synthesis

• Protein synthesis starts in the nucleus (where DNA is located) and finishes on the ribosomes in the cytoplasm.

Two Main Stages of Protein Synthesis

1. Transcription (in the nucleus)

2. Translation (on the ribosome in the cytoplasm)

Key Terminology

• Amino Acids: Monomers/building blocks of proteins.

• Base Triplet: Sequence of three nitrogenous bases on a DNA strand.

• Codon: Sequence of three nitrogenous bases on mRNA, complementary to a DNA base triplet.

• Anti-codon: Sequence of three nitrogenous bases on tRNA, complementary to an mRNA codon.

• Transcription: DNA genetic code is copied into mRNA (in the nucleus).

• Translation: mRNA genetic code is decoded to produce a specific amino acid sequence (on ribosomes in the cytoplasm).

• Peptide Bond: Chemical bond between adjacent amino acids.

• RNA Polymerase: Enzyme that controls transcription.

• STOP Codons: mRNA codons that signal the end of translation.

Transcription (DNA to mRNA)

• Location: Nucleoplasm within the nucleus.

• Purpose: To create an mRNA molecule carrying the genetic code for one specific protein (gene) from the DNA template.

Process

1. Initiation: RNA polymerase binds to the start of a specific gene on DNA. Promoters signal the start of a gene.

2. Unwinding & Unzipping: The DNA double helix unwinds, and hydrogen bonds between base pairs break, causing the DNA to unzip. This creates a transcription bubble.

3. Template Strand: One of the DNA strands acts as a template for mRNA synthesis. This strand is also known as the non-coding strand.

4. mRNA Synthesis: Free RNA nucleotides pair with complementary bases on the DNA template strand. A pairs with U, T pairs with A, C pairs with G, and G pairs with C. RNA polymerase facilitates this process by catalyzing the formation of phosphodiester bonds between RNA nucleotides.

5. mRNA Formed: A single strand of mRNA, containing codons complementary to the DNA base triplets, is synthesized. This mRNA molecule is also known as the primary transcript.

6. Termination & Release: The mRNA molecule detaches from the DNA template. Termination signals in the DNA sequence cause RNA polymerase to stop transcription.

7. DNA Rewinds: The DNA strands re-zip (hydrogen bonds reform), and the double helix winds up again. This restores the original structure of the DNA.

8. mRNA Exit: The mRNA strand leaves the nucleus through a nuclear pore. Nuclear pores are channels in the nuclear envelope that allow the transport of molecules in and out of the nucleus.

9. Ribosome Attachment: The mRNA molecule travels to the cytoplasm and attaches to a ribosome. Ribosomes are the sites of protein synthesis.

Translation (mRNA to Protein)

• Location: Cytoplasm on a ribosome.

• Purpose: To decode the sequence of codons on mRNA and assemble the corresponding sequence of amino acids into a polypeptide chain (protein).

• Molecules Involved: mRNA, tRNA, ribosome, amino acids.

Process

1. Initiation: The mRNA molecule, bound to the ribosome, presents its sequence of codons. The start codon (usually AUG) signals the beginning of translation.

2. tRNA Role: tRNA molecules with specific anticodons bind to specific amino acids. Each tRNA molecule carries a specific amino acid corresponding to its anticodon.

3. Codon-Anticodon Recognition: A tRNA molecule with an anticodon complementary to the first mRNA codon on the ribosome binds to the mRNA. This ensures the correct amino acid is added to the growing polypeptide chain.

4. Amino Acid Delivery: The tRNA delivers its specific amino acid to the ribosome. The ribosome facilitates the formation of peptide bonds between the amino acids.

5. Elongation: The ribosome moves along the mRNA to the next codon. Another tRNA brings the next amino acid. A peptide bond forms between the amino acids. The first tRNA detaches and can pick up another molecule of the same amino acid. This repeats. This process continues until the entire mRNA sequence has been translated.

6. Termination: Elongation continues until the ribosome encounters a STOP codon on the mRNA. No tRNA molecules bind to STOP codons, so protein synthesis terminates, and the polypeptide chain is released. Release factors help detach the polypeptide chain from the ribosome.

Examples Illustrating Protein Synthesis

Example 1: Answering a Question about DNA's Role in Transcription

• Question 4.3.1: Describe the role of DNA during transcription in protein synthesis. (4 marks)

• Answer:

  • DNA codes for a particular protein/polypeptide/amino acid sequence.

  • One strand is used as a template.

  • To form mRNA.

  • DNA cannot leave the nucleus.

Example 2: Determining the mRNA Codon Sequence from a DNA Sequence

• Question 4.3.2: The diagram below shows the sequence of nitrogenous bases of a small part of a strand of DNA which codes for part of a protein molecule. CGG--- TAT--- CCT Write down the mRNA codon sequence that reads from left to right from the DNA sequence above. (3 marks)

• Steps:

  1. Write down the DNA code: CGG--- TAT--- CCT

  2. Write down the complementary RNA nitrogen base sequence: GCC--- AUA--- GGA (Uracil replaces Thymine in RNA)

Example 3: Finding the Amino Acid Sequence from mRNA Codons Using tRNA Anticodons

• Question 4.3.3: Select and write down from the list above, the amino acids (in the correct sequence) that would be required for the base sequence of mRNA shown below. GGG--- CCA--- AGU

• List of tRNA Anticodons and Corresponding Amino Acids:

  • CAA - Valine

  • CCC - Glycine

  • CGU - Alanine

  • AAA - Phenylalanine

  • UUA - Asparagine

  • UAC - Methionine

  • GGU - Proline

  • ACC - Tryptophan

  • UCA - Serine

• Steps:

  1. mRNA sequence: GGG--- CCA--- AGU

  2. Find/write down the tRNA anticodons: CCC--- GGU--- UCA

  3. Use the table to find the corresponding amino acids: Glycine, Proline, Serine

November 2013 Question Example

• Question 2.2: A diagram shows a ribosome with mRNA (Molecule X) and tRNA (Molecule Y), with structure 1, 2, and 3 identified. The mRNA sequence reads CAU GGG AUG.

  • Question 2.2.1: Name the stage of protein synthesis represented in the diagram above. (1)

  • Answer: translation

  • Question 2.2.2: Identify:

    • (a) Molecule X (1)

    • Answer: mRNA

    • (b) Molecule Y (1)

    • Answer: tRNA

    • (c) Structure 1 (1)

    • Answer: Amino acid

  • Question 2.2.3 The table below shows the DNA base triplets that code for different amino acids found in human proteins.

  • Using the information in the table and the diagram above, write down the sequence of the amino acids that correspond with structures 1, 2 and 3.

  • Amino Acid- Leucine - GAA - Proline - GGG - Lycine - TTT - Histidine - GTA - Serine - TCA - Methionine - TAC - Glycine - CCC - Glutamine - GTC

  • Answer: histidine, glycine, methionine

The Genetic Code

• The order of nitrogen bases on DNA determines the sequence of bases on mRNA.

• The sequence of bases on mRNA determines the sequence of amino acids in the protein.

• DNA contains the genetic code for forming a particular protein.

Terminology Review

• Amino acid: Monomer of a protein.

• Dipeptide: Two amino acids joined together.

• Polypeptide chain: More than two amino acids joined together.

• Dehydration synthesis: Combining amino acids by releasing water.

• Protein synthesis: The process of making proteins.

• Transcription: Making mRNA in the nucleus.

• Translation: Combining amino acids in the cytoplasm based on mRNA codons.

• Peptide bonds: Bonds between amino acids.

• Codon: Triplet of nitrogen bases on mRNA.

• Anticodon: Triplet of bases on tRNA.

Final Assessment Questions and Solutions

1. The portion of DNA that carries the genetic code for the formation of a particular protein by specifying its amino acid sequence.

   • A. Genetic code

   • Correct Answer: A

2. The anticodon is the triplet of bases on…

   • B. tRNA

   • Correct Answer: B

3. The codon is the triplet of bases on…

   • C. mRNA

   • Correct Answer: C

4. The site of protein synthesis…

   • A. Ribosomes

   • Correct Answer: A

5. For the tRNA sequence: CCA--- UAU--- GGU. The sequence of codons on mRNA would be…

   • B. GGU--- AUA --- CCA

   • Correct Answer: B

6. For the tRNA sequence: CCA--- UAU--- GGU. The sequence of nitrogen bases on DNA would be…

   • D. CCA--- TAT--- GGT

   • Correct Answer: D

7. The enzyme that is responsible for transcription is …

   • D. Both A and B [Transcriptase (in some contexts) and RNA polymerase]

   • Correct Answer: D

8. Transcription is the process during which…

   • A. mRNA is made

   • Correct Answer: A

9. Transcription occurs in the…

   • C. Nucleus

   • Correct Answer: C

10. Translation is the process during which…

    • B. tRNA picks up free amino acids

    • Correct Answer: B

11. Translation occurs in/on the…

    • B. Ribosome

    • Correct Answer: B

12. The arrangement of amino acids during translation is determined by the…

    • D. All of the above [Order of nitrogen bases on DNA, Sequence of codons of mRNA, Sequence of anticodons on tRNA]

    • **Correct