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STUDY QUESTIONS:

1. Differentiate DNA from RNA. How do they differ in terms of their monosaccharide (sugar)
components and nitrogen bases?
DIFFERENCE BETWEEN DNA FROM RNA?
*DNA contains the sugar deoxyribose, while RNA contains the sugar ribose. The
only difference between ribose and deoxyribose is that ribose has one more -OH group than
deoxyribose, which has -H attached to the second (2') carbon in the ring. DNA is a double-stranded
molecule, while RNA is a single-stranded molecule.
* Composition of Bases and Sugars -DNA= deoxyribose sugar phosphate backbone adenine, guanine,
cytosine, thymine bases. -RNA= ribose sugar phosphate backbone, adenine, guanine, cytosine, uracil
bases
* Ribose and Deoxyribose. The 5-carbon sugars ribose and deoxyribose are important components of
nucleotides, and are found in RNA and DNA, respectively.
*DNA NITROGEN BASES: The four nitrogen bases found in DNA are adenine, cytosine, guanine, and
thymine. Each of these bases are often abbreviated a single letter: A (adenine), C (cytosine), G (guanine),
T (thymine). The bases come in two categories: thymine and cytosine are pyrimidines, while adenine
and guanine are purines ().
*RNA NITROGEN BASES: The nitrogenous bases in DNA are adenine (A), guanine (G), thymine (T), and
cytosine (C). The nitrogenous bases in RNA are the same, with one exception: adenine (A), guanine (G),
uracil (U), and cytosine (C).

2. Define the following: a) chromosomes; b) genes; c) histones; d) nucleosomes


*CHROMOSOMES A chromosome is a string of DNA wrapped around associated proteins that give the
connected nucleic acid bases a structure. A chromosome is a strand of DNA that is encoded with genes.
In most cells, humans have 22 pairs of these chromosomes plus the two sex chromosomes (XX in
females and XY in males) for a total of 46. The word chromosome was originally coined in German from
the Greek words khroma, meaning color, and soma meaning body
*GENES The basic biological unit of heredity. A segment of deoxyribonucleic acid (DNA) needed to
contribute to a function. a gene is defined as "a DNA segment that contributes to phenotype/function.
*HISTONES The proteins in the core particle and linker proteins are called histones. any of a group of
five small basic proteins, occurring in the nucleus of eukaryotic cells, that organize DNA strands into
nucleosomes by forming molecular complexes around which the DNA winds. Their function is to package
DNA into structural units called nucleosomes. Histones are the main proteins in chromatin. Chromatin is
a combination of DNA and protein which makes up the contents of a cell nucleus. Because DNA wraps
around histones, they also play a role in gene regulation.
*NUCLEOSOMES A nucleosome is a section of DNA that is wrapped around a core of proteins.
Inside the nucleus, DNA forms a complex with proteins called chromatin, which allows the DNA
to be condensed into a smaller volume. ... The nucleosome is the fundamental subunit of
chromatin.

3. Name all the ribonucleosides and deoxyribonucleosides.


* The ribonucleosides are uridine, cytidine, adenosine, and guanosine, and the deoxyribonucleosides
are thymidine (or deoxythymidine), deoxycytidine, deoxyadenosine, and deoxyguanosine.
* The four common deoxyribonucleotides are categorized as the purine (deoxyadenosine, dA, and
deoxyguanosine, dG) or pyrimidine (deoxythymidine, dT, and deoxycytosine, dC) nucleotides.
4. Name all the ribonucleotides and deoxynucleotides. Write their abbreviations. How are nucleotides
formed? How are the nucleotides in DNA joined or linked together?

How are nucleotides formed?


- A nucleotide is formed from a carbohydrate residue connected to a heterocyclic base by a β-D-
glycosidic bond and to a phosphate group at C-5' (compounds containing the phosphate group at C-3'
are also known). The molecules derived from nucleotides by removing the phosphate group are the
nucleosides.
How are the nucleotides in DNA joined or linked together?
Nucleotides are joined together by covalent bonds between the phosphate group of one nucleotide and
the third carbon atom of the pentose sugar in the next nucleotide. This produces an alternating
backbone of sugar - phosphate - sugar - phosphate all along the polynucleotide chain. When nucleotides
are incorporated into DNA, adjacent nucleotides are linked by a phosphodiester bond: a covalent bond
is formed between the 5' phosphate group of one nucleotide and the 3'-OH group of another (see
below). In this manner, each strand of DNA has a “backbone” of phosphate-sugar-phosphate-sugar-
phosphate.

5. Give the composition of a polynucleotide. What does its primary structure indicate? What is the
significance of the base sequence? What is the 5' end? 3' end? How is a polynucleotide named?
* A polynucleotide strand is made of a sugar-phosphate backbone (like the string in a strand of flags)
and a variety of bases (like the flags), one per nucleotide. A polynucleotide is made when a polymerase
enzyme joins nucleotides together. The strand has two different ends, which we call 3' and 5'.
* The string is like a backbone that holds the flags together. A polynucleotide has a backbone, too. This
polynucleotide backbone is made of the sugar and phosphate parts of nucleotides, so we call it a sugar-
phosphate backbone. a polynucleotide strand has a sequence of bases called nitrogenous bases.
Instead of colors, the bases have different chemical names. In DNA, the bases are adenine, guanine,
cytosine, and thymine. This means that a polynucleotide's sequence might look like
ACGTCGTATATCGTAGCTGTCAGTCGAGTAC...RNA's polynucleotides are a little different; instead of
thymine, they have uracil. They also have a different type of sugar in their backbone.
*Base sequence are important because it is the order of NUCLEOTIDES in a NUCLEIC ACID MOLECULE.
The nucleotide sequence within a gene determines the AMINO ACID sequence of a PROTEIN product or
the RIBONUCLEOTIDE sequence of an RNA product. Also, The sequence of bases in the DNA determines
the sequence of amino acids in the protein, which determine how the protein can fold and what its
function will be.
* The 5' end? 3' end, it is the One end of the chain carries a free phosphate group attached to the 5'-
carbon atom; this is called the 5' end of the molecule. The other end has a free hydroxyl (-OH) group at
the 3'-carbon and is called the 3' end of the molecule. Each DNA strand has two ends. The 5' end of
the DNA is the one with the terminal phosphate group on the 5' carbon of the deoxyribose; the 3' end is
the one with a terminal hydroxyl (OH) group on the deoxyribose of the 3' carbon of the deoxyribose.
* The name of this polynucleotide comes from the sugar ribonucleic acid, abbreviated to the three
letters RNA. Adenine, guanine, cytosine and uracil are the four nitrogenous bases always found in RNA.
There are several different forms of RNA, each playing a slightly different role in the cell.

6. Describe the DNA model proposed by Watson and Crick.

* The Watson-Crick model of the DNA molecule is a coiled ladder structure forming a double helix. The
ladder is composed of a phosphate group, a sugar group and nitrogen bases. The sugar and phosphate
groups bond together to form the side rails while 2 nitrogen groups bind together to form the rung.
Each nitrogen group is bonded to one of the sugar-phosphate groups and then to one nitrogen group.

7. What complementary base pairs are hydrogen bonded together?

* Each nucleotide base can hydrogen-bond with a specific partner base in a process known as
complementary base pairing: Cytosine forms three hydrogen bonds with guanine, and adenine forms
two hydrogen bonds with thymine. These hydrogen-bonded nitrogenous bases are often referred to as
base pairs. The nitrogen bases are held together by hydrogen bonds: adenine and thymine form two
hydrogen bonds; cytosine and guanine form three hydrogen bonds. Two hydrogen bonds form between
adenine and thymine or adenine and uracil. Complementary pairs always involve one purine and one
pyrimidine base

8. What are the three steps of protein synthesis? describe each step.
*The 3 steps of protein synthesis includes three steps: initiation, elongation, and termination. After the
mRNA is processed, it carries the instructions to a ribosome in the cytoplasm. Translation occurs at the
ribosome, which consists of rRNA and proteins.
* Initiation is the beginning of transcription. It occurs when the enzyme RNA polymerase binds to a
region of a gene called the promoter. This signals the DNA to unwind so the enzyme can “read” the
bases in one of the DNA strands. The enzyme is ready to make a strand of mRNA with a complementary
sequence of bases.
* Elongation is the addition of nucleotides to the mRNA strand.
* Termination is the ending of transcription. The mRNA strand is complete, and it detaches from DNA.

9. In what ways are replication and transcription similar? In what ways are they different?

Some similarities between transcription and DNA replication is that they both use DNA and RNA, they
both occur in the nucleus, and they are both catalyzed by a polymerase enzyme. Transcription is the first
step in protein synthesis. It occurs in the nucleus when the enzyme RNA polymerase reads DNA to
create a copy called messenger RNA (mRNA). DNA replication is the process of creating new strands of
DNA for cell division. DNA replication also occurs in the nucleus. During DNA replication, the DNA unzips
and reveals the nucleotides. An RNA primer is created for DNA polymerase to hook onto so it can start
copying the DNA. The end product of DNA replication is two identical daughter molecules of DNA,
whereas the end product of transcription is one molecule of mRNA.

10. Differentiate the three types of RNA.


* In both prokaryotes and eukaryotes, there are three main types of RNA – messenger RNA (mRNA),
ribosomal RNA (rRNA), and transfer RNA (tRNA).
* mRNA, or messenger RNA, is the link between a gene and a protein. The gene is transcribed by RNA
polymerase, and the resulting mRNA travels to the cytoplasm, where it is translated by ribosomes into a
protein with the help of tRNA. This form of RNA is extensively altered post-transcriptionally with
modifications such as methylguanosine caps and polyadenosine tails. Eukaryotic mRNA frequently includes
introns which must be spliced out of the message to form the mature mRNA molecule.
* rRNA, or ribosomal RNA, is a major component of ribosomes. After transcription, these RNA molecules
travel to the cytoplasm and join with other rRNAs and many proteins to form a ribosome. rRNA is used both
for structural and functional purposes. Many reactions in the translational process are catalyzed by key
portions of certain rRNAs in the ribosome.
* tRNA, or transfer RNA, is the "decoder" of the mRNA message during protein translation. After
transcription, tRNA is extensively modified to include nonstandard bases such as pseudouridine, inosine, and
methylguanosine. By themselves, ribosomes cannot form a protein when the mRNA makes contact. The
anticodon, a string of three key bases on the tRNA, match with three bases on the mRNA message called the
codon. That is only the first function of tRNA, as each molecule also carries with it an amino acid which
matches the mRNA codon. The ribosome functions to polymerize the amino acids linked to the tRNA into a
functional protein.

11. For the given DNA segment 3' - GGTATACGG - 5', what is the sequence of the mRNA molecule?

5' - CCA UAU GCC - 3'

What is the sequence of the informational strand of the DNA molecule?

Deoxythymidine monophosphate (dTMP)

12. What is a codon? anticodon? For a given mRNA molecule, how are the codons written? What
determines the order of amino acids in a protein molecule?
* A codon is a sequence of three DNA or RNA nucleotides that corresponds with a specific amino acid
or stop signal during protein synthesis.

* anticodon is a trinucleotide sequence complementary to that of a corresponding codon in a


messenger RNA (mRNA) sequence. An anticodon is found at one end of a transfer RNA (tRNA)
molecule.

*mRNA codons are written from 5' to 3' , and they specify the order of amino acids in a protein from
N-terminus (methionine) to C-terminus.
*The actual order of the amino acids in the protein is called its primary structure and is determined by
DNA.
13. Refer to slide 44. Fill in the base, codon, anticodon, or amino acid needed to complete the following
table that relates the sequences of DNA, mRNA, tRNA and the resulting polypeptide. Use the GENETIC
CODE presented on Video # 4 in order to determine the amino acids in the polypeptide. This is how you
should use it. Start with the 1st letter at the center. Continue with the 2nd letter in the middle, and end
up with the 3rd letter situated on the edge. Then find the amino acid that corresponds to the mRNA
codon.

DNA 5’ end 3’ end


informational
strand
DNA template 3’end TTG ATA GGT TGC TTC TAC 5’ end
strand
mRNA codons 5’ end 3’ end
tRNA anticodons
Polypeptide

14. Differentiate the three types of mutation.


*BASE SUBSITUTIONS Single base substitutions are called point mutations, recall the point mutation
GluVal which causes sickle-cell disease. Point mutations are the most common type of mutation and
there are two types WHICH ARE TRANSITION AND TRANSVERSION.
*DELETIONS A deletion, resulting in a frameshift, results when one or more base pairs are lost from
the DNA (see Figure above). If one or two bases are deleted the translational frame is altered resulting in
a garbled message and nonfunctional product. A deletion of three or more bases leave the reading
frame intact. A deletion of one or more codons results in a protein missing one or more amino acids.
This may be deleterious or not.
*INSERTIONS The insertion of additional base pairs may lead to frameshifts depending on whether or
not multiples of three base pairs are inserted. Combinations of insertions and deletions leading to a
variety of outcomes are also possible.

15. Why is sickle cell anemia fatal?

Sickle cells that block blood flow to organs deprive the affected organs of blood and oxygen. In sickle
cell anemia, blood is also chronically low in oxygen. This lack of oxygen-rich blood can damage nerves
and organs, including your kidneys, liver and spleen, and can be fatal.

16. Other than cystic fibrosis and galactosemia, give examples of genetic diseases.
* Phenylketonuria (PKU) is an inborn error of metabolism that results in decreased metabolism of the
amino acid phenylalanine. 
* Huntington's disease is a progressive brain disorder caused by a single defective gene on chromosome
4 — one of the 23 human chromosomes that carry a person's entire genetic code. 
* Marfan syndrome (MFS) is a genetic disorder of the connective tissue. The degree to which people are
affected varies. People with Marfan tend to be tall and thin, with long arms, legs, fingers and toes.
17. What is recombinant DNA or rDNA? What are the four elements needed to amplify DNA by
polymerase chain reaction or PCR?

* Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of


genetic recombination (such as molecular cloning) to bring together genetic material from multiple
sources, creating sequences that would not otherwise be found in the genome.
* 4 elements needed to amplify DNA by polymerase chain reaction or PCR IS DNA Template, Taq DNA
Polymerase, Oligonucleotide Primers, and Nucleotides.

18. What is the importance of a host organism to a virus? What is the importance of vaccine? What
diseases are viral in origin?
* Viruses depend on the host cells that they infect to reproduce. When found outside
of host cells, viruses exist as a protein coat or capsid, sometimes enclosed within a
membrane. The capsid encloses either DNA or RNA which codes for the virus elements.
* A vaccine activates our immune system without making us sick. Many dangerous infectious
diseases can be prevented in this simple and effective way. From birth, we are constantly
exposed to many different viruses, bacteria and other microbes. Most are not harmful, many
are beneficial but some can cause disease.
* Polio, or poliomyelitis is a viral infection that can cause paralysis and death in its most
severe forms. It can spread easily from person to person.

20. Define the following. a) retrovirus; b) reverse transcription; c) reverse transcriptase. What causes
AIDS?
* A retrovirus is a type of RNA virus that inserts a copy of its genome into the DNA of a host
cell that it invades, thus changing the genome of that cell.
* reverse transcriptionthe reverse of normal transcription, occurring in some RNA viruses, in which a
sequence of nucleotides is copied from an RNA template during the synthesis of a molecule of DNA.
* reverse transcriptase an enzyme that catalyzes the formation of DNA from an RNA
template in reverse transcription.
* HIV infection is caused by the human immunodeficiency virus. You can get HIV from contact
with infected blood, semen, or vaginal fluids. Most people get the virus by having unprotected
sex with someone who has HIV. Another common way of getting it is by sharing drug needles
with someone who is infected with HIV.