Biochemistry Ch 6. DNA and Biotechnology Flashcards
Deoxyribonucleic acid (DNA)
Macromolecule that stores genetic information all living organisms
Nucleosides
Contain a five carbon sugar bonded to a nitrogenous base
Nucleotides
Nucleosides with one to three phosphate groups added, in DNA contain deoxyribose, in RNA contain ribose
Deoxyribose
5 carbon sugar bonded to nitrogenous base In DNA
Ribose
5 carbon sugar bonded to nitrogenous base in RNA
5 nucleotides
Adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)
Adenine
A purine, pairs with T in DNA and U in RNA via two hydrogen bonds
Guanine
A purine, pairs with C in DNA and RNA via three hydrogen bonds
Thymine
A pyrimidine, pairs with A in DNA using two hydrogen bonds
Cytosine
A pyrimidine, pairs with G in DNA and RNA via three hydrogen bonds
Uracil
A pyrimidine, pairs with A in RNA using two hydrogen bonds
Watson-Crick model
How DNA is organized, the backbone is composed of alternating sugar and phosphate groups, always read 5’ to 3’, two strands with antiparallel polarity that are wound into a double helix
How is DNA always read
5’ to 3’
Antiparallel
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Double helix
How two stands of DNA are wound
Purine
A and G, always pair with pyrimidines (A with T and G with C in DNA and A with U in RNA), biological aromatic heterocycle
Pyrimidine
U, T, and C, always pair with purines (A with T and G with C in DNA and A with U in RNA), biological aromatic heterocyle
Aromatic compounds
Cyclic, planar, and conjugated, contain 4n+2pi electrons
Huckels rule
Says aromatics contain 4n+2pi electrons where n is an integer
Heterocycles
Ring structures that contain at least two different elements in the ring
Chargaffs rules
States that purines and pyrimidines are equal in number in a DNA molecules and that because of base pairing, the amount of adenine equals the amount of thymine and the amount of cytosine equals the amount of guanine
B-DNA
most common DNA form with right handed helix
Z-DNA
Zigzag shape of DNA at a lower concentration, may be seen with high GC content or high salt concentration
Denatured
DNA strands that are pulled apart, can be done by heat, alkaline, pH, and chemicals like formaldehyde and urea
Reannealing
When DNA strands are brought back together after the removal of conditions that cause denaturing
Human chromosomes
DNA is organized into 46 chromosomes in human cells
Histone proteins
Proteins that DNA is wound around in eukaryotes to form nucleosomes, includes H2A, H2B, H3, and H4
Nucleosomes
DNA that is wrapped around histones, may be stabilized further by another histone protein (H1)
Chromatin
DNA and its associated histones in the nucleus
Heterochromatin
Dense, transcriptionally silent DNA that appears dark under light microscopy
Euchromatin
Less dense, transcriptionally active DNA that appears light under light microscopy
Telomeres
The ends of chromosomes, contain high GC content to prevent unraveling of the DNA, during replication, telomeres are slightly shortened although this can be partially reversed by the enzyme telomerase
Centromeres
Located in the middle of the chromosome and holds sister chromatids together until they are separated during anaphase in mitosis, also contain a high GC content to maintain a strong bond between chromatids
Replisome
aka replication complex, a set of specialized proteins that assist the DNA polymerases
Replication complex
A set of specialized proteins that assist the DNA polymerases
Origin of replication
Location where DNA is first unwound during replication by helicases
Helicases
Unwind DNA, produce two replication forks at the origin of replication on either side of the origin
Eukaryote origins of replication
Have linear chromosomes that contain many origins of replication
Prokaryote origins of replication
Have a circular chromosome that contains only one origin of replication
Replication forks
Formed on either side of the origin of replication by helicase at the beginning of DNA replication
Single-stranded DNA-binding proteins
Keep unwound stands of DNA from reannealing or being degraded
Supercoiling
Causes torsional strain on the DNA molecules which can be released by DNA topoisomerases
DNA topoisomerases
Relieve torsional strain in supercoiled DNA by creating nicks
Semiconservative
Describes DNA replication because one old parent strand and one new daughter strand is incorporated into each of the two new DNA molecules
Parent strand
From original DNA molecule
Daughter strand
New DNA strand
Primase
Puts down a small RNA primer on a new DNA strand because DNA cannot be synthesized without an adjacent nucleotide to hook onto
DNA polymerase II
In prokaryotes, can synthesize a new strand of DNA, they read the template DNA 3’ to 5’ and synthesize the new stand 5’ to 3’
DNA polymerases alpha, delta, and epsilon
In eukaryotes, can synthesize a new strand of DNA, they read the template DNA 3’ to 5’ and synthesize the new stand 5’ to 3’
Eukaryote DNA polymerase types
Alpha, delta, and epsilon
Leading strand
Requires only one primer and can then by synthesized continuously in its entirety
Lagging strand
Requires many primers and is synthesized in discrete sections called Okazaki fragments
Okazaki fragments
Discrete sections of DNA formed on the lagging strand
DNA polymerase I
In prokaryotes, removes RNA primer and fills spot in with DNA
Dna polymerase delta
In eukaryotes, removes RNA primer and fills spot in with DNA
DNA ligase
Fuses the DNA strands together to create one complete molecule
Oncogenes
Develop from mutations of proto-oncogenes and promote cell cycling, may lead to cancer
Proto-oncogenes
Mutate into oncogenes
Cancer
Unchecked cell proliferation with the ability to spread by local invasion or metastasize
Metastasize
Migrate to distance sites via the bloodstream or lymphatic system
Tumor suppressor genes
Code for proteins that reduce cell cycling or promote DNA repair, mutations of tumor suppressor genes can also lead to cancer
Polymerase proofreading
During replication, DNA polymerase proofreads its work and excises incorrectly matched bases, the daughter strand is identified by its lack of methylation and corrected accordingly
Mismatch repair
Also occurs during the G2 phase of the cell cycle, using the genes MSH2 and MLH1
Nucleotide excision repair
Fixes helix-deforming lesions of DNA (such as thymine dimers) via a cut and patch process that requires an excision endonuclease
Excision endonuclease
Necessary for nucleotide excision repair which fixes helix-deforming lesions of DNA (such as thymine dimers) via a cut and patch process
Base excision repair
Fixes non deforming lesions of the DNA helix (such as a cytosine deamination) by removing a base, leaving an apurinic/apyrimidinic (AP) site
Apurinic/apryrimidinic site
AP site, left when a base is removed during base excision repair
AP endonuclease
Removes the damaged sequence when can be filled in with the correct bases
Recombinant DNA
DNA composed of nucleotides from two different sources
DNA cloning
Introduces a fragment of DNA into a vector plasmid, once the fragment binds to the plasmid, it can be introduced into a bacterial cell and permitted to replicate, generating many copies of the fragment of interest, one replicated, the bacterial cells can be used to create a protein of interest or can by lysed to allow for isolation of the fragment of interest from the vector
Vector plasmid
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Restriction enzyme
aka restriction endonuclease - cuts both the plasmid and the fragment, which are left with sticky ends
Sticky ends
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Vectors
Contain an origin of replication, the fragment of interest, and at least one gene for antibiotic resistance (to permit for selection of the colony after replication)
DNA libraries
Large collections of known DNA sequences
Genomic libraries
Contain large fragments of DNA, including both coding and nonvoting regions of the genome, they cannot be used to make recombinant proteins or for gene therapy
cDNA libraries
aka expression libraries, contain smaller fragments of DNA and only include the eons of genes expressed by the sample tissue, they can be used to make recombinant proteins or for gene therapy
Hybridization
The joining of complementary base pair sequences
Polymerase chain reaction (PCR)
An automated process by which millions of copies of a DNA sequence can be created from a very small sample of hybridization
Agarose gel electrophoresis
Can separate DNA molecules by size
Southern blotting
Can be used to detect the presence and quantity of various DNA strands in a sample, after electrophoresis, the sample is transferred to a membrane that can be probed with simple stranded DNA molecules to look for a sequence of interest
DNA sequencing
Uses dideoxyribonucleotides which terminate the DNA chain because they lack a 3’ -OH group, the resulting fragments can be separated by gel electrophoresis and the sequence can be read directly from the gel
Didoxyribonucleotides
Terminate the DNA chain because they lack a 3’ -OH group
Gene therapy
A method of curing genetic deficiencies by introducing a functional gene with a viral vector
Transgenic mice
Created by integrating a gene of interest into the germ line or embryonic stem cells of a developing mouse, can be mated to select from the transgender
Chimeras
Organisms that contain cells from two different lineages (such as mice formed by integration of transgenic embryonic stem cells into a normal mouse blastocyst)
Knockout mice
Created by deleting a gene of interest
Biotechnology ethics
Brings up a number of safety and ethical issues including pathogen resistance and the ethics of choosing individuals for specific traits
