DNA and Biotechnology Flashcards
nucleosides
five-carbon sugar, bonded to a nitrogenous base and formed by covalently linking the base of C-1’ to the sugar, carbon atoms in sugar have prime to distinguish them from nitrogenous base
nucleotides
when one or more phosphate groups are attached to C-5’ of a nucleoside, nucleotides are the building block of DNA
If the pentose is a ribose, the nucleic acid is…
RNA
If the pentose is a deoxyribose, the nucleic acid is …?
DNA
deoxyribose is a ribose with the 2’ OH group replaced by a H
Bond breaking is…?
Endothermic
Bond making is….?
Exothermic
What is the backbone of DNA composed of?
Alternating sugar and phosphate groups, it is read 5’- 3’, it is formed as nucleotides are joined by 3’-5’ phosphodiester bonds, carries a negative charge
5’ end of DNA will have an -OH or phosphate group bonded to C-5’ of the sugar while the 3’ end has a free -OH on C-3’ of the sugar
Purines
Al Gore is Pure
adenine and guanine, both found in DNA and RNA, two rings
Pyrimidines
Pyramids are CUT, only contain one ring, cytosine, uracil, and thymine
thymine is only in DNA
uracil is only found in RNA
What are the 4 rules for something to be aromatic?
- compound is cyclic
- compound is planar
- compound is conjugated, alternating single and multiple bonds or lone pairs, creating at least one unhybridized p-orbital for each atom in the ring
- follows Huckel’s rule: 4n+2
ex. benzene
complementary base pairing
A is paired with T (via two hydrogen bonds); G always pairs with C (via three hydrogen bonds), hydrogen bonds provide stability to the structure
Chargaff’s Rues
amount of A equals the amount of T; the amount of G equals the amount of C
%A=%T
%G= %C
B-DNA
double helix of most DNA is a right-handed helix, forming B-DNA, makes a turn every 3.4 nm and contains about 10 bases within that span
Z-DNA
zigzag appearance; it is a left-handed helix that has a turn every 4.6 nm and contains 12 bases in each turn, unstable and hard to research
denatured
will melt DNA into two single strands that have separated from each other…heat, alkaline (basic) pH, and chemicals like formaldehyde and urea are all able to denature DNA
reannealed
when denatured, single-stranded DNA is brought back together (can occur if the denaturing condition is slowly removed)
probe DNA
DNA with known sequence, can be used to provide evidence of a gene of interest
how many chromosomes are in humans?
46 chromosomes
DNA is divided up among the 46 chromosomes found in the nucleus of the cell
histones
a group of small basic proteins
When DNA is wound around histones it forms…?
chromatin
DNA wrapped around a protein complex forms a ….?
Nucleosome –> create a much more organized and compacted DNA
Nucleoproteins
proteins that associate with DNA, example histones, others stimulate processes like transcription
What is compacted chromatin called? (Occurs during interphase)
heterochromatin
dark, dense, silent
What is dispersed chromatin called?
euchromatin, appears lights under light microscopy
light, uncondensed, expressed
telomere
a simple repeating unit (TTAGGG) at the end of the DNA, forms a telomere
have high GC content, makes them notably strong
What enzyme helps rebuild telomeres?
telomerase, more expressed in rapidly dividing cells
Centromeres
a region of DNA found in the center of chromosomes, often referred to as the site of constriction, because they form noticeable indentations
repliosome/replication complex
a set of specialized proteins that assist the DNA polymerases
DNA unwinds at points called the origins of replication, the generation of new DNA proceeds in both directions, creating replication forks on both sides of the origin
sister chromatids
two identical copies of the same chromosome formed by DNA replication, attached to each other by a structure called the centromere
helicase
the enzyme responsible for unwinding the DNA, generating two single-stranded template strands ahead of the polymerase
single-stranded DNA binding proteins will bind to the unraveled strand, preventing both the re-association of the DNA strands and the degradation o fDNA by nucleases
supercoiling
a wrapping of DNA on itself as its helical structure is pushed even further toward the telomeres during replication (like a telephone cord that’s all wrapped up)
parental strands
serve as a template for the generation of the new daughter strands
replication is semiconservative
DNA polymerases
responsible for reading the DNA template, or parental strand, and synthesizing the new daughter strand
reads 3’ to 5’; synthesizes the complementary strand 5’ to 3’
lagging strand
strand that is copied in a direction opposite the direction of the replication fork
Okazaki fragments
small strands that are produced on the lagging strand during replication
primase
synthesizes a short primer in the 5’ to 3’ direction to start replication on each strand
DNA polymerase III (prokaryotes)
DNA polymerase alpha, delta, epsilon
will begin synthesizing the daughter strand of DNA in the 5’ to 3’ manner
DNA polymerase I
DNA polymerase delta
replacement of RNA with DNA (gets rid of spot where the RNA primer had been)
DNA ligase
seals the ends of the DNA molecules together, creating one continuous strand of DNA
DNA topoisomerases/DNA gyrase
removal of positive supercoils ahead of advancing replication forks
cancer
cell proliferate excessively bc they are able to divide when they shouldn’t
metastasis
migration to distant tissues by the bloodstream or lymphatic system
oncogenes
mutated genes that cause cancer
proto-oncogenes before they are mutated
tumor suppressor genes/ antioncogenes
p53, Rb…encode proteins that inhibit the cell cycle or participate in DNA repair processes; normally function to stop tumor progression
mismatch repair
cells have machinery in the G2 phase of the cell cycle, enzymes are encoded by genes, detect and remove errors introduced in replication that were missed during the S phase of the cell cycle
nucleotide excision repair (NER)
thymine dimers are eliminated from DNA NER mechanism, excision endonuclease makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligonucleotide
base excision repair
first, the affected base is recognized and removed by a glycosylase enzyme, leaving behind an apurinic/apyrimidinic (AP) site, also called an abasic site…AP site is recognized by an AP endonuclease that removes the damaged sequence from the DNA…DNA polymerase and DNA ligase can then fill in the gap and seal the strand, as described above
recombinant DNA technology
allows a DNA fragment from any source to be multiplied by either gene cloning or polymerase chain reaction (PCR), provides the reagents necessary for genetic testing, such as carrier detection and prenatal diagnosis of genetic disease, also useful for gene therapy
DNA cloning
a technique that can produce large amounts of a desired sequence; requires that the investigator ligate the DNA of interest into a piece of nucleic acid referred to as a vector, forming a recombinant vector
vectors are usually bacterial or viral plasmids
vectors
usually bacterial or viral plasmids that can be transferred to a host bacterium after insertion of the DNA of interest
restriction enzymes (restriction endonucleases)
enzymes that recognize specific double-stranded DNA sequences, sequences are palindromic, can cut through the backbones of the double helix
DNA libraries
large collections of known DNA sequences
genomic libraries
contain large fragments of DNA and include both coding (exon) and noncoding (introns) regions of the genome
cDNA
complementary DNA, constructed by reverse transcribing processed mRNA, shorter, lacks introns, sometimes called expression libraries
hybridization
the joining of complementary base pair sequences
DNA-DNA recognition or DNA-RNA recognition
polymerase chain reaction (PCR)
automated process that can produce millions of copies of a DNA sequence without amplifying the DNA in bacteria; requires primers that are complementary to the DNA that flanks the region of interest, nucleotides (dATP, dTTP, dCTP, and dGTP) and DNA polymerase
gel electrophoresis
technique to separate macromolecules, like DNA and proteins, by size and charge, uses agarose gel, long the DNA strand, the slower it moves
Southern Blot
gel electrophoresis is often used, used to detect the presence and quantity of various DNA strands in a sample; DNA is cut by restriction enzymes and then separated by gel electrophoresis
probe will bind to its complementary sequence and form double-stranded DNA
DNA sequencing
template DNA, primers, an appropriate DNA polymerase, and all four deoxyribonucleotide triphosphates; fragments are separated by gel electrophoresis
gene therapy
offers potential cures for individuals with inherited diseases, intended for diseases in which a given gene is mutated or inactive, giving rise to a pathology; vectors are used to transfer the cloned gene into the target cells’ DNA
transgenic mice
mice that are altered at their germ line by introducing a cloned gene into fertilized ova or into embryonic stem cells; cloned gene is known as the “transgene”
better for studying dominant genes
knockout mice
a gene has been intentionally deleted (knocked out) in a mouse, provide valuable models in which to study human disease
chimera
offspring have patches of cells, including germ cells, derived from each of the two lineages
