Comprehension Assignment 1 Flashcards
Define molecular biology
The study of essential cellular macromolecules, including DNA, RNA, and proteins, and the biological
pathways that link their biosynthesis.
Or
The study of biological phenomena at the molecular level, in particular, the study of: the molecular
structure of DNA and the information it encodes and the biochemical basis of gene expression and
regulation
Fill in the blank: The process by which individuals best adapted to exploit the prevailing resources are the most
likely to survive and reproduce is called_______
natural selection
What are Mendel’s 3 laws (1 of these is not always considered a law)? Describe in your own words what each
means.
Law of Dominance: One allele masks (dominant) the effect of another (recessive)
Law of segregation: Allele Pairs Segregate during Gamete Formation
Law of Independent Assortment: Different Genes Assort Independently during Gamete Formation
Sodium hydroxide degrades both proteins and nucleic acids, while phenol denatures proteins but not nucleic
acids. In the transformation experiments performed by Griffith with Streptococcus pneumoniae, what result would
be expected if an extract of S-strain bacteria was treated with phenol and then was injected into mice along with
R-strain bacteria?
The mice would die as the S strain bacteria DNA would be able to transform the R-strain bacteria
___ is the hereditary material: each ______ is a single molecule
of DNA and ________ are sequences of DNA
DNA, Chromosome, Genes
Fill in the blanks: Nucleic acids are composed of repeating units called _________. Each of these
units contain three components _____, ____, ______. Information is encoded in the sequence of these components
Nucleic acids are composed of repeating units called _Nucleotides_. Each of these
units contain three components __Pentose Sugar___, _Phosphate_, Nitrogenous Base. Information
is encoded in the sequence of these components
Describe an interaction (not a bond) that stabilizes the secondary structure of DNA:
Hydrophobic interactions, Base Stacking, Van der Waals forces
Provide at least 4 descriptors of the DNA helix proposed by Watson and Crick (ex. right-handed)
DNA is a double-helix
the two strands run antiparallel
sugar phosphate backbones
purines pair with pyrimidines inside / complementary base pairing
major/minor groves
B-form
What is Hoogsteen base pairing and where might you find it?
Hoogsteen base pair is a variation of base pairing in nucleic acids that can result in the formation of triplex DNA within long sequences containing only pyrimidines or only purines in a given strand
T/F:
a. Inverted repeats can form hairpins that are important for slowing or preventing protein synthesis.
b. GC vs CG base pairing can be easily distinguished by DNA binding proteins in the minor groove.
c. DNA that is overwound would be best described as positively supercoiled.
d. DNA in humans is normally negatively supercoiled.
a. Inverted repeats can form hairpins that are important for slowing or preventing protein synthesis. True
b. GC vs CG base pairing can be easily distinguished by DNA binding proteins in the minor groove. False
c. DNA that is overwound would be best described as positively supercoiled. True
d. DNA in humans is normally negatively supercoiled. True
Which term below best describes the unusual secondary structure that the following sequence may exhibit?
5’-TACGTACGTACGTACG-3’
3’-ATGCATGCATGCATGC-5’
slipped structure
An intermediate in production of a DNA nucleotides is ribose 5-phosphate. What still needs to be changed to make this a DNA nucleotide? Indicate the location(s) that must change
Remove the 1’ and 2’ hydroxyl and add the base to the 1’ carbon
What does melting point refer to with regard to double stranded DNA and how does it relate to hybridization?
Melting point is the temperature that half of the DNA is denatured. DNA can be denatured to single stranded DNA. Hybridization is the complementary base pairing of denatured strands from two different
sources.
What is the appropriate complementary DNA sequence to the following: 5’-GTACGGTCAAT-3’
5’ATTGACCGTAC3’
What is the defining feature that differentiates DNA and RNA?
Type of sugar in nucleotides: Deoxyribose vs Ribose
uracil: pyrimidine or a purine?
pyrimidine
Helical forms adopted by double-stranded RNA typically are ___ form, unlike DNA which is ___form.
Helical forms adopted by double-stranded RNA typically are _A___ form, unlike DNA which is _B____form.
Why is RNA 3D structure important?
Functions! Example: tRNA, rRNA, riboswitches
What feature of RNA is directly or indirectly responsible for the unique structural properties of RNA?
2’ hydroxyl group on ribose sugar
Besides mRNA, name 4 other types of functional RNAs and describe their function.
rRNA: essential component of the ribosome
tRNA: charged with a specific amino acid. tRNA delivers to the ribosome interaction of anticodon with codon
snRNAs: pre-mRNA splicing, preparing mRNA for translation
snoRNA: rRNA processing
What is a RNP? Provide 2 examples, one that has a component that acts as a ribozyme and the other without
Ribonucleoprotein – has RNA and Protein components. Examples include ribozymes: RNaseP, Ribosome, Spliceosome and not a ribozyme: Telomerase and SRP
What is meant by the tertiary structure of RNA? Provide 2 examples of RNA tertiary structures.
Tertiary structure of RNA is the 3-D structure that results from interactions between preformed secondary structural domains. Five examples of tertiary structure include pseudoknots, A-minor motifs, Tetraloops, ribose zippers, kink-turns
Can a genome be made of RNA? If so, provide an example. If not, why?
Yes, a genome can be made of RNA – eukaryotic RNA viruses, retroviruses, viroids, virusoids, satellite RNAs
Which is more stable DNA or RNA? Why?
DNA is more stable. RNA nucleotides may come apart more readily due to the 2’ hydroxyl group
Why is protein folding important?
Structure determines function
How do cells make sure that proteins fold correctly?
Some proteins fold correctly spontaneously, most require molecular chaperone proteins to fold correctly
Describe the 4 levels of structure for a protein. What are the key features of each? (this should be a comprehensive answer)
Primary structure – Amino acid sequence of polypeptide held together by peptide bonds
Secondary structure – alpha helix, beta conformation, and turns formed through hydrogen bonding of the backbone.
Tertiary structure – Multiple weak interactions and possibly disulfide bridges between R groups that produce the 3D structure of a single polypeptide.
Quaternary structure – Multiple polypeptides held together.
Infectious proteins that cause misfolding of endogenous proteins are called __
prions
You have isolated and characterized a novel protein. The protein catalyzes the breakdown of a large substrate.
The protein has two binding sites, one is small, possibly a regulatory molecule binding site; and the other one is large, most likely the site that the large substrate binds. What do these findings suggest to you about the function
of this protein?
The protein is an enzyme that is controlled by an allosteric effector
_____ different genetically-encoded amino acids are found in the proteins of cells; they are distinguished
by____
_____22________ different genetically-encoded amino acids are found in the proteins of cells; they are distinguished
by______the R-group
For the following 20-residue sequence in a protein, list five amino acid residues that are likely to be buried in the
protein, inaccessible to water. Pick five that are good candidates for surface residues.
ELLQERTLVPAGVSITFKLD
Deeply Buried: Leucine (L2, 3, 8, 19), Phenylalanine (F17), Isolucine (I15), Valine (V9,13)
Possibly: Glycine (G), Alanine (A), Proline (P),
Surface: Asparagine (D20), Lysine (K18), Threonine (T7, 16), Serine (S14), Arganine (R6), Glutamine (E1,5), Glutamine (Q4)
