02 Processes Involving the Genetic Material Flashcards
Prokaryotes and Eukaryotes similarities:
- Both contain genome consist of DNA Molecules and also contains genes.
- Genomes serve as storage or genetic information of both organisms.
- Both undergoes transcription and translation.
- Genomes of both organism duplicates and inherit to next generations.
Genome is larger in size than prokaryotes
Eukaryotes
Contains nucleus and other membrane-bound organelles.
o Ribosomes, endoplasmic reticulum, golgi apparatus, vacuoles, lysosomes, mitochondria, and, in plants, chloroplasts.
Eukaryotes
Genome is smaller in size than the eukaryotes
Prokaryotes
Does not contain nucleus and membrane bound organelles
Prokaryotes
Chromosomes are multiple and in linear shape, they also have telomeres.
o They are diploid, in humans, cells other than human sex cells, are diploid and have 23 pairs of chromosomes. This gives 46 chromosomes in total.
Eukaryotes
the specific DNA–protein structures found at both ends of each chromosome, protect the genome from nucleolytic degradation, unnecessary recombination, repair, and interchromosomal fusion.
Telomeres
Eukaryotes wrap their DNA around proteins called _____to help package the DNA into smaller spaces.
histones
A protein that provides structural support to a chromosome. In order for very long DNA molecules to fit into the cell nucleus, they wrap around complexes of histone proteins, giving the chromosome a more compact shape.
Histones
Extrachromosomal DNA is present in all eukaryotic cells like the _____
Mitochondria
is a main source of this extrachromosomal DNA in eukaryotes. The fact that this organelle contains its own DNA supports the hypothesis that mitochondria are descended from specialized bacteria that somehow survived endocytosis by another species of prokaryote or some other cell type, and became incorporated into the cytoplasm.
Mitochondrial DNA
Contains single circular chromosome or DNA which is found in the central part of the cell called the nucleoid
Prokaryotes
where prokaryotes assemble their genetic information. (Nucleus in eukaryotes)
Nucleoid
DNA is not associated with Histone
Prokaryotes
Most prokaryotes do not have histones. The way prokaryotes compress their DNA into smaller spaces is through_______
supercoiling
Prokaryotes may also contain extrachromosomal DNA molecules called _______
plasmid
separate from the prokaryotic chromosome and replicate independently of it
Plasmids
Extrachromosomal small circular DNA molecule that can self-replicate in the cell
Prokaryotes
DNA or deoxyribonucleic acid is a type of molecule known as a ______. It consists of a 5-carbon deoxyribose sugar, a phosphate, and a nitrogenous base.
It consists of two spiral nucleic acid chains that are twisted into
nucleic acid
Double Helix shape
This twisting allows DNA to be more compact. In order to fit within the nucleus, DNA is packed into tightly coiled structures called _____. `
chromatin
_____ condenses to form chromosomes during cell division.
Chromatin
Prior to DNA replication, the chromatin ____ giving cell replication machinery access to the DNA strands
loosens
Is the process by which a double stranded DNA molecule is copied to produce two identical DNA molecules.
DNA replication
is one of the most basic processes that occurs within a cell.
DNA replication
Each time a cell divides, the two resulting daughter cells must contain exactly the same genetic information, or DNA, as the parent cell. To accomplish this, each strand of existing DNA acts as a _____ for replication.
template
Replication occurs in three major steps:
the opening of the double helix and separation of the DNA strands,
the priming of the template strand
the assembly of the new DNA segment.
DNA replication:
During separation, the two strands of the DNA double helix uncoil at a specific location called the ____.
Several enzymes and proteins then work together to prepare, or ____, the strands for duplication.
Finally, a special enzyme called _____ organizes the assembly of the new DNA strands.
origin
prime
DNA polymerase
Universal Features of DNA Replication Process:
DNA replication is _____
DNA replication occurs at a _____
DNA replication is mostly _____
DNA replication occurs in the ___
DNA replication takes place as a ____ and a ______
A _____ is needed to initiate synthesis of DNA strand
______ bubbles form after initiation of DNA synthesis along one template strand.
DNA replication begins at specific regions of ______
Many proteins assist DNA replication
DNA associates with _____ to form nucleosomes soon after its synthesis
semiconservative specific time bidirectional and discontinuous 5'-3’ direction continuous leading strand, discontinuous lagging strand. primer Bidirectional replication chromosomes.
histones
- DNA replication is a semiconservative process because when a new double stranded DNA molecule is formed, one strand will be from the original template molecule and one strand will be newly synthesized.
- This occurs because each nitrogenous base can only pair with its complementary partner: Adenine (A) pairs with Thymine (T) and Cytosine(C) pairs with Guanine (G)
DNA replication occurs at a specific time.
- It occurs in the ____ of cell cycle, before mitosis and cell division. In ______, the cell synthesizes a complete copy of the DNA in its nucleus.
S phase
DNA replication is mostly bidirectional and discontinuous.
- At an origin of replication, two _______ are formed that are extended in two directions.
replication forks
A ______ is a structure that forms within the long helical DNA during DNA replication. It is created by helicases which break the hydrogen bonds holding the two DNA strands together in the helix. The resulting structure has two branching prongs, each one made up of an angle strand of DNA
replication fork
On the lagging strand, Okazaki fragments are formed in a _______.
discontinuous manner
are short sequences of DNA nucleotides which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication
Okazaki fragments
DNA replication occurs in the 5’-3’ direction.
- Why not 3’-5’? It’s because 3’ contains the ______ whereas 5’ contains the _____ group which nucleotides are not able to attach. So, DNA polymerase can only add nucleotides to the 3’ OH group of the growing DNA strand.
free hydroxyl group
phosphate
In the figure, we can see the leading strand that replicates ____ in direction of fork movement while lagging strand as we can see, replicates ______ in direction opposite to fork movement that’s why small fragments are formed, labeled in the middle, which is known as Okazaki fragments from 5’ to 3’
continuously
discontinuously
This means DNA polymerase alone can’t be able to replicate the DNA strand. It requires a _____ in order to initiate replication. ____ which is a primer is needed because it helps in the synthesis of Okazaki fragments
primer
Primase
_____ - where DNA replication is moving along in both directions from the starting point. This creates two replication forks, moving in opposite directions.
______ are created when the enzyme helicase separates the two strands of DNA so that they can be replicated.
Bidirectional replication
Bubbles
Many proteins assist DNA replication.
That means the various enzymes require further senses of the DNA replication. This includes DNA gyrase, helicase, primosome, primase, Single stranded binding protein (SSB protein), polymerase 3, Polymerase 1(DNA poly 1) and Ligase.
→ Initiation
o _____ - where DNA replication starts.
o _____ - an unwound and open region of DNA where DNA replication occurs. They are created when the enzyme helicase separates the two strands of DNA so that they can be replicated.
o ______ - the area where the replication of DNA will actually take place
• ____ - unwinds the strands of DNA for it to be replicated
Origin of Replication
Replication Bubble
Replication Fork
Helicase
→ Elongation
o ______ - lays down RNA primers which enable Type 3 DNA polymerase to carry out its function
Primase Enzyme
→ Elongation
o ______- function is to synthesize nucleotides from 5’ to 3’. In short it functions in the duplication of the chromosomal DNA. It also has a proofreading function which corrects any mistakes in the duplication process.
• _____ - needs only one RNA primer, replicated continuously
• _____ - needs multiple RNA primers, replicated discontinuously
DNA polymerase 3
Leading strand
Lagging Strand
→ Elongation
o _____ - fill DNA gaps that arise during DNA replication, repair, and recombination
DNA Polymerase 1
→ Elongation
o ____- fuse the DNA ends together in the Lagging strand
Ligase
→ Elongation
It forms a single lagging strand by attaching (with DNA ligase) multiple Okazaki fragments. And then each of them grows away from the replication fork, until they meet up.
Unfortunately, DNA polymerase can’t join two Okazaki fragments, so they’re joined together by another enzyme, DNA ligase, which results in a finished strand of DNA called the lagging strand.
→ Termination
o DNA polymerase leaves strand at _____ (_____ nucleotide sequences)
o _____: maximum number of times cell’s DNA can be replicated
- Due to repeated shortening of telomeres during termination step
telomere (TTAGGG)
Hayflick limit
Telomere: At the end of the chromosome is a region of DNA where there are repeating sequences of TTAGGG nucleotides. The DNA sequence in the ____ signals the DNA polymerase to hop off of the strand right before replicating the DNA right up to the very end.
The result is that each time the DNA strand is replicated, the new strand is just slightly _____ than the template strand because a bit of the telomere itself is lost.
telomere
shorter
Stages of DNA replication
Initiation
Elongation
Termination
In Prokaryotes
o ______: is the major replicative polymerase, functioning in the synthesis of both the leading strand of DNA and lagging strand.
o ______: then removes RNA primers and fills the gaps between Okazaki fragments.
Polymerase III
Polymerase I
→ In Eukaryotes
o ______: Synthesize lagging strand
o _______: Fills up the gaps left by removal of primers
o _______: Synthesize leading strand
o _______: Complete lagging strand in telomere regions of chromosomes.
DNA polymerase α
DNA polymerase β
DNA polymerase theta
DNA Telomerase
Replication Proteins:
→ Helicase and Single-Strand DNA Binding Proteins
_____is the enzyme that harnesses the chemical energy from the ATP hydrolysis to separate the two DNA strands at the replication fork
When the two strands are separated, _______ bind selectively to single-stranded DNA as soon as it forms.
This also allows enzymes to attach to the newly opened single strand and initiate elongation. SSBs are removed as DNA synthesis proceeds.
Helicase
single-strand DNA binding proteins (SSBs)
______ fights positive supercoils by putting negative supercoils ahead of the replication fork. Thus, the torsional strain is released, and replication can continue.
DNA gyrase (Type II topoisomerase)
_____ is responsible for copying a short stretch of the DNA template strand to produce the RNA primer sequence
The use of RNA primer for DNA replication is common to all _____.
Primase
prokaryotes
Normally, the polymerase-α subunit-primase complex synthesizes a stretch of 10–30 nucleotides of RNA. Subsequently, α -catalytic subunit continues to synthesize a short stretch of DNA before the DNA polymerase takes over the replication process. This phenomenon is called ______
polymerase switching.
Once the replication is initiated, the synthesis of the new DNA strand is directed by one of the polymerases, ______
DNA polymerase III.
As the replication fork moves, the RNA primer is removed and is replaced by newly formed _____. These reactions are performed by DNA polymerase I’s exonuclease activity and polymerization activity which is called _____
deoxynucleotides
Okazaki maturation process.
o Just after RNA removal, DNA polymerase I uses its polymerase activity to fill in the gap left by the RNA with new DNA.
o When it reaches the beginning of the next DNA segment, the DNA polymerase cannot seal the final nick in the DNA backbone that remains.
o Finally, ______ is the enzyme responsible for sealing the nick between the new strands synthesized by polymerase III and polymerase I.
DNA ligase
It is essential that the ___________ be as high as possible to prevent mutations, which are errors in replication and can lead to diseases. A major function of replicative DNA polymerases is to replicate DNA with very high accuracy. The fidelity of DNA replication relies on proofreading mechanism & polymerase exonuclease activity which are a single strand repair mechanism.
fidelity & accuracy of the replication process
Proofreading Mechanism – ____
Proofreading polymerases have several checkpoints to prevent incorrect nucleotide incorporation during the DNA ___ process.
DNA Polymerase III
extension
Polymerase Exonuclease Activity – ______
DNA Polymerase I
Proofreading Mechanism – DNA Polymerase III
If an incorrect base does bind to the active site, incorporation is _____, increasing the opportunity for the incorrect nucleotide to dissociate and a correct nucleotide to bind.
→ Alternatively, if an incorrect nucleotide is incorporated the proofreading polymerase detects the perturbation caused by the wrong paired bases and shifts the three-prime end of the growing strand to the polymerases proofreading exonuclease active site domain where the 3’-to- 5’ prime exonuclease activity removes the wrong paired base.
→ With the wrong paired base polymerase shifts the strand back into the polymerase domain and continues adding bases and extending the DNA.
slowed
Polymerase Exonuclease Activity – DNA Polymerase I
- If one or more bases have been damaged by an external agent, or if a mismatch was missed by the proofreading activity, _____can use its nick translation process to repair such DNA mistakes as it moves along the DNA. This polymerase removes RNA Primer in 5’-to- 3’ prime directions.
→ First, a distortion in the DNA helix is recognized, and the region containing the distortion is removed.
→ The gap in the damaged strand is replaced by the action of a DNA polymerase that uses the intact, undamaged strand as a template, and synthesizes DNA in the 5′-to-3′ direction.
→ Finally, a _____ seals the nick in the strand that has undergone repair.
polymerase I
ligase
There are three alternative models of DNA replication
Conservative model
Semiconservative model
Dispersive model
In the ______model, the two parental strands of DNA rejoin, after acting as templates for the new DNA strands.
This means the parental double helix is restored.
The _____ would yield one helix of new DNA and one helix of the original DNA.
conservative model
In the _______, the two strands of the parental molecule separate, and each strand functions as a template for synthesis of a new, complementary strand.
semiconservative model
In the________model, each strand of both daughter molecules contains a mixture of the original DNA, and the newly synthesized DNA.
dispersive
The _______ of DNA replication is the correct model, because each daughter DNA molecule consists of one parental strand and one new strand.
semiconservative model
A _______ of DNA replication illustrates how the two strands of the parental DNA molecule separate, and how each strand functions as a template for synthesis of a new, complementary strand.
semiconservative model
DNA replication can be described as _____. This means that each strand of the double helix acts as a template, based on which a new, complementary strand will form. Eventually the original chromosome will split into two exact copies, each made of one of the original strands, and one of the newly made ones.
semiconservative
Replication Pattern
→ Bidirectional Replication - most eukaryotic and bacterial or prokaryotic DNAs replicate ______.
o ______cells - have many replicons and they begin simultaneously
o _____ cells - have only one replicon
bidirectionally
Eukaryotic
Prokaryotic
_____ - common bacterial DNA replication
Rolling Circle Replication
Termination of Replication
o _____ - occurs when two replication forks moving away from the single origin of replication meet on the opposite side of the circle in the circular chromosome of bacteria.
o _____ - termination is completed at multiple points since it has multiple origins.
• During the elongation, the two replication forks from different replication bubbles will meet in the same way as the two bacterial forks.
Prokaryotes
Eukaryotes
→ Replication at the Telomere
o Eukaryotic chromosomes end in distinctive sequences called ______ that help preserve the integrity and stability of the chromosome.
o During the replication, the ____ on the leading strand template may proceed to the end.
o Results in net telomere elongation and allows telomeres to be maintained around an equilibrium length
telomeres
50 to 30 syntheses
→ Mitochondrial Replication
o ______ must be duplicated during the cell cycle and segregated to the daughter cells. The process at each stage of mitochondria duplication is governed by a ______ of each copy.
o Mitochondria divide by developing a ring around the organelle that constricts to pinch it into two halves.
o The distribution of mitochondrial genomes to daughter mitochondria does __ depend on their parental origins
Mitochondria
random distribution
not
DNA repair pathway disruption, it affects the pathway by the interstrand crosslink. During DNA Replication, interstrand crosslinks block cell division by keeping together the two strands that makeup DNA, In. The repression of Cell Division results in the Death of hematopoietic cells by apoptosis. It is hard to repair since it presents biallelic mutations that alter the correct function
Fanconi Anemia
____mutation means it affects both the maternal and paternal copy of the same gene, both have defected/mutated copies of the particular allele.
Biallelic
Is due to a mutation in a gene whose product is involved in nucleotide excision repair. People suffering from this disorder are extremely prone to UV-induced skin cancers as a result of exposure to sunlight and other diseases due to repair defects.
Xeroderma pigmentosum
