BIO 3350: BIOINFORMATICS
EXAM # 1 STUDY GUIDE QUESTIONS
TEXTBOOK READING: Zvelebil, pp. 3-23 and pp.25-43
ONLINE ACTIVITIES: 2 (Biological Information Flow) and 3 (Hemoglobin)
LECTURES: 1 (What is Bioinformatics?), 2 (DNA and the Genetic Code), 3 (Gene Structure and Control), 4 (Protein
Structure)
WHAT IS BIOINFORMATICS?
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What is informatics? What is bioinformatics?
Be able to compare and contrast related fields such as bioinformatics, medical informatics, clinical
genomics, and biomedical informatics.
What distinct subfields intersect in bioinformatics?
What is the over-all goal of bioinformatics? Give a concrete example of how bioinformatics advances
biological knowledge.
NUCLEIC ACID STRUCTURE AND THE CENTRAL DOGMA
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Discuss the importance of biological sequences and biological structures, in terms of biological function.
Discuss the similarities and differences between DNA and RNA.
What are the three parts of the nucleotide? Be able to distinguish between them given a chemical
structure.
What is the Watson-Crick base pairing? How does the base pairing occur chemically (i.e., what kinds of
bonds occur between base pairs)?
Be able to produce a complementary strand of a DNA sequence in the context of a double helix, and
indicate orientation.
Explain the meaning of the 5' and 3' orientation of nucleic acids. How does it arise, and why is it important
to indicate orientation?
What is the Central Dogma? What is transcription? What is translation?
Be able to transcribe a DNA sequence into an mRNA sequence, and then translate an mRNA sequence into
an amino acid sequence using the standard genetic code. Again, you should know how to indicate the
orientation of the resulting mRNA sequence as well as the orientation of the resulting amino acid
sequence.
Be able to identify the roles of the following molecules have in the processes involved in the Central
Dogma: RNA polymerase, sigma factor, transcription initiation factors, enhancers, and the ribosome.
Be able to distinguish between the coding/sense and the noncoding/antisense strands of DNA.
What is a reading frame? Be able to identify the six reading frames given a DNA sequence. What is an
open reading frame (ORF)?
How does identifying sufficiently long ORFs evidence that genes possibly exist in a given DNA sequence?
What three different types of RNA, and what are their roles?
What is the Genetic Code? Discuss some properties of the Genetic Code. What is special about the codon
for Methionine? What are "stop" codons? The Genetic Code is said to be “degenerate”—what does this
mean?
What is a gene? Compare and contrast eukaryotic and prokaryotic genes.
Explain the phenomenon of "overlapping genes".
17. What segments of the gene are involved in the regulation of transcription? Be able to explain how they
work to regulate transcription. Why is the regulation of transcription important in normal cell activity?
18. What is the function of the promoter region of a gene? Compare and contrast eukaryotic and prokaryotic
promoter regions. What is the Pribnow box? What is the TATA box?
19. What is meant by a consensus sequence?
20. What is splicing? What are introns and exons?
21. What is alternative splicing? Explain the implications of alternative splicing in creating diversity of protein
products, and also in finding new genes in a genome.
22. What are silent, missense, nonsense, and frameshift mutations? What effect does each have, in terms of
the resulting amino acid sequence? How can mutations cause biological malfunction or disease?
23. Be able to discuss Slide 21 of Lecture 2 (DNA and the Genetic Code).
PROTEIN STRUCTURE
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Be able to enumerate all 20 amino acids (spelled correctly), their three-letter codes, and their one-letter
codes.
Be familiar with the different functions of proteins in living systems.
What is the advantage of visually representing complex molecular structures in different ways?
Describe what primary, secondary, tertiary, and quaternary structures are.
Describe the chemical structure of amino acids. Which part remains constant among all amino acids, and
which part is different from one amino acid to another?
What are some dominant properties of amino acid side chains? Describe each characteristic, name
examples of amino acids for each one, and discuss how these characteristics affect protein folding.
Discuss how the properties of acidity, basicity, and polarity arise for some amino acids.
How does water interact with hydrophobic and hydrophilic molecules? How does water interact with
amino acid side chains, and how does this facilitate the folding of proteins?
Describe how amino acids are linked together to form protein chains.
What does the Ramachandran plot describe? How is it useful in describing protein structure? What are
some of the uses for Ramachandran plots?
What physical forces act on the amino acid chain to fold it into a compact structure? Explain the role of
hydrophobicity in inducing the spontaneous folding of protein chains.
What is hydrogen bonding? How does it arise? Explain the role of hydrogen bonding in stabilizing protein
folds.
"The stable folded state of a protein represents a state of low energy." Be able to expound on this
fundamental idea.
What is the protein folding problem? Be able to describe the need for the computational solution to the
protein folding problem.
What are the two major challenges to the computational solution to the protein folding problem?