DG Midterm #1 Spring 2021 From ULA Review

Exam 1 Review Sheet Fall 2020
Definitions:
● Liter: a metric unit of capacity

● Milliliter: one thousandth of a liter
● Microliter: one millionth of a liter
● Molar concentration: defined as the amount of a constituent divided by the volume of the
mixture (the Molarity = 2x? 4x? 10x?)
● DNA: (deoxyribonucleic acid), a self-replicating material which is present in nearly all
living organisms as the main constituent of chromosomes. It is the carrier of genetic
information
● mRNA: (messenger RNA) molecule in cells that carries codes from the DNA in the
nucleus to the sites of protein synthesis in the cytoplasm (the ribosomes)
● premRNA: a precursor mRNA, is a type of primary transcript that becomes a mRNA
● tRNA: (transfer ribonucleic acid) a type of RNA molecule that helps decode a mRNA
sequence into a protein. Function at specific sites in the ribosome during translation.
● Intron: a segment of a DNA or RNA molecule which does not code for proteins and
interrupts the sequence of genes.
● Exon: a segment of a DNA or RNA molecule containing information coding for a protein
or peptide sequence.
● rRNA: (Ribosomal RNA) is part of the ribosome, or protein builders, of the cell. rRNA are
responsible for reading the order of amino acids and linking amino acids together. They
do this through a highly complex sequence.
● Spliceosome: a large and complex molecular machine found primarily within the nucleus
of eukaryotic cells. Spliceosomes remove introns from a transcribed pre-mRNA.
● Ribosome: A sphere-shaped structure within the cytoplasm of a cell that is composed of
RNA and protein and is the site of protein synthesis. They exist in both eukaryotic and
prokaryotic cells. Ribosomes are responsible for translation, or the process our cells use
to make proteins.
● cDNA: (complementary DNA) is DNA synthesized from a single-stranded RNA. cDNA is
often used to clone eukaryotic genes in prokaryotes.
● Reverse transcription: The process of making a double stranded DNA molecule from a
single stranded RNA template through the enzyme
● Reverse transcriptase: A DNA polymerase enzyme that catalyzes the process of reverse
transcription.
● Protein: polymers of amino acids. They have a variety of functions in cells. Major
functions include acting as enzymes, receptors, transport molecules, regulatory proteins
for gene expression, and so on.
● DNA Polymerase: An enzyme assisting in DNA replication.
● RNA Polymerase: an enzyme that is responsible for making RNA from a DNA template.
● Polymerase Chain Reaction: (PCR) a method widely used in molecular biology to make
several copies of a specific DNA segment. A powerful technique used to isolate and
amplify specific regions of DNA.
● Annealing: The part of PCR after denaturing where the reaction is then cooled to allow
the two primers to base pair to the primer-binding sites.
● Denaturing: The first part of PCR where the double-stranded DNA containing the target
sequence (two strands) are separated by heating.
● Extension: The last part of PCR after annealing. After the temperature is raised, Taq
polymerase then synthesizes the first set of complementary strands in the reaction.
● Polymorphism: when two individuals have sequence differences at the same place in the
genome
● Insertion Deletion (indel): occurs when one or more nucleotide of DNA is present in one
individual and absent in another. Indels are the results of errors during the DNA
replication process.
● Single Nucleotide Polymorphism (SNP): A difference of one nucleotide. Many SNPs do
not change the protein sequence (like TTT and TTC which both code for phenylalanine).
● Transposable Elements (TE): A third type of variation is due to the insertion of mobile
pieces of DNA. TEs have a characteristic structure (large deletions/changes in the
sequence).
● BLAST:
○ One of the techniques used for bioinformatics
● Blast Hit:
● Multiple Sequence Alignment: a sequence alignment of three or more biological
sequences, generally protein, DNA, or RNA.
● Transformation: the process of introducing DNA into a cell. Very inefficient and only a
tiny percent of cells will contain the plasmid (less than 1 per million).
● Primers: a short nucleic acid sequence that provides a starting point for DNA synthesis
● Taq: (Thermus aquaticus) an enzyme that copies DNA. It is isolated from a heat-loving
bacteria that is naturally found in hot springs, so the enzyme doesn't break down at the
high temperatures necessary for copying DNA using a polymerase chain reaction.
● Negative control: is part of a well-designed scientific experiment. The negative control
group is a group in which no response is expected. It is the opposite of the positive
control, in which a known response is expected.
● Master mix: a premixed concentrated solution that has all of the components for a
real-time PCR reaction that are not sample-specific.
● Antibiotic selection: To recover only the cells that take up a plasmid, called
transformants, antibiotic selection is used. The plasmid contains a gene for resistance to
antibiotics in the growth medium. Transformants will divide while all other cells will die.
● Plasmid: a small, circular, double-stranded DNA molecule that is distinct from a cell's
chromosomal DNA. Naturally exist in bacterial cells, and they also occur in some
eukaryotes. H
● Bacterial transformation: The piece of DNA or gene of interest is cut from its original
DNA source using a restriction enzyme and then pasted into the plasmid by ligation. The
plasmid containing the foreign DNA is now ready to be inserted into bacteria.
● Constitutive promoter: An unregulated promoter that allows for continual transcription of
its associated gene. If a gene is preceded by a promoter region that always promotes
transcription, it is said that the gene has a constitutive promoter.
● Conditional promoter: If the gene is transcribed conditionally, it may refer to proteins
having to bind to the promoter region so that transcription can take place.
● Gene expression: the process by which information from a gene is used in the synthesis
of a functional gene product. These products are often proteins.
● Synonymous mutations: SNPs that do not change the protein sequence (like TTT and
TTC which both code for phenylalanine).
● BLAST: Bioinformatics. Is an algorithm and program for comparing primary biological
sequence information, such as the amino-acid sequences of proteins or the nucleotides
of DNA and/or RNA sequences.
● Site-directed Mutagenesis: technique used to introduce a mutation (dpGreen NortfT
example), is a method to create specific, targeted changes in double stranded plasmid
DNA.
Kahoot: https://create.kahoot.it/details/c98ecc6e-d658-4198-a45f-d129aa7859a0
You should be able to:

1. Calculate the part of the stock solution and water needed to perform a
dilution using c1v1=c2v2.
c1= 2x, v1= volume of MyTaq to use, c2= 1x (final concentration of MyTaq), v2= 15ul
(total volume)
(1x/2x) * 15ul = volume 2x MyTaq * v1
v1= 7.5 ul
2. Diagram and understand the process of genetic information transfer (gene

expression).
https://www.youtube.com/watch?v=2zAGAmTkZNY
3. Understand differences between genomic DNA and cDNA (mRNA), i.e

intron/exon structure.
4. Describe the steps involved in DNA amplification using PCR.
5. Understand the function of PCR primers.

6. Use BLAST to search a DNA database.
7. Understand and interpret the BLAST output (graph, table, alignment).
8. Use a multiple sequence alignment program and interpret the output.

9. Discuss the different types of DNA polymorphisms and possible effects on
gene function.
DNA polymorphisms are the different DNA sequences among individuals, groups, or
populations. Polymorphism at the DNA level includes a wide range of variations from
single base pair change, many base pairs, and repeated sequences.
10. Design a PCR experiment and interpret the results.
11. Discuss the different types of DNA polymorphisms and possible effects on gene
function.
12. Describe significant features of Transposable elements - TEs (autonomous and

non-autonomous), TIRs.
13. Design a PCR experiment and interpret the results.
14. Recognize and explain the use and need for positive and negative controls.
15. Design a PCR reaction table.
Example: Given primers and materials design an experiment?

Isolate cDNA from gDNA. Synthesize cDNA from reverse transcriptase
11. Design a PCR reaction table.
12. Recognize and explain the use and need for positive and negative controls.
The negative control is used to show that any positive effects of the new treatment
aren't the result of the placebo effect. The positive control is used to detect any
problems with the experiment and to benchmark results against another medication.

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Exam 1 Review Sheet Fall 2020

● Liter: a metric unit of capacity

You should be able to:

(1x/2x) * 15ul = volume 2x MyTaq * v1

2. Diagram and understand the process of genetic information transfer (gene

3. Understand differences between genomic DNA and cDNA (mRNA), i.e

5. Understand the function of PCR primers.

8. Use a multiple sequence alignment program and interpret the output.

10. Design a PCR experiment and interpret the results.

12. Describe significant features of Transposable elements - TEs (autonomous and

13. Design a PCR experiment and interpret the results.

15. Design a PCR reaction table.

Example: Given primers and materials design an experiment?

11. Design a PCR reaction table.

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