Week 4 Application Questions Flashcards
Part A: Nucleic Acids
1. (Have to look at diagram of a structure of a DNA molecule)
a) On the diagram, label the 5’-ends, 3’-ends, and all the phosphodiester bonds.
Part A: Nucleic Acids
1. (Have to look at diagram of a structure of a DNA molecule)
b) On the diagram, label the purines and the pyrimidines.
Part A: Nucleic Acids
1. (Have to look at diagram of a structure of a DNA molecule)
c) The enzyme DNA polymerase synthesizes DNA polymers from nucleotide monomers.
Name the parts of the nucleotide molecules that are involved in this chemical reaction (use the carbon numbering to identify the positions).
Part A: Nucleic Acids
1. (Have to look at diagram of a structure of a DNA molecule)
d) If you were to compare this structure to the structure of an RNA molecule, describe all the chemical differences you would observe.
Part A: Nucleic Acids
1. (Have to look at diagram of a structure of a DNA molecule)
e) When DNA is heated it denatures, which means that the two strands of the double helix separate from each other. Explain why this occurs.
- H-bonds are weak bonds
- Increased molecular motion
caused by heat will break them - When H-bonds break,
two strands come apart - Covalent bonds don’t break
so denatured DNA exists
as single strands connected by phosphodiester bonds
Part A: Nucleic Acids
1. (Have to look at diagram of a structure of a DNA molecule)
f) Examine the T=A base pair in the structure above. Explain, based on the chemical properties of the nitrogenous bases, why T is not able to form a base pair with G.
- To form an H-bond, need a
δ+ H to line up with a δ– atom - T and G do not contain
compatible groups to form
H-bonds - Only T-A and C-G can base pair
Part B: Proteins
2. The HBB gene encodes beta-globin, the larger of the two polypeptide subunits that make up the human protein hemoglobin. The first part of the HBB gene has the DNA sequence (order of nitrogenous bases) in one strand of the double-helix of:
5’—A T G G T C C A T C T A A C T C C T G A G G A G A A G—3’
a) What would the sequence (order of nitrogenous bases) of the other strand of the double helix be?
Write the sequence of the second strand below the first strand, showing where base pairs would form, and label the ends.
3’— T A C C A G G T A G A T T G A G G A C T C C T C T T C —5’
Part B: Proteins
2. The HBB gene encodes beta-globin, the larger of the two polypeptide subunits that make up the human protein hemoglobin. The first part of the HBB gene has the DNA sequence (order of nitrogenous bases) in one strand of the double-helix of:
5’—A T G G T C C A T C T A A C T C C T G A G G A G A A G—3’
b) What would the sequence (order of nitrogenous bases) be if the sequence written above was an RNA molecule rather than a DNA molecule? Write the sequence above or below on of the strands above and label the ends.
5’—A U G G U C C A U C U A A C U C C U G A G G A G A A G—3
Part B: Proteins
3a) The SARS- CoV-2 virus is covered in spike proteins (Fig 1) consisting of two subunits: a spherical or globular part and a flexible stalk.
How would you describe the structure of the protein (the green structures are carbohydrates)?
– Quaternary structure: two subunits (min of 2
polypeptides)
Part B: Proteins
3a) The SARS- CoV-2 virus is covered in spike proteins (Fig 1) consisting of two subunits: a spherical or globular part and a flexible stalk.
What kind of bonds do you think are holding
this shape together?
– held together by ionic bonds, disulfide bridges, hydrophobic interactions, hydrogen bonds but not: peptide bonds
Part B: Proteins
3a) The SARS- CoV-2 virus is covered in spike proteins (Fig 1) consisting of two subunits: a spherical or globular part and a flexible stalk.
Do you think this is a mostly hydrophobic or hydrophilic molecule/protein? Why?
– The spherical part should be hydrophilic, (virus is in water droplets), the stalk should have a hydrophobic end to be anchored in the lipid bilayer.
Part B: Proteins
3b) Governments all over the world are 3wconcerned about new strains of SARS- CoV-2 that are more infectious because of changes in the shape of spike protein. One of the observed changes is called D614G: at that location (614) the amino acid Aspartic Acid (D) has changed to Glycine (G).
What change has occurred at the nucleic acid (RNA)
level?
Based on what you know about functional groups, polarity, bonding and protein folding describe or characterize this change and what could be behind this change?
- GAU sequence has changed to GGU = substitution of one base: A to G
- Old sequence ….5’GAU3’…
- New sequence…5’GGU3’…
- This change in the RNA sequence results in a aspartic acid amino acid (D) being
changed to a glycine amino acid (V) in the beta-globin polypeptide. - this change is Non-conservative change
Explain how you were able to determine this: - Conservative: New AA has same properties as old AA
- Non-conservative: New AA has different properties than old AA
Aspartic acid is neg. charged, charged; glycine is non-polar, = no ionic bonds possible
– Non-conservative change when
* Bonds and shape of proteins are changed due to
different polarity and/or
* A measurable change in behaviour of the protein
Part B: Proteins
3b) Governments all over the world are 3wconcerned about new strains of SARS- CoV-2 that are more infectious because of changes in the shape of spike protein. One of the observed changes is called D614G: at that location (614) the amino acid Aspartic Acid (D) has changed to Glycine (G).
Why would the exchange of a single amino acid result in a change of protein function/effectiveness?
– Change to primary amino acid sequence of protein
– New amino acid has different properties than old amino acid
* Non-polar instead of polar, charged
– New amino acid forms different bonds with different amino acids
* Wants to form hydrophobic interactions with other non-polar amino acids (not ionic bonds)
– Creates a 3D different shape in the tertiary & quaternary structure
* Forms fibers instead of clusters
– Alters function of protein
* Can’t carry oxygen as well, distorts the shape of red blood cells
Part B: Proteins
4. Go to the following website and read about how to cook an egg: https://www.livescience.com/28575-science-of-cooking-perfect-egg.html
Based on the information in this article and what you have learned in this topic:
a) In this article, the author talks about denaturing the proteins in the egg yolk. Based on our discussion of protein denaturation in this topic, what is happening to the different levels of protein structure (primary, secondary, and tertiary) in the yolk proteins as the egg is cooked.
- level of structure that is NOT affected is:
– Primary - bonds NOT be broken during cooking:
– Peptide bonds
Part B: Proteins
4. Go to the following website and read about how to cook an egg: https://www.livescience.com/28575-science-of-cooking-perfect-egg.html
Based on the information in this article and what you have learned in this topic:
b) Do all the proteins in the egg yolk denature at the same temperature? Explain why or why not, based on your understanding of protein folding.
c) What factors other than heat do you think could denature a
protein?
- No
– Different proteins have a unique shape, made up of lots of different numbers and
types of bonds
– Each protein will denature at a different temperature, depending on how much
heat/ kinetic energy is needed to break those bonds to unfold the protein.
- – Chemical factors: pH change (presence of acids or bases) ,
presence of ions (e.g. salts, heavy metals), presence of organic molecules (e.g. ethanol as a solvent)
– Physical factors: Heat/movement/agitation: forms of kinetic energy (e.g. beating egg whites), UV radiation
