Chapter 6: DNA and Biotechnology Flashcards
What does DNA stand for?
Deoxyribonucleic acid
Where is the bulk of DNA found in eukaryotic cells? Where is it also present?
- In chromosomes in the nucleus
- Mitochondria and chloroplasts
Define nucleosides.
- Composed of five-carbon sugar (pentose) bound to a nitrogenous base
In nucleosides, how are nitrogenous bases linked to sugars?
Covalently linking the base to C-1’ of the sugar
When are nucleotides formed? What is attached to where?
When one or more phosphate groups are attached to C-5’ of a nucleoside
How are nucleotides named?
- According to the number of phosphates bound
- ex: Adenosine di- and triphosphate
What are the building blocks of DNA?
Nucleotides
Nucleic acids are classified according to what?
According to the pentose they contain
What is the difference between the pentose in RNA and DNA?
RNA: ribose
DNA: deoxyribose
What is deoxyribose? How is it different than ribose?
Ribose with the 2’-OH group replaced by -H
Name the 5 nitrogenous bases. Which one is only present in DNA? Which one is only present in RNA?
- Adenine
- Guanine
- Cytosine
- Uracil (RNA)
- Thymine (DNA)
What is the backbone of DNA composed of? In what direction is DNA read from?
- Alternating sugar and phosphate groups
- Read from 5’ to 3’
How are nucleotides joined together? What type of bond?
3’-5’ phosphodiester bonds
- Phosphate group links the 3’ carbon of one sugar to the 5’ phosphate group of the next incoming sugar
What is the overall charge of DNA and RNA strands? Why?
- Negative
- Phosphates carry a negative charge
What does the 5’ end of DNA contain? What does the 3’ end contain?
5’: -OH or phosphate group bound to C-5’ of the sugar
3’: free -OH on C-3’ of the sugar
How would you write (5’-ATG-3’) backwards?
3’-GTA-5’
Write the following DNA strand while showing the position of phosphates: 5’-ATG-3’
pApTpG
DNA is generally ______-stranded and RNA is generally ______-stranded.
double, single
What are the two families of nitrogen-containing bases found in nucleotides?
Purines and pyrimidines
How do the ring structures of purines and pyrimidines differ?
Purine: two rings
Pyrimidine: one ring
What are the two purines found in nucleic acids?
Adenine (A) and Guanine (G)
What are the three pyrimidines found in nucleic acids?
Cytosine (C), Uracil (U), and Thymine (T)
Purines and pyrimidines are examples of biological _______ _______
aromatic heterocycles
In chemistry, the term aromatic describes any unusually stable ring that adheres to the which four specific rules?
1) Compound is cyclic
2) Compound is planar
3) Compound is conjugated
4) Compound respects Huckel’s rule
What is a conjugated compound?
Has alternating single and multiple bonds, or lone pairs, creating at least one unhybridized p-orbital for each atom in the ring
What is Huckel’s rule?
Compound has 4n + 2 (where n is any integer) pi electrons
What is the cause of the extra stability in aromatic compounds?
The delocalized pi electrons, which can travel throughout the entire compound using available p-orbitals
Are aromatic compounds reactive?
No, they are fairly unreactive
What are heterocycles?
Ring structrues that contain at least two different elements in the ring
Who presented the three-dimensional structure of DNA in 1953?
James Watson and Francis Crick
What are the key features of the Watson-Crick model?
- Two strands of DNA are antiparallel (opposite direction)
- Sugar-phosphate backbone is on the outside of the helix while the nitrogenous bases are on the inside
- Complementary base pairings
- Chargaff’s rule
Where is the sugar-phosphate backbone located in DNA? Where are the nitrogenous bases located?
Sugar-phosphate backbone: outside of the helix
Nitrogenous bases: inside
What is adenine (A) always paired with? Through how many hydrogen bonds?
- Thymine (T) - DNA or Uracil (U) - RNA
- 2 hydrogen bonds
What is guanine (G) always paired with? Through how many hydrogen bonds?
- Cytosine (C)
- 3 hydrogen bonds
What would be the complimentary strand of DNA for the following strand: 5’-ATCG-3’
5’-CGAT-3’
Which complementary pair is stronger? Why?
- G-C
- Because of the three hydrogen bonds
What does Chargaff’s rules state?
- Total purines will be equal to total pyrimidines
- %A = %T
- %G = %C
What hand is the DNA helix? What is it called?
- Right-handed helix
- B-DNA
How often does the helix in B-DNA make a turn? How many bases does it contain within that span?
- 3.4 nm
- 10 bases
How can major and minor grooves be identified? What is their role?
- Between the interlocking strands and are often the site of protein binding
- Provide binding sites for regulatory proteins
Apart from B-DNA, what is another form of DNA? Why is it called that?
- Z-DNA
- For its zigzag appearance
What hand is Z-DNA? How often does the helix make a turn? How many bases does it contain within that span?
- Left-handed helix
- 4.6 nm
- 12 bases
What contributes to the formation of Z-DNA?
High GC-content or high salt concentration
Has Z-DNA been attributed biological activity? Why or why not?
No, partly because it is unstable and difficult to research
How can DNA be denatured? What does that result in?
- By conditions that disrupt hydrogen bonding and base-pairing
- Resulting in the “melting” of the double helix into two single strands that have separated from each other
What does not break during DNA denaturation?
The covalent links between the nucleotides in the backbone of the DNA
What is commonly used to denature DNA?
Heat, alkaline pH, and chemicals (formaldehyde)
How can denatured be brought back together? What is this called?
- Reannealed
- If the denaturing condition is slowly removed
Annealing of complementary DNA strands is an important step in many laboratory processes. Give examples.
Polymerase chain reactions (PCR) and the detection of specific DNA sequences
How does PCR and detection of specific DNA sequences work?
- Probe DNA (DNA with known sequence) is added to a mixture of target DNA sequences
- Probe DNA binds to target DNA sequences, evidence of the presence of the gene of interest
How many phosphate groups can nucleotides contain?
One to three phosphate groups
How does the aromaticity of purines and pyrimidines underscore their genetic function?
- Make compounds stable and unreactive
- Important for storing genetic information and avoiding spontaneous mutations
If a strand of RNA contained 15% cytosine, 15% adenine, 35% guanine, and 35% uracil, would you violate Chargaff’s rules? Why or why not?
- No
- RNA is single-stranded, so the complementarity seen in DNA does not hold true
In humans, DNA is divided up among the ___ chromosomes found in the nucleus of the cell.
46
The DNA that makes up a chromosome is wound around a group of small basic proteins called ______, forming ______
histones, chromatin
How many histone proteins are found in eukaryotic cells? What are they?
- H2A, H2B, H3, H4
- H1
How does a nucleosome form?
- Two copies each of the histone proteins H2A, H2B, H3, and H4 form a histone core
- 200 base pairs of DNA are wrapped around this protein complex, forming a nucleosome
What does the histone H1 do?
Seals off the DNA as it enters and leaves the nucleosome, adding stability to the structure
What contributes to the compaction of DNA?
- Supercoiling of the DNA double helix
- Nucleosomes
What are nucleoproteins? Give an example.
- Proteins that associate with DNA
- Histones
What would be the consequence of a nucleosome without the histone H1?
Sensitive to nuclease
As a whole, DNA and its associated histones make up ______ in the nucleus
chromatin
What is heterochromatin? How does it appear under light microscopy?
Dense, transcriptionally silent DNA that appears dark under light microscopy
What is euchromatin? How does it appear under light microscopy?
Less dense, transcriptionally active DNA that appears light under light microscopy
A small percentage of the chromatin remains compacted during interphase and is referred to as ____________.
heterochromatin
Why can’t DNA replication extend all the way to the end of a chromosome? What is the solution?
- Results in losing sequences and information with each round of replication
- Solution
What are telomeres? What do they contain? Why?
- The ends of chromosomes
- Contain high GC-content to prevent unraveling of the DNA
What happens to telomeres during replication? How can this be (partially) reversed?
- Slightly shortened
- By the enzyme telomerase
In each round of DNA replication, some of the sequence is lost. How can it be replaced?
By the enzyme telomerase
Telomerase is more highly expressed in which kinds of cells?
Rapidly dividing cells
Where are centromeres located? What is their major function?
- Located in the middle of chromosomes
- Hold sister chromatids together until they are separated during anaphase in mitosis
What contains a high GC-content to maintain a strong bond between chromatids?
Centromeres
Which histone is not part of the histone core around which DNA wraps to form chromatin?
H1
What property of telomeres and centromeres allow them to stay tightly raveled, even when the rest of DNA is uncondensed?
High GC-content increases hydrogen bonding, making the association between DNA strands very strong at telomeres and centromeres
What is the replisome or replication complex?
Set of specialized proteins that assist the DNA polymerases
To being the process of replication, DNA unwinds at points called _______________
origins of replication
The generation of new DNA proceeds in ____ directions, creating ______________ on both sides of the origin
- both
- replication forks (2 in total)
What enzymes unwound DNA during DNA replication?
Helicases
Prokaryotes have a ______ chromosome that contains ___ origin of replication
circular, one
Eukaryotes have a ______ chromosome that contains ___ origin of replication
linear, many
What are unwound strands of DNA kept from reannealing or being degraded by during DNA replication?
Single-stranded DNA-binding proteins
During DNA replication, as the replication forks move toward each other and ___________ are created, the chromatids will remain connected at the _________.
sister chromatids, centromere
What is supercoiling? When does it happen?
- Wrapping of DNA on itself as its helical structure is pushed ever further toward the telomeres during replication
- As the helicase unwinds the DNA during DNA replication
What enzymes introduces negative supercoils to alleviate the torsional stress and reduce the risk of strand breakage?
DNA topoisomerase II (DNA gyrase)
How does DNA topoisomerase II (DNA gyrase) work?
Alleviates torsional stress by working ahead of helicase, nicking both strands, passing the DNA strands through the nick and then resealing both strands
Why is the replication process is termed semiconservative?
Because one parental strand is retained in each of the two resulting identical double-stranded DNA molecules
Which enzyme is responsible for reading the DNA template, or parental strand, and synthesizing the new daughter strand?
DNA polymerases
