Study guide for 3rd Test BSC 2010 L
1. Compare and contrast DNA and RNA.
DNA
Localization Nucleus
Bases and Sugar DNA is a long polymer
with a deoxyribose and
phosphate backbone
and four different bases:
A, G, C and T.
Stands for DeoxyriboNucleicAcid
Fuction Medium of long-term
storage and
transmission of genetic
information
Pairing of bases A-T and G-C
Stability Deoxyribose sugar in DNA
is less reactive because of
C-H bonds. Stable in
alkaline conditions. DNA
has smaller grooves where
the damaging enzyme can
attach which makes it
harder for the enzyme to
attack DNA.
Structure Typically a double-
stranded molecule
with a long chain of
nucleotides
Unique The helix geometry of DNA
is of BForm. DNA is
completely protected by
the body i.e. the body
destroys enzymes that
cleave DNA. DNA can be
damaged by exposure to
Ultraviolet rays
RNA
Cytoplasm & Nucleus
RNA is a polymer with a
ribose and phosphate
backbone and four
different bases: A,G, C
and U.
RiboNucleicAcid
The main job of RNA is to
transfer the genetic code
need for the creation of
proteins from the nucleus
to the ribosome. This
process prevents the DNA
from having to leave the
nucleus, so it stays safe.
Without RNA, proteins
could never be made
A-U and G-C
Ribose sugar is more
reactive because of C-OH
(hydroxyl) bonds. Not
stable in alkaline
conditions. RNA on the
other hand has larger
grooves which makes it
easier to be attacked by
enzymes.
A single-stranded molecule
in most
of its biological roles and
has shorter chain of
nucleotides
The helix geometry of RNA
is of A-Form. RNA strands
are continually made,
broken down and reused.
RNA is more resistant to
damage by Ultra-violet
rays.
 2. What are the characteristics of DNA? (i.e. semi-conservative, bidirectional,
chemical bonds that keep the molecule together)

DNA Characteristics:

-Semiconservative Replication
-double helix
-five-carbon sugar deoxyribose
-a phosphate group
-hold genetic information
-antiparallel
-held by hydrogen bonds.

3. What are the characteristics of RNA?

-single stranded
-contain ribose
-contain uricil...
-unlike DNA which contains thymine instead

4. How many types of RNA are there? What are their functions?

-Ribosomal RNA (rRNA): Is a RNA that forms part of ribosomes, which provide the
site where translation occurs
-Transfer RNA (tRNA): An RNA that carries amino acids and is used to translate
mRNA into polypeptides.
-Messenger RNA (mRNA): RNA that contains the information to specify a polypeptide
with a particular amino acid sequence.

mRNA - carries the message from the DNA

tRNA - carries the amino acid to help synthesize the protein
rRNA - makes up the ribosomes where the protein synthesis occurs

5. What is the central dogma in molecular biology?

The central dogma of molecular biology states that biological information flows in
only one direction, from DNA to RNA to proteins.
(transcription) (translation)
DNA ------------ RNA ----------- Proteins

6. What is the difference between protein synthesis and gene expression?

Protein synthesis:
The process by which amino acids are linearly arranged into proteins through the
involvement of ribosomal RNA, transfer RNA, messenger RNA, and various enzymes.

Gene Expression:
The appearance in a phenotype of a characteristic or effect attributed to a particular
gene.
The process by which possession of a gene leads to the appearance in the phenotype
of the corresponding character.

7. What is the relationship between codon, anticodon and aminoacid?

Anticodon: A three- nucleotide sequence in tRNA that is complementary to a codon in
mRNA.
Amino acid: The building blocks of proteins. Amino acids have a common structure in
which a carbon atom, called the a-carbon, is linked to an amino group (NH2) and a
carbosyl group (COOH). The a-carbon also is linked to a hydrogen atom and a particular
side chain.
Codon: A sequence of 3 nucleotide bases that specifies a particular amino acid or a stop
codon; codons function during translation.

8. Compare and contrast genotype vs phenotype

Genotype: The genetic composition of a individual.

Phenotype: The characteristics of an organism that are the results of the expression
of its genes.

9. What are restriction enzymes? How are they used in molecular biology?

Restriction enzyme: AN enzyme that recognizes particular DNA sequences and

cleaves the DNA backbone at two sites.

10. What is the basis of gel electrophoresis?

Gel electrophoresis is a method for separation and analysis of macromolecules (DNA,

RNA and proteins) and their fragments, based on their size and charge.

11. What is the basis of PCR? How does it work?

The polymerase chain reaction (PCR) is a technology in molecular biology used to

amplify a single copy or a few copies of a piece of DNA across several orders of
magnitude, generating thousands to millions of copies of a particular DNA sequence.

12. Be able to describe the setup for agarose gel electrophoresis.

After the gel has solidified, the comb is removed, using care not to rip the bottom of
the wells. The gel, still in its plastic tray, is inserted horizontally into the
electrophoresis chamber and just covered with buffer. Samples containing DNA
mixed with loading buffer are then pipeted into the sample wells, the lid and power
leads are placed on the apparatus, and a current is applied. You can confirm that
current is flowing by observing bubbles coming off the electrodes. DNA will migrate
towards the positive electrode, which is usually colored red.

13. What is the purpose of restriction enzyme digestion previous to gel

electrophoresis?
Restriction enzymes are enzymes isolated from bacteria that recognize specific sequences in
DNA and then cut the DNA to produce fragments, called restriction fragments. Restriction
enzymes play a very important role in the construction of recombinant DNA molecules, as is
done in gene cloning experiments. Another application of restriction enzymes is to map the
locations of restriction sites in DNA.
 14. What is the basis of STR analysis?

Short tandem repeat analysis (STR) is a molecular biology method used to compare
specific loci on DNA from two or more samples. A locus (plural loci) is the specific
location of a gene, DNA sequence, or position on a chromosome.

15. What are operons? What types of operons are there?

Operon: An arrangement of two or more genes in bacteria that are under the
transcriptional control of a single promoter. Lac operon, trp operon

16. What is meant by inducible operon. Describe using the Lac Operon.

Inducible operon: In this type of operon, the presence of a small effector molecule
causes transcription to occur.

The lac operon (lactose operon) is an operon required for the transport and
metabolism of lactose in Escherichia coli and some other enteric bacteria. It has
three adjacent structural genes, lacZ, lacY, and lacA. The genes encode -
galactosidase, lactose permease, and galactoside O-acetyltransferase, respectively.

17. What is transcription? Localization in prokaryotic and eukaryotic.

Transcription: The use of a gene sequence to make a copy of RNA.

=Transcription is the first step of gene expression, in which a particular segment of
DNA is copied into RNA (mRNA, tRNA or rRNA) by the enzyme RNA polymerase. Both
RNA and DNA are nucleic acids, which use base pairs of nucleotides as a
complementary language.
It takes place in the nucleus of a eukaryotic cell and it takes place in the cytoplasm
of an prokaryotic cell

18. What is translation? Localization in prokaryotic and eukaryotic.

Translation: The process of synthesizing a specific polypeptide on a ribosome. Occurs

in the cytoplasm for eukaryotes and prokaryotes.

In molecular biology and genetics, translation is the process in which cellular

ribosomes create proteins. In translation, messenger RNA (mRNA)produced by
transcription from DNAis decoded by a ribosome to produce a specific amino acid
chain, or polypeptide.

19. What are the base pairing rules for DNA? For RNA?

DNA: A-T and C-G RNA: A-U and C-G

20. What is involved in making recombinant DNA?

Plasmids are used as vectors in producing recombinant DNA as explained below. The
required gene is cut from a DNA molecule using a restriction enzyme. A bacterial
plasmid is isolated and cut with the same restriction enzyme.
 21. What are vectors? What are examples of vectors used in biotechnology?

Vector: A type of DNA that acts as a carrier of DNA segment that is to be cloned.
Examples: plasmid vectors, viral vectors, cosmids, and artificial chromosomes.

22. What are plasmids? Whats their importance?

Plasmids: A small circular piece of DNA found naturally in many strains of bacteria
and occasionally in eukaryotic cells; can be used as a vector in cloning experiments.

Importance:
Plasmids are small pieces of circular DNA that are often found as part of the genetic
information in bacteria and prokaryotes. They often contain special genes that
convey special abilities, e.g. a resistance to certain antibiotics.
Plasmids are very important in biotechnology for research. Researchers can alter
plasmids and observe the immediate effects they have on the prokaryote as well on
its offspring. Researchers can add or delete genes, and observe their effects. They
can also use plasmids to grow certain organic compounds, such as synthetic insulin.

23. What are these enzymes used for: restriction enzymes, DNA ligase, reverse
transcriptase

Restriction enzymes: Also known as restriction endonucleases, are enzymes that cut
a DNA molecule at a particular place. They are essential tools for recombinant DNA
technology. The enzyme "scans" a DNA molecule, looking for a particular sequence,
usually of four to six nucleotides.

DNA Ligase: DNA ligase is a specific type of enzyme, a ligase, (EC 6.5.1.1) that
facilitates the joining of DNA strands together by catalyzing the formation of a
phosphodiester bond.

Reverse transcriptase (RT): is an enzyme used to generate complementary DNA

(cDNA) from an RNA template, a process termed reverse transcription. It is mainly
associated with retroviruses.

24. What are Punnett squares? What do they show?

Punnett Squares: A common method for predicting the outcome of simple genetic
crosses. The diagram is used by biologists to determine the probability of an
offspring having a particular genotype. Shows the possible phenotypes of crossing
two individuals.

25. Know how to solve Punnet squares.

26. What is a dominant trait?

Dominant: A term that describes the displayed trait in a heterozygote

27. What is a recessive trait?

Recessive: A term that describes a trait that is masked by the presence of a

dominant trait in a heterozygote.
 28. What is the nomenclature to represent dominant and recessive genes?
Lower case for recessive and Capitalized for dominant.

29. What is a test cross? What is its significance?

Testcross: A cross to determine if an individual with a dominant phenotype is a

homozygote or heterozygote. Also, a cross to determine if two different genes are
linked.

30. What is an allele?

Allele: A variant form of a gene. An allele is a viable DNA (deoxyribonucleic acid)

coding that occupies a given locus (position) on a chromosome. Usually alleles are
sequences that code for a gene, but sometimes the term is used to refer to a non-
gene sequence.

31. How do homozygous and heterozygous alleles differ?

Blood type is determined by three different alleles: A, B, and O. The O allele is

recessive and the A and B alleles are co-dominant. A homozygous individual will
have one of the following genotypes, AA, BB, or OO. A heterozygous individual will
have an AO, BO, or AB genotype.

32. What is codominance?

Codominance: Is the phenomenon in which a single individual expresses two alleles.

33. What is incomplete dominance?

Incomplete dominance: The phenomenon in which a heterozygote that carries two

different alleles exhibits a phenotype that is intermediate between the corresponding
homozygous individual

34. Know how to calculate phenotypic and genotypic ratios.

DNA and PCR-Gel Electrophoresis lab

What are the general steps used to extract DNA from any biological sample (i.e.
Halobacterium, strawberries, cheek cells)? Be able to explain the steps and
principles behind these simple extractions.
Explain the significance of:
1- Using different temperatures for PCR
2- using an electrolyte solution for electrophoresis,
3- the correct orientation of the gel in the electrophoresis box
4- the addition of marker dye to the sample
5- adding a marker lane
6- staining and washing excess dye from gels
7- be able to interpret banding patterns in electrophoresis

Transformation Lab
What are the basic steps in any transformation experiment? What were the
reagents/bacteria/plasmids used for the transformation experiment and what was
the purpose of using them? What were the characteristics of the plasmid used in this
lab: pGLO? What kind of genetic markers did it have? What conditions were used to
make the cells likely to take up plasmids? How can you determine whether the
plasmids had in fact entered the bacterial cells and that transformation had
occurred?
Be able to describe the organization of operons in bacteria. What are the regions of
a typical operon and their function? How does the operon look when induced? When
repressed? Practice using diagrams to represent regulatory, operator and structural
genes regions in operons
Know how both, the Lac and arabinose operon work. .
What observation was used in this lab to establish whether the ara C regulatory
protein was active?

Mendelian Genetics Lab

Be able to solve Punnett square for simple monohybrid crosses. Be able to resolve
crosses between homozygous parents, homozygous vs heterozygous parents, or
both heterozygous parents.
Differentiate between genotypic and phenotypic ratios for monohybrid crosses and
dihybrid crosses. How do phenotypic ratios for codominance and incomplete
dominance compare to the ratios predicted by Mendels Laws.