DNA (pp.4-8, handout 4) Flashcards
purines
Type of nitrogenous base with a double ring found in DNA and RNA
Guanine and Adenine
GAPUR
pyrimidines
Type of nitrogenous base with a single ring found in DNA and RNA
cytosine and thymine
PYRCT
DNA
deoxyribonucleic acid.
- the central dogma of genetics is that all genes are made of DNA
base pairs
adenine and thymine (DNA) / adenine and uracil (RNA) (2 hydrogen bonds)
guanine and cytosine (DNA) (3 hydrogen bonds)
RNA
ribonucleic acid.
right-handed helix
In a right-handed helix, as the observer looks down, the helix axis (in either direction), each strand turns clockwise as it moves away from the observer
one turn is 34 angstrom and has 10 base pairs
Nucleotides contain…
1) a phosphate group
2) pentose (five-carbon sugar)
3) nitrogen-containing base
What is the pentose for DNA
deoxyribose
B-form
The normal form of the DNA double helix, as originally described by Watson and Crick
- aqueous environments with low salt concentrations
What is the pentose of RNA
ribose
What are the nitrogenous bases
adenine and thymine (corresponds with DNA)
guanine and cytosine (corresponds with DNA)
uracil (corresponds with RNA)
A-form
An alternative form of the double helix, with 11 base pairs per turn, often found for double-stranded RNA, but rarely for DNA
found in DNA in high salt environments
Z-form
An alternative form of double helix with left-handed turns and 12 base pairs per turn. Both DNA and dsRNA may be found in the Z-form
occurs when proteins bind to DNA and create a zig-zagged phosphate backbone
What is a phosphodiester bond
how phosphate connects to sugars. connect the nucleotides into a chain that runs in the 5’ to 3’ direction.
5’ -OH of one nucleotide’s sugar is linked to a phosphate group by an oxygen. The 3’ -OH of the next nucleotide’s sugar is linked to the other side of the phosphate.
DNA double helix
TEAMROSALIND
most stable structure: when one single strand of nucleotides aligns with another strand to form a double stranded molecule.
supercoiling
Higher level coiling of DNA that is already a double helix.
The DNA is twisted in a left-handed direction containing around 200 nucleotides per supercoil. The supercoils then forms loops and connects to a protein scaffold.
performed by DNA gyrase.
DNA Gyrase
An enzyme that introduces negative (left-handed) supercoils into DNA, a member of the type II topoisomerase family
the only one that can do negative coils…..#biologyissocool
antiparallel
as each base forms H-bonds with another base in the other strand, the strands run in opposite directions to each other
5’ ———————- 3’
3’ ———————- 5’
restriction enzymes
(also known as restriction endonucleases) allows DNA to be cut and rejoined in predictable ways
antisense strand
one of the strands in DNA that contains the complementary sequence to the strand and to the mRNA transcript generated from the gene
the non-coding DNA strand of a gene, serves as the template for producing messenger RNA (mRNA), which directs the synthesis of a protein.
sense strand
the strand of DNA that reads as the code for the expressed genes
topoisomerase I
Enzyme that alters the level of supercoiling or catenation of DNA (i.e., changes the topological conformation) - removes extra super coils
polymer
molecular chain of building blocks stitched from end to end
histones
DNA is supercoiled and wrapped around the histones so that everything ‘fits’
Special positively charged protein that binds to DNA (neutralizes negatively charged phosphate) and helps to maintain the structure of chromosomes in eukaryotes
eukaryotic (plant and animal) DNA is too complex for just supercoiling.
tails stick out of nucleosomes to assist in regulation
in regions of dna expression, histones roam freely
monomer
the building blocks making the links in the polymer chain
chromatin
Complex mixture of DNA plus protein that constitutes eukaryotic chromosomes.
dna is supercoiled, wrapped around histones to become chromatin and then all squished up to make chromosomes
looks like beads on a string
nucleosome
Subunit of a eukaryotic chromosome consisting of DNA coiled around histone proteins (the beads on chromatin)
structural unit of chromatin.
contains of 200 base pairs and 9 histones
tetra-nucleotide theory
People believed that DNA was simply repeating a nucleotide sequence and could not be complex enough to carry hereditary information
heterochromatin
condensed histones that prevent other protein from accessing DNA
Tightly packed form of chromatin that is found in centromeres and telomeres; histone 3 is di- and tri-methylated on lysine 9 (H3K9) in these regions of the genome
Chargaff’s Rules
The number of Adenines always equals the number of Thymines
The number of Guanines always equal the number of Cytosines
What is the DNA backbone made up of?
A phosphate and a pentose (5-carbon sugar)
30-nanometer fiber
Chain of nucleosomes that is arranged helically, approximately 30 nm in diameter
chromatin cannot condense enough to fit eukaryotic DNA so it is coiled into this structures that has six nucleosomes per turn.
structure loops back and forth and is tethered to a protein scaffold or chromosome axis
How many hydrogen bonds bind Adenine and Thymine?
2 hydrogen bonds
How many hydrogen bonds bind Guanine and Cytosine
3 Hydrogen bonds
matrix attachment regions (MAR)
Site on eukaryotic DNA that binds to proteins of the nuclear matrix or of the chromosomal scaffold—same as SAR sites
aka place where chromatin loopies from 30nm fiber attach to protein or chromosome.
70% A/T concentration causes bentness and promotes connections between DNA and proteins
Semiconservative replication
During the replication process each new double helix contains one original strand and one newly synthesized strand
purpose of bacteria in biotechnology
bacteria are treated as workhorses due to their prevalence on earth and ability to thrive in extreme conditions
which enzyme aids in DNA copying from the template strand?
DNA Polymerase - proofreads and replicates!
DNA polymerase
An enzyme that elongates strands of DNA, especially when chromosomes are being replicated - synthesizes a new strand of DNA in the 5’ –> 3’ direction
think DNA replication!!
nucleoside
a nitrogen base linked to a sugar - no phosphate group!
thermostable
Able to withstand high temperatures without loss of function
nucleotide
a nitrogenous base linked to a sugar and one or more phosphate groups
nucleoside triphosphate
a nitrogenous base linked to a sugar and three phosphates
polymerase chain reaction (PCR)
Amplification of a DNA sequence by repeated cycles of strand separation and replication
takes one segments and amplifies and replicates it really quickly so you get alot of copies of one dna segment
carried out at high temperatures
Nucleophilic attack
occurs when an electron-rich species “attacks” an electron-deficient species, forming a new bond between the nucleophile and the carbocation
amino acids
monomer building blocks (20 different ones) of proteins whose sequence is determine by the nitrogen bases within the genetic code.
sequence of amino acids determine a proteins 3D structure which determines its function.
What other enzymes also participate in unzipping and unwinding the double helix?
DNA helicase and DNA topoisomerase
codons
three base sequences that represent amino acids (found inside of DNA sequences is singles or multiples)
degeneracy of the genetic code
multiple codons specifying the same amino acid
The two antiparallel strands are replicated ___________
simultaneously
What are RNA primers used for?
To initiate a new strand
The parent strand at the 3’ end determines __________ in a continuous replication
the leading strand
The parent strand at the 5’ end determines __________ in a continuous replication
the lagging strand
What are Okazaki fragments
the lagging strand fragments
what process does the central dogma of biology follow?
DNA → transcription → RNA → translation → polypeptide → folding → functional protein (3D)
RNA primers are removed by __________ and the fragments are joined by _________
DNA polymerase DNA ligase
transcription
the process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA).
walter sutton
observed chromosomes in pairs that sorted independently to gametes
thomas hunt morgan
fly guy!!! bred flies and tracked their phenotypes (worked better than peas bc they reproduce faster and have more traits to consider)
what are the ten features of DNA that watson and crick identified?
1) double-stranded helix that spirals in the right hand direction
2) anti-parallel
3) backbones outside, bases inside
4) bases perpendicular to helix axis
5) bases held together by hydrogen bond
6) 2nm diameter for double helix
7) base-pairing
8) major and minor grooves
9) one revolution = 10 monomers
10) complementarity
what two things does DNA polymerase need?
1) template strand to direct the sequence
2) a short piece of stranded DNA to prime the enzyme
what is the significance of a covalent bond?
because it has chemical potential, breaking the bond releases energy
