AP Biology

Protein Synthesis – Part 1

(Associated Learning Objectives: 1.14, 1.15, 1.16, 2.22, 2.31, 2.33, 2.36, 2.37, 3.4, 3.6, 3.18, 3.24, 3.25, 4.1, 4.2, 4.3, 4.4)

Important concepts from previous units:

1)Proteins are constructed from the macromolecules called amino acids.

2)Amino Acids are linked by a covalent peptide bond by a hydrolysis reaction.

3)DNA is more stable than RNA; but RNA evolved before DNA did.

  1. George Beadle and Edward Tatum (1934)
  2. They develop the one gene-one enzyme hypothesis. This proposes that a single gene has the genetic information for making one enzyme. This is later changed to become the one gene - one polypeptide (protein) hypothesis; as enzymes are a type of polypeptide (protein).
  1. Transcription (means “ the process of making a working copy of an original”)
  2. This process is the making of a disposablecopy of DNA but in the form of RNA.The disposable copy will become known as mRNA – messenger RNA. It is a disposable copy of the “Million Dollar DNA Blueprint”.
  3. The message (mRNA) will be sent to the construction site (ribosomes)for building the protein.
  4. RNA nucleotides use Ribose instead of Deoxyribose as the five carbon sugar.This makes the RNA less stable than DNA; that is good since the cell only needs it to send a temporary message on how to construct the protein.
  5. In RNA, Uracil replaces Thymine.Thymine can’t exit nuclear pores. Remember, ribosomes are out in the cytoplasm, so Thymine needs to be substituted by Uracil.
  6. DNA serves as a template (guide) for making the mRNA. A = U and C = G (Still can use Chargaff’s Rule.)
  7. In Eukaryotic cells, the mRNA mustfirst be “modified” before translation can occur. The modification occurs in the nucleus. (Prokaryotes DO NOT modify the mRNA. They sent it to the ribosome “as is”.)
  8. Primary Transcript (before modification) is modified to produce the secondary transcript (aftermodification has occurred). The secondary transcript is what will be sent out of the nucleus to the ribosome.
  9. This is considered the first part of Protein Synthesis.
  1. Translation (means “The process of taking from one language and changingto another language”)
  2. In this process, the cell is turningnucleotide language (DNA/RNA) into amino acid language to make proteins. Remember, amino acids are the building blocks of proteins.
  3. This process occurs at the Ribosome. The ribosome has a nickname… “the Translator”. It is also considered a “construction site” since the cell is building a protein.
  4. This is considered the second part of Protein Synthesis.
  1. Codon “A.K.A Triplet Code” (This is the amino acid language.)
  2. Codons are determined by the template strand of DNA (Important Blueprint Information) but are READ ON THE RNA! (The mRNA is what is being translated; not the DNA.)
  3. The codons MUST be read 5’ 3’on the mRNA!(Because this is how the mRNA was made. You do not write a sentence and then read it backwards do you. It would make no sense.)
  4. RNA Codon Chart for Amino Acids (Contains the 20 known amino acids for living organisms.)
  5. The chart was started by Marshall Nirenberg (early 1960’s) (He won a Noble Prize for this.)
  6. UUU- Phenylalanine was the first one recorded.
  7. 61of the 64 possible codons ( 4³) codes for an Amino Acid.
  8. 4 refers to the four nucleotides possible (A, C, U, G); 3 refers to the number of pieces in a UNIT (codon).
  9. AUG is the start codon or Methionine. It depends on the position in the mRNA. If it is the first codon on the 5’ end, it will be the start codon. If it is not the first, it will be regular methionine.
  10. UAA, UAG, and UGA are thestop codons.These codons stop the process of transcription.
  11. Redundancy is wasteful, so enter Inosine.This nucleotide can act as a “Wild Card”. When put in the third position of an anticodon, it can represent any nucleotide. (This is useful for such amino acidsequences such as Serine or Arginine.)
  12. This chart is universal for all living organisms and vituses.(Viruses are not living.) This hits on the theme of Unity and Diversity. Unity in that it indicates Common Ancestry among all organisms and viruses. Diversity is in the differences of the sequencesof amino acids strung together to make a protein.)
  13. Remember, RNA evolved first (but it is unstable) then mutated to DNA (which is more stable). This is why ALL living organisms and most viruses are DNA based.
  14. Reading Frame - This term refers to a set of 3 consecutive nucleotides read in 5’  3’direction.
  15. RNASynthesis and Modification -The makingof mRNA.This process occurs at the nucleolus. (Remember,

the nucleolus is “like” a copy machine because we are making a cheap

disposable copyof the DNA sequence.)

  1. Three Phases of production to a transcription unit - piece of mRNA.
  2. Initiation - This is building our factory to make mRNA basically.
  3. A protein called a Transcription Factor attaches to the TATA box todetermine the direction the “factory” will proceed. The TATA box is part of the promoter sequence. (Look at the TATA sequence, can you see it running in different directions. This orients the “factory” to the direction it will transcribe.)
  4. Then additional transcriptionfactors (proteins and enzymes) are added to the “factory”.
  5. Finally, RNA Polymerase II joins to complete the factory.The whole “factory” is called a Transcription Initiation Complex. (Can you see the definition in the term? Transcription is the process being done. Initiation refers to the beginning process. Complex indicates we have many parts involved in making the structure.)
  6. This is a step by stepcontrolled process. (The cell “controls” each step to help make sure nothing goes wrong.)
  7. Elongation - This refers to the actual makingof the mRNA molecule.
  8. This must bemade in the 5’  3’ direction!
  9. RNA Polymerase IIseparates the DNA Double Helix to make room to work.
  10. RNA Polymerase IIalso adds nucleosides to the growing molecule.

i. Nucleosides come from the cytoplasm.Lysosomes recycle and provide them.

  1. After RNA Polymerase II has past the DNA transcription point, the DNA reforms the helix.
  2. Cells can make multiple copies of RNA because the DNA is left intact and protected in the nucleus.
  1. Termination(Just like it sounds… stop the transcription.)
  2. A stop codon is made (for the ribosome) and the “factory” molecule slows down.
  3. RNA Polymerase IIslows down until it stops transcription by forming anAAUAAA sequence and is then released from the DNA.
  1. Modification of the Primary Transcript for EUKARYOTIC Cells (This also occurs in the nucleus.)
  2. Front end (5’)modification of the mRNA molecule.
  3. A 5’ protective capis added. (This would be like you putting on a hard hat to protect your headwhen you go outside into a “construction site”.)
  4. This cap acts as a signal to the ribosome particles, telling it where to attach.
  5. Back end (3’) modification of the mRNA molecule.
  6. A Poly A Tail is added. (“poly” means “many”; 50-250 Adenines will be added onto the tail.)
  7. This acts as protection against digestive enzymes in the cytoplasm. (Remember, it is a construction site and things are being broken down as well as being built.)
  8. Middle modification of the mRNA molecule. (This modification is referred to as RNAAlternative Splicing.)
  9. During this step, remove the non-coding introns (These act as spacers) using Spliceosomes. (A spliceosome is a collection of snRNPs.)

i. snRNP’s (smallnuclear ribonucleic proteins act as scissors.) Remember, Ribozymes are RNA molecules that act as enzymes.

  1. Then rearrange the separatedcoding exons (important blueprint pieces.) to the needed configuration. This is why it is called alternative; pieces (exons) can be rearranged in different orders.(This is REALLY important in the making of antibodies by our immune system. Remember the variable portion of the antibody structure.)
  2. “Stitch” the pieces together to make the finalized secondary mRNA transcript that is know ready for transport to the ribosomes for translation into proteins.