Long Answer Question 5

Question 1

Protein and amino acid composition (2)

Answer 1

• Proteins are composed of amino acid monomers
• Amino acid has central carbon atom bonded to a hydrogen atom and three functional groups: amino group (–NH2), acid group (–COOH), and an R group, which determines the uniqueness of the amino acid

Question 2

What are the levels of protein organization? (4)

Answer 2

• Primary structure - a linear sequence of amino acids joined by polypeptide bonds
• Secondary structure - coiled primary structure that results in an alpha helix structure with H bonds between amino acids OR a folded primary structure that results in a 𝛃 pleated sheet similar to a handheld fan
• Tertiary structure- globular twisted shape caused by covalent bonds (usually disulfide bonds) between R groups that make polypeptides fold and twist
• Quaternary structure - 2 or more polypeptides joined together to make a protein; cube-ish

Question 3

• What are nucleic acids?

- State the structure and composition of nucleotides

Answer 3

• Two types of nucleic acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
• Both are polymers of nucleotides; every nucleotide is a molecular complex of 3 subunits: phosphate (phosphoric acid), pentose sugar, and a nitrogen-containing base
  DNA is stored in nucleus

Question 4

• Describe DNA composition in terms of its nucleotide composition and possible bases.
• Describe DNA polynucleotide structure using the terms: backbone, hydrogen bonding, and complementary base pairing
• Describe DNA strand configuration in a molecule using the term: antiparallel

Answer 4

• A DNA molecule is made up from a chain of nucleotides. Each nucleotide is made up from a complex of 3 subunits: phosphoric acid (phosphate), pentose sugar (deoxyribose), and a nitrogen-containing base. There are four possible bases. Two are purines with a double ring (adenine[A] and guanine[G]) and two are pyrimidines with a single ring (thymine[T] and cytosine[C]).
• A DNA polynucleotide strand has a backbone made of alternating phosphate and sugar molecules, bases attach to sugar and project to one side. DNA has two strands that twist about each other to form a double helix. The strands are held together by hydrogen bonding between bases: A always pairs with T forming 2 hydrogen bonds and G is always paired with C forming 3 hydrogen bonds. A purine is always paired with a pyrimidine to create complementary base pairing.
• Two DNA strands are antiparallel, meaning they are oriented in opposite directions. The fifth carbon atom (5’) is the uppermost on one strand and the third carbon atom (3’) is the uppermost on the other strand

Question 5

Transcription, discuss function of mRNA. (4)

Answer 5

• Transcription begins when enzyme RNA polymerase binds tightly to a promoter, which is a region of DNA that contains a special sequence of nucleotides. This enzyme opens up the DNA helix just before the promoter so complementary base pairing occurs (like DNA replication). - RNA polymerase inserts RNA nucleotides resulting in an mRNA molecule.
• Messenger RNA (mRNA) carries genetic information from DNA to ribosomes for protein synthesis. mRNA has a sequence of bases complementary to DNA: A, T, C, G in DNA translate to U, A, G, C, in mRNA.
• mRNA must be processed before entering cytoplasm. Newly synthesized primary mRNA molecules become mature mRNA after processing and enter the cytoplasm.

Question 6

What is a ribosome and how are they made? (3)

Answer 6

• Ribosomes: small structural bodies found in cytoplasm and on ER where translation occurs. It is composed of many proteins and several ribosomal rRNAs (rRNA).
• rRNA is produced in to nucleolus within the nucleus, then it joins with proteins manufactured and imported from cytoplasm to for 2 ribosomal subunits, one large and one small.
• Subunits leave nucleus and join together in cytoplasm to form a ribosome as protein synthesis begins

Question 7

Describe Initiation Step of Translation. (3)

- discuss tRNA

Answer 7

• Initiation: brings all translation components together and initiation factor proteins assemble small ribosomal unit, mRNA, initiator tRNA and large ribosomal unit for start of protein synthesis.
• In prokaryotes, small ribosomal unit attaches to mRNA in vicinity if start codon, initiator tRNA pairs with this codon in the P site, then large ribosomal unit joins the small ribosomal unit. Ribosomes have one binding site for mRNA and three for tRNA.
• Transfer RNA (tRNA) molecules bring amino acids to ribosomes, the site of protein synthesis. The single-stranded polynucleotide doubles back on itself so complementary base pairing creates a boot-like shape, on one end is an amino acid and on the other is an anticodon.

Question 8

Describe Elongation Step of Translation (4)

Answer 8

• Elongation: protein synthesis where polypeptide increases in length one amino acid at a time, requires tRNA molecules and elongation factors that facilitate binding of tRNA anticodons to mRNA codons at ribosome. - tRNA with attached peptide is at the P site and tRNA carrying next amino acid in chain is arriving at the A site.
• Once in place at the A site, the peptide chain will be transferred to the A site tRNA. Energy and the ribosomal subunit is needed to bring about transfer: energy contributes to peptide bond formation making resulting polypeptide chain one amino acid longer.
• Once translocation occurs, mRNA moves forward one codon length and peptide-bearing tRNA is now at ribosome P site. The “spent” tRNA exits.

Question 9

Describe Termination Step of Translation (3)

Answer 9

• Termination: the final step of protein synthesis. The polypeptide and the assembled components separate.
• This occurs at the stop codon and requires a protein called a release factor. This cleaves polypeptide from last tRNA and the polypeptide is set free.
• It begins to take its own 3D shape. The ribosome will dissociate into 2 subunits.

Question 10

Pathway of ribosomes, mRNA, and synthesized proteins.

Answer 10

• mRNA sequence is made from transcription in the nucleus. After processing it matures and leaves for the cytoplasm through a nuclear pore of the nuclear envelope
• Ribosomal subunits made in nucleolus leave the nucleus through nuclear pores in the nuclear envelope. They attach to the rough endoplasmic reticulum
• Ribosomes produce proteins that will be folded, processed and packaged into vesicles in the rough ER. Most vesicles will be sent to the Golgi body

Question 11

Why is water important for the overall structure and function of proteins and nucleic acids and their processes in protein synthesis. (5)

Answer 11

• The release factor in the termination step of translation requires water to hydrolyze the bond between the last tRNA at the P site and the polypeptide
• In order for a chain of amino acids to be made, water must be removed in a dehydration reaction to create the peptide bonds, forming the amino acid chain in protein synthesis
• Water contributes to structure protein and processes with water are required for proteins to be synthesized and to function properly
• Nucleic acids (DNA and RNA) need water to be synthesized and function in protein synthesis; nucleotide monomers require removal of water to form nucleic acid polymers
• Water is required for hydrogen bonding between bases in DNA to form correct double helix structure and complete complementary base pairing

Question 12

Main subtopics of this question (7)

Answer 12

• protein and amino acid composition, levels of protein organization
• structure and composition of nucleic acids
• structure and composition of DNA
• transcription and mRNA definition
• ribosome and rRNA definition
• steps of translation: initiation, elongation, termination
• pathway of ribosomes, mRNA and synthesized proteins