Nucleic Acids Flashcards
What is DNA?
genetic material that is contained in the chromosomes of the nucleus.
What does DNA consists of?
- two polynucleotide strands paired together and held by hydrogen bonds between the nitrogenous bases
- pairing bases: A and T, C and G (complementary pairing)
- nucleotides are joined by covalent bonds
State the definition of nucleotides
Repeating units linked together to form chains or strands.
What nucleotides contain?
- nitrogenous base (cytosine, guanine, adenine, thymine)
- sugar - deoxyribose (DNA) and ribose (DNA)
- phosphate
How to differentiate between the deoxyribose and ribose?
Ribose has hydroxyl (OH) group at position 2. However, Deoxyribose has hydrogen atom (H) at the same position.
What are pyrimidines in DNA?
types of base pairs
Explain the DNA replication
It is the duplication of DNA by making a copy of an existing molecule (interphase). It leads to creation of two molecules of DNA
- one composed of original strand
- the second one is newly synthesized strand (semi-conservative strand)
What are the models of DNA replication
- conservative
- semi-conservative
- dispersive model
Explain the semi-conservative model
two parental strands separate an each functions as the template of a new complementary strand.
Explain the conservative model of DNA replication
parental double helix remains intact (unbroken) and new copy is made.
Explain the dispersive model of DNA replication
each strand contains a mixture of old and newly synthesized parts.
What is the process of DNA replication?
- Unwinding the DNA molecule- hydrogen bonds holding the strands have to be broken. Helicase is the enzyme that holds strands apart while replication occurs.
- Creating the new DNA strands involves the activity of an enzyme known as DNA polymerase. Fresh nucleotides containing complementary bases align themselves opposite the exposed bases of the strands. DNA polymerase then forms covalent bonds, linking the phosphate of the new nucleotide to the sugar of the preceding nucleotide.
- Rewinding the DNA molecule- each of new double-helix. DNA molecules have one strand of the original DNA and new strand. Two DNA strands wind up into double helix.
What are Okazaki fragments?
small sections of DNA that are formed during the synthesis of the lagging strand during DNA replication.
What is the function of RNA primer?
added by DNA primase to synthesize the new strands of DNA
What are topoisomerases?
enzymes that regulate the overwinding or underwinding of DNA. for example gyrase
What is the function of DNA polymerase I?
filling the DNA gaps that arise during DNA replication.
What is the function of the DNA polymerase III?
binding nucleotides together and forming a new strand
The function of ligase
Joining DNA molecules together
define transcription
the genetic information of DNA is transcribed into a molecule of mRNA by complementary base pairing.
Define translation
Process of protein production using mRNA molecule as a guide.
Define central dogma
states that information passes from genes on the DNA to RNA copy
Steps of transcription
- After DNA polymerase binds to the promoter of the DNA, DNA strands unwind and polymerase initiates RNA synthesis at the start point.
- Initiation- DNA is unwinded and RNA transcript 5’ -> 3’ is elongated. DNA strands re-form a double helix.
- Termination- the RNA transcript is released and polymerase detaches from DNA.
What is the difference between the antisense strand and sense strand of DNA?
- antisense strand is the non-coding DNA strand of a gene. it serves as the template for producing messenger RNA
- sense strand is the one coding of mRNA, the strand will be synthesized with this strand as the template.
What is the post-transcriptional modification?
It helps the RNA molecule to be recognized by molecules that take part in the translation into proteins.
Steps of the post-transcriptional modification (nucleus)?
- When a split gene is transcribed into mRNA, newly formed mRNA contains sequences of introns and exons.
- Introns are removed and the remaining coding portions of mRNA are spliced together.
- The mRNA passes out into cytoplasm to ribosomes where it is involved in protein synthesis.
Difference between the exons and introns
exons carry genetic information but introns are the units of non-coding sequences, so they do not carry any genetic information.
How are amino acids activated?
They are combined with short lengths of different tRNA molecules involved in the protein synthesis. tRNA catalyzes an ATP- requiring reaction.
The process of translation
- Anticodon (tRNA) pairs with mRNA codon in the A site. Hydrolysis of GTP increases efficiently.
- tRNA calalyzes the formation of peptide bonds. This step removes the polypeptide from tRNA in the P site to tRNA in A site.
- tRNA is translocated to P site and tRNA in P site is moved to E site, where it is released.Next codon can be translated in A site.
What happens in the A site?
It carries/holds tRNA carrying the amino acids.
The function of P site
It holds the tRNA with the polypeptide chain
The function of E site
releases the protein (tRNA with polypeptide chain)
Describe the function of ribosomes in the translation
- site of protein synthesis
- several ribosomes move along the mRNA at one time
What is the pylosome?
mRNA + ribosomes + growing protein chains
Define nucleic acids
Information molecules of cells found throughout the living world. We include RNA and DNA
How the components of nucleotides are combined?
through the condensation reaction with the formation of two molecules of water.
What is the DNA of prokaryotes?
- Found in the nucleoid region
- Single circular chromosome
- Naked DNA
- Lack of histones
- Contains plasmids
- Replicated through binary fission
DNA in eukaryotes
- Enclosed within a membrane-bound nucleus
- Linear chromosomes, typically multiple, organized with histone proteins into chromatin
- Replicated during the S phase of the cell cycle
What the protein does in the DNA in eukaryotes?
it helps to supercoil the DNA to package up the chromatin.
Nucleosome
globular structure that consists of the molecule of DNA wrapped around a core of eight histone proteins.
Function of nucleosomes
helps to supercoil the chromosomes and help to regulate the transcription
What does nucleosome consists of?
- histone tails
- amino acids
- DNA
How the packaging of DNA looks like?
- DNA double helix is wrapped around histones to form nucleosomes
- the whole thread is coiled up which forms the chromatin fiber
- then the chromatin fiber is again coiled, and the coiles are looped around the non-histone proteins
- the whole structure is folded (supercoiled) into much condensated metaphase chromosome
Types of DNA sequences
Repetitive sequences
Structural DNA
Protein-coding genes
What are highly repetitive sequences
- they do not have coding functions
- dispersed region of the repetitive DNA
What is the structural DNA?
highly coiled DNA that does not have a coding function
- occurs around the centromere
What are protein-coding genes?
- they provide the base sequence essential to produce proteins
What are non-coding DNA types?
- satellite DNA
- telomeres
- introns
- non-coding RNA genes
- gene regulatory sequences
Telomeres
regions of repetitive DNA at the end of the chromosome
Non-coding RNA genes
Codes for RNA molecules that are not translated into protein
Gene regulatory sequences
involved in transcription and include the promoters of DNA
What established the unique importance of DNA as genetic material?
experiment with a bacteriophage virus
Steps of replication of the phage
Bacterial phage attaches to the bacterial wall and then injects the virus DNA. Virus DNA takes over the host’s synthesis process. New viruses are assembled and then escape to repeat the infection cycle.
What was the Martha Chase and Alfred Hershey experiment?
They used a bacteriophage that parasites the bacterium E. Coli to find out if the genetic information lies in the protein (coat) or the DNA (core).
Explain the steps of Martha Chase and Alfred Hershey experiment
FIRST BATCH: phages with radioactive sulfur - phage protein
SECOND BATCH: phages with radioactive DNA-phage DNA
1. Mixed radioactively labeled phages with bacteria. The phages infected the bacterial cells.
2. Mixed the mixture in a blender to free phage parts outside the bacteria from cells.
3. Centrifuged the mixture so that bacteria formed a pellet (bacterial contents) at the bottom of the test tube. Lighter parts remained in the liquid.
4. Measured the radioactivity of the pellet and the liquid.
What were the results of the Martha Chase and Alfred Hershey experiment?
Phage DNA entered the bacterial cells but phage proteins did not. Hershey and Chase concluded that DNA, not protein, functions as the genetic material of the phage.
DNA replication takes place where?
interphase
Contents of interphase and their functions
- first phase of growth (G1) - cytoplasm active, new organelles are formed, preparation for phase S
- synthesis of DNA (S) - chromosomes are copied as well as histone proteins
- second phase of growth (G2) - more growth of cell and preparation for mitosis
Explain the Meselson and Stahl experiment
- First step: Dna contains nitrogen atoms (bases). First grew E.coli cells in heavy nitrogen (15N). When cells are centrifuged, the DNA will show up heavy.
- Second step: Transferred E.Coli cells into a medium with light nitrogen (14N). Cells were allowed one round of replication. Then they were centrifuged.
THE SEMI-CONSERVATIVE DNA AND DISPERSIVE DNA HAVE SHOWED UP - Third step: Cells were allowed to grow for a second round of replication in the (14N) and they were centrifuged once again.
THE THE SEMI-CONSERVATIVE DNA HAS SHOWED UP
What was the conclusion of the Meselson and Stahl experiment
DNA replicated semi-conservatively, meaning that each strand in DNA molecule serves as a template for synthesis of new complementary strand.
In what direction DNA replication occurs?
5’ -> 3’ direction
What are dideoxynucleotides?
lack the 3’- hydroxyl group necessary for forming a phosphodiester bond. It prevents the elongation of nucleotide chain and terminates replication (blocks it).
What is the sequence of three bases on the mRNA called?
codon
What is the degenerative code?
amino acids have two or three similar codons that code for them.
What is the formation of tRNA?
- aminoacyl - tRNA synthetase catalyzes an ATP- requiring reaction
- carboxyl group of amino acid becomes attached to the 3 end of tRNA
- aminoacyl-tRNA is released
Why transcription needs to be regulated?
to prevent production of unwanted proteins or enzymes and to prevent the energy and amino acids being used up unnecessarily.
What are the 3 methods of regulation of transcription?
- nucleosomes
- regulatory proteins called transcription factors
- methylation of DNA
Explain the regulation of transcription by nucleosomes
- acetylation of nucleosomes - adding the acetyl group to the tail which neutralizes the charge, making the DNA less tightly coiled and increasing transcription
- methylation of nucleosomes- adding methyl group to the tail to maintain the positive charge, making the DNA more coiled and reducing transcription
where methylation and acetylation of histone proteins take place?
- methylation: heterochromatin
- acetylation: eurochromatin
State the definition of epigenetics
It is the study of changes in the phenotypes as the result of variations in gene expression levels. It shows that DNA methylation may change over time. Environmental factors such as diet, pathogen exposure can influence the level of DNA methylation.
What are the epigenetic tags?
the chemical modifications of chromatin such as acetylation and methylation and DNA methylation
Epigenome
sum of all epigenetic tags
What are the transcription factors?
They are needed to initiate transcription. They bind to the enhancer region and cause the promoter to come together with enhancer -> starts transcription.
What is the asymmetric segregation of cellular determinants?
cells divide unequally, distributing specific molecules unevenly between daughter cells, influencing their function.
Differences between the prokaryotic and eukaryotic transcription
- coupled transcription and translation in prokaryotes
- occurs in the cytoplasm in prokaryotes, and in nucleus in eukaryotes
- RNAs processed in cytoplasm in prokaryotes and in nucleus in eukaryotes
Explain the Griffith’s Experiment
- involved the use of two strains of a deadly virulent strain (S) and non-virulent strain (R)
- Griffith infected mice with the non-virulent bacteria and the mice survived
- then he infected mice with virulent bacteria, the mice died
- Griffith then infected mice with heat-killed virulent bacteria and the mice survived but the bacteria was killed
- but when he infected th mice with a mix of heat-killed bacteria (S) and living bacteria (R), the mice died
- result: development of vaccine against the pneumonia
DNA sequencing
DNA sequencing is the process of determining the order of nucleotides in a DNA molecule.
Steps of DNA sequencing
- Obtaining DNA from a biological sample.
- Breaking DNA into smaller pieces.
- Determining the sequence of nucleotides in each fragment.
- Aligning and assembling sequences to reconstruct the original DNA sequence.
- Analyzing the sequence for genetic information or variations.
How DNA sequencing regulates the transcription?
DNA sequencing identifies regulatory elements and transcription start sites.
