Transcription, Translation, and Protein Study Guide

What is the Central Dogma of Biology?
DNA>RNA>PROTEIN The Central Dogma of Biology is used to describe the “one gene-one protein” mechanism that allows for DNA to produce a code specific to an amino acid sequence needed for structural and functional proteins. This premise is losing some hold on biology since it has been discovered that NOT all genes code for the production of proteins but rather RNA.

Describe the 3 main types of RNA, their function, and their location in the cell.
mRNA – found in nucleus and cytoplasm; makes a nucleotide copy of DNA so it can be read at the nucleus for the production of an amino acid sequence.
rRNA – found in the ribosomal structure itself; responsible for the physical production of an amino acid sequence.
tRNA – found in the cytoplasm; responsible for the matching of a correct amino acid to the codon sequence found on mRNA.

Differences between DNA and RNA.
DNAdouble stranded moleculerestricted to nucleusdeoxyribose sugarATGC
RNAsingle stranded moleculenucleus and cytoplasmribose sugarAUGC

What is transcription? Can you transcribe a segment of DNA into mRNA?
Transcription is the construction of a nucleotide copy of mRNA from the order of nucleotide bases in DNA. When a mRNA is made, introns/non-coding sequences are removed and exons are spliced together. The resulting mRNA contains all of the codons necessary for the production of specific proteins.

What is a ribosome? Where are ribosomes located in EUKARYOTIC cells?
A ribosome is an organelle found either free or fixed (to the rough endoplasmic reticulum) in the cytoplasm of a eukaryotic cell. It is composed of rRNA.

What is the structural components of the EUKARYOTIC ribosome? Be specific.
Large subunit (60s)Small subunit

28s rRNA +5s rRNA + 6s rRNA18s rRNA

4700 nucleotides 120 nucleotides 160 nucleotides1874 nucleotides

and 49 proteinsand 33 proteins

What is the function of transfer RNA? What does tRNA look like? Where does the amino acid bind to the tRNA molecule?
To match the codon of mRNA and transfer an AMINO ACID to the growing polypeptide chain.

Describe the codon dictionary. Can you read a codon chart? How many start codons? Stop codons? What are they?
The codon dictionary is an arrangement of 64 different combinations of AUGC that dictate a specific amino acid for each 3 letter combination. 61 of the codons will produce a match for one of 20 biologically necessary amino acids (some amino acids have more than 1 possible codon sequence) and 3 codons produce the STOP sequence for the termination of the reading frame for an amino acid sequence. 1 codon sequence acts as a start codon but can also be read as methionine. If it appears AFTER stop, AUG is read as a start codon; if it is read after start but BEFORE stop, it is read as the amino acid methionine.

What are the 3 main steps of Translation?
1. Initiation

  • mRNA binds to small subunit of rRNA with initiation factors and initiator tRNA with START/methionine with mRNA in the P site.
  • START/initiate the production of polypeptide chain. It binds to UAC as the anticodon.
  • Initiating factors are released, the large subunit binds to the small subunit.

2. Elongation
The lengthening of the growing polypeptide chain by one amino acid is call elongation. The binding sites created by the initiation process are called the P (peptidyl) site and the A (aminoacyl) site. The mRNA moves through the assembled ribosome beginning at the P site allowing the amino acids to be bound together by peptide bonds. The E site is the location in the ribosome that uncharged tRNA exits the complex. Peptidyl transferanse is the enzyme that catalyzes the formation is the peptide bonds between the amino acids in the P and A sites.

  • Step 1: A second charged tRNA enters the A site while the initiator sequence (UAC) is still in the P site.
  • Step 2: A peptide bond forms between the first amino acid (in the P site) and the 2nd amino acid (in the A site). The uncharged tRNA in the P site moves to the E site as the mRNA is shifted 3 bases to the left and the dipeptide moves into the P site. (Note the color sequence of the growing amino acid chain.
  • Step 3:First elongation step is complete, the 3rd charged tRNA moves into the A site
  • Steps 4 and 5: 2nd elongation step begins as a tripeptide is formed. Uncharged tRNA moves into the E site.

3. Termination
The final phase of translation is signaled by the appearance of one or more of three STOPcodons appearing in the A site. The codons do not specify an amino acid and they DO NOT call for a charged tRNA. Often, these codons appear as consecutive stop sequences at the end of mRNA.

Be able to TRANSCRIBE and TRANSLATE a DNA sequence into an amino acid sequence.

What was significant about inborn errors of metabolism that provided information to researchers about protein structure and function?
Observable inborn errors in metabolism provided a way for scientists to study the IMPACT that changes/alterations in DNA affected an individual. Since all of these conditions were caused by faulty ferments (enzymes) and all belonged to the protein classification, changing sequences provided valuable information on mutations.

Provide detailed information about PKU.
Phenylketonuria is the most common inborn error of metabolism in the US. Almost every newborn is screened for this condition within hours after birth. If they test positive, a specific diet must be followed in order to prevent buildup of the amino acid phenylalanine in nervous tissue. Essentially, PKU is lacking the enzyme phenylalanine hydroxylase that allows for phenylalanine to be converted into tyrosine which can be further metabolized into other needed products.

Provide detailed information about sickle cell anemia and describe the significance of sickle cell disease that made it a useful tool in studying genetic mutations and protein structure/function.
Sickle cell disease provided evidence that a single amino acid change in a sequence can lead to disease. The change alters the shape of the erythrocytes in those impacted by this mutation. The mutation occurs in the 6th position of the beta subunit of the hemoglobin molecule can alters the shape of hemoglobin when in a low oxygen or stress environment.
Hemoglobin is a quaternary protein made of 4 tertiary subunits, 2 alpha and 2 beta, held together by a central molecule of iron.

Identify an amino acid structure, the significance of the R group, and the chemistry of linking amino acids together.

The R-group is also referred to as a side chain and is what gives the amino acid its chemical characteristics/behavior.
When amino acids are linked together, the enzyme peptidyl transferase forms a peptide bonds through dehydration synthesis, removing water to link the amine group of one amino acid to the carboxyl group of the adjacent amino acid.

What 4 categories do all 20 biologically needed amino acids belong? (You DO NOT need to know which amino acids fit into which group for this test.) What are the characteristics of each of these categories? How do they play a role in the formation of a protein?
Hydrophobic: will turn the side chain away from water in the middle of the tertiary structure.
Hydrophilic: will turn the side chain toward the water and remain on the outer portion of the tertiary structure.
Acidic: has a slight negative charge and will form a salt bridge with a basic side chain
Basic: has a slight positive charge and will forma salt bridge with an acidic side chain

What are the 4 structures that make a 3-dimensional protein? Describe each arrangement and how it is held together.
Primary: straight chain of amino acids

Secondary: alpha helix and/or beta pleated sheet; held together by hydrogen bonds

Tertiary: globular structure formed by the association of amino acids to each other based on their side chain group

Quarternary: 2 or more tertiary structures held together by a central molecule.
What are the RULES for protein folding?
See half note sheet