dna structure and replication Flashcards
it is the different building blocks combine in sequences which enables to carry information
nucleic acids
what are the 2 classes of nucleic acids
DNA and RNA
it is the single building block of DNA
nucleotide
nucleotide consist of
1 deoxyribose sugar (5 carbon sugar)
1 phosphate group (phosphorus atom bonded to 4 oxygen atoms)
1 nitrogenous base
- purines: adenine and guanine
- pyrimidines: cytosine and thymine
it forms the “rails” of the DNA helix, providing structure
sugar-phosphate backbone
purines vs pyrimidine
purines: 2 ring structure
pyrimidine: 1 ring structure
their pairing (1 big and 1 small) ensures that the DNA helix maintains a consistent width throughout
phosphodiester bond vs hydrogen bond
phosphodiester bond:
Link the sugar of one nucleotide to the phosphate group of the next in the DNA backbone.
hydrogen bond:
Hold the complementary nitrogenous bases (A-T, G-C) together between the two DNA strands.
why must dna be replicated
To ensure that genetic information is passed to daughter cells during cell division, maintaining the continuity of genetic information across generations.
dna sequences are measured in
measured in numbers of base pairs
- kilobase (kb): thousands
- mega base (mb): millions
it is the information-containing parts of DNA because they form sequences
nitrogenous bases
it is a chain that forms when nucleotides link together that held together phosphodiester bons
polynucleotide chains
what are phosphodiester bonds
they are formed between deoxyribose sugars and the phosphate groups
it is a continuous link that are formed between deoxyribose sugars and the phosphate groups
sugar-phosphate backbone
it is when in a DNA molecule, the two polynucleotide chains run in opposite directions
antiparallelism
briefly explain antiparallelism
One chain runs from the 5′ end (5 prime) to the 3′ end (3 prime)
while the other runs from the 3′ end to the 5′ end
= head-to-toe alignment.
5’ -
3’ -
*structure of sugar-phosphate backbone structure
5’ - have phosphate group attached to 5th C
3’ - end w hydroxyl grp attached to 3rd C
explain how the sugar-phosphate backbone is formed
These carbons are numbered from 1 to 5, starting from the carbon next to the nitrogenous base and moving
clockwise
nucleotides and pairing
adenine pairs w thymine
guanine pairs w cytosine
A & T - 2 hydrogen bonds
G & C - 3 hydrogen bonds
true or false:
a single strand of DNA will form a helix
flase - will not
purine-pyrimidine couples are called
complementary base pairs
why is the hydrogen bonds are weak individually but strong collectively
the bonds are between base pairs
that maintains the stability of the DNA structure
they are strong collectively butt weak enough to allow the strands to separate when needed
this is formed when the DNA strands twist and when they are antiparallel
double helix structure
true or false:
DNA molecules are extremely long
true
how long is the the DNA of the smallest human chromosome, if stretched out
14 millimeters (thousandths of meter)
*but it is packed into a chromosomes that during cell division, its only 2 micrometers (millionths of a meter)
how is the DNA in chromosomes is highly compacted
by shrinking its length by a factor of 7000 to fit inside the cell nucleus
what are the role of proteins in DNA folding
○ Scaffold Proteins
Provide a framework for organizing DNA strands
○ Histones
DNA wraps around these proteins to form structures called nucleosomes.
Each nucleosome consists of 8 histone proteins and 147 DNA base pairs.
each nucleosome consists of
8 histone proteins
147 DNA bases
aka “DNA bead”
what is the structure of the nucleosomes
the 5th histones anchors nucleosomes to short linker regions of DNA, which tightens the nucleosomes into 30 nm fibers.
true or false:
at any given time, only small sections of the DNA double helix are exposed.
true
*most of the DNA is wrapped up
what do the chromatin consists of
aka “colored material”
■ 30% histone proteins
■ 30% scaffold protein and other other DNA-binding proteins
■ 30% DNA
■ 10% RNA
what happens when a chromatin is loose
(not condensed into chromosomes)
it forms loops at abt 10000 places in the genome
it bring together parts of the DNA sequence within the same long molecule to form the overall “loop-ome” structure
CTCF
CCCTC-binding
briefly explain the sites of chromatin attachment to the nuclear membrane
they are not random and the
placement may control which genes a cell is using to make proteins
closed chromatin vs open chromatin
closed chromatin:
heterochromatin
more densely packed
open chromatin:
euchromatin
less compact structure
this help form and maintain the chromatin loops
CTCF anchor protein
loop domain
- large loops of DNA formed by chromatin
it is a genetically rare disease that resembles rapid aging in children
progeria
this bring together regions of the genome that work together
chromatin loops
*a way for the cell to organize its genetic material, bringing tgt parts tht need to work tgt and influence which genes r active (gene regulation)
what happens if there is an alteration in a chromatin loops
it may contribute to disease like cancer
briefly explain the positioning of loops within the nucleus
linked to which genes are active in a particular cell.
why do the DNA must be copied or replicated
so that the genetic information it contains can be passed on to future cell generations while also guiding the production of proteins
who uncovered the double helix structure of DNA in 1953
James Watson and Francis Crick
*the mechanism for DNA replication became clear
briefly explain the DNA replication process
2 strands of the double helix unwind and separate
each strand serve as a template to attract complementary bases from free nucleotides available in the cell
= 2 identical DNA double helices
briefly explain semiconservative replication
semi - half
conservative - to keep
each new DNA molecule keeps half of the original DNA
(1 old strand and 1 new strand = genetic info is accurately copied and passed on)
who provided proof for semiconservative replication.
Researchers Matthew Meselson and Franklin Stahl
Their experiment showed that after replication, DNA molecules had a mix of heavy and light strands, confirming the semiconservative model.
where do the replication occurs
it occurs during the S phase of the cell cycle
in order, what are the enzyme used in DNA replication
helicase - unwinds parental double helix
binding proteins - stabilize separate strands
primase - adds short primer to template strand
DNA polymerase - bind nucleotides to form new strands
ligase - joins okazaki fragments and seals other nicks in sugar-phosphate backbone
*okazaki fragments that are up to 150 nucleotides long
in the step of DNA replication,
what happens in unwinding and separation of DNA
helicase enzyme breaks the hydrogen bonds between base pairs = double helix to unwind and separate into 2 single strands
= formed replication fork, where the DNA is opened for replication.
in the step of DNA replication,
what happens in stabilizing strands
binding proteins attach to the single DNA strands, keeping them apart to prevent re-annealing of the hydrogen bonds
in the step of DNA replication,
what happens in formation of RNA primer
primase enzymes synthesize RNA primer (short RNA sequences)
this is cos the main enzyme that replicates DNA, DNAPolymerase cannot initiate replication on its own - it can only add nucleotides to an existing strand
in the step of DNA replication,
what happens in extension of the DNA strand
DNA polymerase:
1) adds DNA nucleotides complementary to the
bases on the parental DNA strand
= form hydrogen bonds with their complementary bases
2) links the sugar-phosphate backbone of the new strand = strong chain.
in the step of DNA replication,
what happens in leading and lagging strand synthesis
leading strand:
antiparallelism of the DNA strands
causes one strand to be synthesized continuously in the 5′ to 3′ direction
lagging strand:
synthesized discontinuously in short fragments called Okazaki fragments since it runs in the opposite direction
DNA polymerase adds nucleotides in pieces, moving from the replication fork outward
in the step of DNA replication,
what happens in sealing the DNA strands
ligase enzyme joins the Okazaki fragments by sealing the sugar-phosphate backbone = DNA strand is continuous
in the step of DNA replication,
what happens in proofreading and rewinding
DNA polymerase has a proofreading function - ensure that incorrect bases are removed and replaced with the correct ones
annealing helicase helps rewind the
DNA that remains unwound during replication.
a powerful biotechnology tool used to amplify a specific DNA sequence outside of cells
Polymerase Chain Reaction
* it can produce millions to billions of copies of a specific DNA sequence in a short period
Polymerase Chain Reaction is a vital technique for replicating DNA and has a wide range of applications such as
forensic analysis
genetic research
ecological studies
what are the steps of PCR
denaturation (heat separation):
DNA containing the target sequence is heated to a high temperature (around 95°C) - break H bonds
annealing (primer building):
temp is lowered, typically to 50-65%, allow primers to bind to complementary sequences at each end of the target DNA
extension (DNA synthesis):
heat-tolerant DNA polymerase (Taq polymerase)
adds nucleotides to the primers, extending them and synthesizing new DNA strands complementary to the original single-stranded templates.
a known target sequence of DNA that is to be amplified
target DNA sequence
two synthetic single-stranded DNA primers that are complementary to the opposite ends of the target sequence
primers
abundant copies of the four nucleotide bases (A, T, G, C) required to build the new DNA strands
DNA nucleotides
a heat-resistant enzyme from the bacterium Thermus aquaticus, which can survive the high temperatures necessary for DNA denaturation during PCR
Taq Polymerase
how does PCR works
3 temperature-dependent steps
denaturation > annealing > extension = amplification to occur exponentially
after each cycle, no. of copies of the target DNA doubles
for instance, after 30 cycles, PCR can generate more than a billion copies of the specific DNA sequences
it is a sanger sequencing
called chain termination
today’s version PCR
- altered bases w fluorescent tags
Why would a DNA structure in which each base type could form hydrogen bonds with any of the other three base types not produce a molecule that is easily replicated
If bases could pair randomly, the complementary base-pairing rule would break down, making it impossible for the DNA to form consistent pairs, and this would prevent accurate copying during replication
What part of the DNA molecule encodes information
The nitrogenous bases (adenine, thymine, cytosine, and guanine) encode genetic information by forming specific sequences
Explain how DNA is a directional molecule in a chemical sense
DNA has directionality because its two strands run antiparallel. One strand runs from the 5′ carbon to the 3′ carbon, while the other runs from 3′ to 5′. DNA polymerase adds nucleotides in the 5′ to 3′ direction
How can very long DNA molecules fit into a cell’s nucleus?
DNA molecules are compacted through several levels of coiling and looping, including wrapping around histone proteins to form nucleosomes, which then coil further into chromatin.
Explain how loop formation enables gene-gene interactions.
Proteins called CTCF bring together different regions of the DNA molecule that contain related genes, allowing them to interact and regulate gene expression.
How are very long strands of DNA replicated without becoming twisted into a huge tangle?
DNA helicase unwinds the strands
an enzyme called annealing helicase helps rewind any sections that remain unwound
Okazaki fragments prevents tangling
List the steps in DNA replication.
DNA unwinds and separates.
RNA primer is added by primase.
DNA polymerase adds nucleotides to form the new strand.
RNA primers are replaced, and DNA ligase seals gaps in the sugar-phosphate backbone
an enzyme that adds new bases to replicating DNA and corrects mismatched base pairs
DNAPolymerase
a locally opened portion of a replicating DNA double helix
replication fork
what are the two jobs that the genetic material carry out
duplicate itself
control the development of the rest of the cell
- Francis Crick and James Watson discovered
who described DNA when he isolated nuclei from white blood cells in pus on soiled bandages
Friedrich Miescher, swiss physician and biochemist
- he discovered in the nuclei an unusual acidic substances containing nitrogen and phosphorus
nuclein -> later called nucleic acid. named by Miescher in 1871
who was the first to link inherited disease and protein
Archibald Garrod, english physician
who took the first step in identifying DNA as the genetic material
Frederick Griffith, english microbiologist
he worked with two types of Streptococcus pneumoniae bacteria
Type R (Rough): These bacteria had a rough surface and were easily recognized and destroyed by the mouse’s immune system, so they didn’t cause disease.
Type S (Smooth): These had a smooth surface due to a protective capsule that hid them from the mouse’s immune system, causing severe infections.
Griffith found that when he mixed harmless type R bacteria with heat-killed type S bacteria (which alone didn’t cause illness), the mixture somehow made the mice sick and die. He called this change transformation, as the type R bacteria had seemingly turned into the deadly type S. He couldn’t identify what part of the dead S bacteria caused this change before his untimely death during World War II.
why did the mouse immune system cant recognize the type S bacteria
as it was enclosed in a polysaccharides capsule (a type of carbohydrate)
however, when the bacteria were heated, it killed them
who continued Frederick Griffith’s work and what did they discover/ their findings
Oswald Avery
Colin MacLeod
Maclyn McCarty
to find out exactly what part of the dead type S bacteria was responsible for transforming the harmless type R bacteria into the deadly form by:
treating the bacteria with
- protease, tht dismantles protein (no change)
- deoxyribonuclease DNase, an enzyme that dismantles dna (have change = disrupt the transformation)
who infected Escherichia coli bacteria with a virus that consisted largely of a protein head or coat surrounding DNA.
Alfred Hershey and Martha Chase
virus infect bacterial cells by injecting their DNA = produce more virus while protein cots remain outside the bacterial cells
what were the experiments and results of Alfred Hershey and Martha Chase
Experiment:
They grew one group of viruses in a medium with radioactive sulfur, which made the protein shells of the viruses radioactive.
They grew another group of viruses in a medium with radioactive phosphorus, which made the DNA inside the viruses radioactive.
Blender test: They mixed these labeled viruses with bacteria and used a blender to shake off the virus shells from the outside of the bacteria. Then, they spun the mixture in a centrifuge to separate the bacteria from the lighter virus shells.
Results:
Sulfur-labeled viruses:
The radioactivity was found only in the fluid with the protein shells, not in the bacteria. This showed that the proteins stayed outside the bacteria.
Phosphorus-labeled viruses:
The radioactivity was found in the bacteria at the bottom of the tube, showing that the DNA had entered the bacteria.
Conclusion: Only the DNA entered the bacteria and directed them to produce more viruses. This experiment confirmed that DNA is the genetic material, not protein.
who identified the 5-C sugar ribose and deoxyribose and when did he discovered it
Phoebus Levene, russian american biochemist
1909 - ribose
1929- deoxyribose
what are the major chemical distinction between RNA and DNA that Levene revealed
RNA:
serve as a carrier of the info in a dna molecule
DNA: instructs the cell to manufacture a particular protein
true or false:
all the three parts of a nucleic acid that are present in equal proportions
true
who showed that DNA in several species contains equak amounts of these bases adenine (A) and thymine (T) and equal amounts of the bases Guanine (G) and cytosine (C)
Erwin Chargaff
it is a technique where DNA is bombarded with X rays
x-ray diffraction
used by English physicist Maurice Wilkins and English chemist Rosalind Franklin
who provided the pivotal clue that there were two forms of DNA
Rosalind Franklin
- She distinguished a dry, crystalline “A” form from the wetter type seen in cells, the “B” form.
- It took her 100 hours to obtain the now famous photo 51 of the B form in May 1952.
the famed biochemist who suggested a triple helix structire for dna
Linus Pauling
- this was proven incorrect
how did Watson and Crick found the answer of the double helix of the dna
using cardboard cutouts of the DNA components
- April 25, 1953: Published their findings in an issue of Nature magazine where they built a more detailed and traditional ball-and-stick metal model.
- received the Nobel Prize
a section of dna molecule whose order of bases specifies the sequences of aa in a protein
gene
it is considered diverse because proteins have diverse functions
inherited traits
how fast the human dna replicates
at a rate of about 50 bases per second
what are the steps in PCR and the required temp
- denaturation, 95 degree Celsius
heated to separate strands - annealing, 55 degree Celsius
primers bind to target dna sequences - extension, 72 degree Celsius
dna polymerase, exends (make it long)
