Nucleic Acids

What are purines and which nucleotides are classified as purines in DNA?

A purine is a type of nitrogen-containing molecule that forms a part of the nucleotides in DNA. Adenine (A) and Guanine (G) are the two nucleotides classified as purines in DNA.

Which nucleotides in DNA are classified as pyrimidines?

Pyrimidines are a type of nitrogen-containing molecule that forms a part of the nucleotides in DNA. Thymine (T) and Cytosine (C) are the two nucleotides classified as pyrimidines in DNA.

What is satellite DNA and how much of the genome does it make up?

Satellite DNA is a type of highly repetitive sequence that is found in DNA. It makes up 5-45% of the genome.

What is meant by the term "junk DNA"?

The term "junk DNA" refers to the large portions of DNA that were once thought to have no function or purpose.

What are introns and how do they relate to DNA?

Introns are non-coding segments of DNA that interrupt the coding regions of a gene. They are transcribed into RNA but are spliced out before the final mRNA is produced.

What are exons and how do they relate to DNA?

Exons are the coding segments of DNA that are transcribed into RNA and translated into proteins. They make up only a small fraction of the total DNA in the genome.

What is DNA replication and why is it important?

DNA replication is the process by which a cell makes an exact copy of its DNA. It is important because it ensures that the genetic information is passed down accurately from one generation of cells to the next.

What was the purpose of the Hershey-Chase Experiment?

To investigate whether genes were made of protein or DNA.

Which virus was used in the Hershey-Chase Experiment?

T2 bacteriophage.

What is the composition of T2 bacteriophage?

T2 bacteriophage consists of a DNA molecule surrounded by a protein coat.

What was the role of radioactive 32P in the experiment?

Radioactive 32P was used to label the DNA in one of the strains of T2.

What was the role of radioactive 35S in the experiment?

Radioactive 35S was used to label the protein in one of the strains of T2.

How did Hershey and Chase follow the T2 while they infected E. coli?

Hershey and Chase mixed the T2 with E. coli and then centrifuged the mixture.

What was found in the solid pellet after centrifugation?

The solid pellet contained the bacteria.

What was found in the liquid supernatant after centrifugation?

The liquid supernatant contained the T2 virus and any remaining protein.

What was the significance of the high proportion of radioactive 32P found in the pellet?

The high proportion of radioactive 32P found in the pellet provided strong evidence that genes are composed of DNA rather than protein.

Where did some of the 35S come from in the experiment?

Some of the 35S came from protein coats still stuck to the bacterial cell walls.

What is the method developed by Maurice Wilkins for producing DNA arrays?

Maurice Wilkins developed a method for producing DNA arrays, an orderly arrangement.

What did Rosalind Franklin develop for producing clear diffraction patterns from DNA?

Rosalind Franklin developed a high resolution detector for producing clear diffraction patterns from DNA.

How are particles arranged in a crystal sample?

Particles in a crystal sample are arranged in regular repeating patterns.

What happens when a beam of X-ray passes through a crystal sample?

When a beam of X-ray passes through a crystal sample, some of it is scattered by the particles in the material.

How can the pattern of scattering in a crystal sample be investigated?

The pattern of scattering in a crystal sample can be investigated by rotating the sample in three different dimensions.

What was used to record diffraction patterns in the X-ray crystallography experiment?

Diffraction patterns were recorded using X-ray films.

What deductions were made about the structure of DNA from the diffraction pattern obtained in the X-ray crystallography experiment?

From the diffraction pattern obtained, it was deduced that the DNA molecule is helical in shape and the distance between the turns of the helix is 3.4 nm apart.

What is a nucleosome?

A nucleosome consists of a DNA molecule wrapped around 8 histone proteins.

How is DNA associated with proteins in eukaryotes?

DNA in eukaryotes are associated with proteins.

What is the structure of a nucleosome?

A nucleosome consists of a DNA molecule wrapped around 8 histone proteins, with DNA wrapping twice around the histone protein core.

What is the role of H1 in a nucleosome?

Another histone protein called H1 binds to the outside of the DNA strand in a nucleosome.

How does DNA wrap around histone proteins in a nucleosome?

The DNA can be wrapped around these histone proteins due to DNA being negatively charged which attracts to the positive charge of the histone proteins.

What are the N-terminal tails of histone proteins?

The histone proteins in the core have N-terminal tails sticking outwards from the nucleosomes.

What happens to nucleosomes during mitosis and meiosis?

The tails of neighboring histones link up during condensation of chromosomes, causing the nucleosomes to pull closer together. This occurs during mitosis and meiosis and is known as supercoiling.

How is transcription regulated by supercoiling?

Supercoiling in general helps regulate transcription because only certain areas of the DNA are accessible for the production of mRNA by transcription.

What happens to N-terminal tails during interphase?

During interphase, N-terminal tails are blocked off with methyl caps (NH3 groups) to allow the DNA to decompose (uncoil); H1 also detaches to loosen DNA.

What is the appearance of DNA during uncoiling?

During uncoiling, it gives the entire DNA the appearance of a 'string of beads'.

What is the structure of DNA?

DNA is a double-stranded molecule formed in the shape of a double helix. Each strand is composed of a backbone of nucleotides.

What is a nucleotide?

A nucleotide is a molecule containing a 5-carbon sugar called the deoxyribose, a phosphate group, and a nitrogenous base.

How is a nucleotide composed?

The phosphate group is covalently bonded to the 5' carbon of the sugar and the nitrogenous base is covalently bonded to the 1' carbon of the sugar.

How are nucleotides held together?

Nucleotides are held together by a covalent bond called a phosphodiester bond between the phosphate group of one nucleotide and the 3' carbon of the sugar of the next nucleotide, which produces a backbone of alternating phosphate and deoxyribose molecules (also known as the sugar-phosphate backbone).

What is the process that links the nucleotides to one another?

Condensation reaction links the nucleotides to one another.

How do DNA strands run in relation to each other?

DNA strands run antiparallel to each other with one strand running in a 5' to 3' direction and the other strand running 3' to 5' when looking at the strands in the same direction.

How are the two sugar-phosphate backbones held together?

The two sugar-phosphate backbones are held together by hydrogen bonds between their nitrogenous bases.

What are the four types of nitrogenous bases found in DNA?

There are four types of nitrogenous bases: Adenine (A), Thymine (T), Cytosine (C), and Guanine (G).

What are the characteristics of purines in DNA?

Adenine and Guanine have two rings in their structures and are referred to as purines.

What are the characteristics of pyrimidines in DNA?

Cytosine and Thymine have one ring in their structures and are referred to as pyrimidines.

What is the base pairing rule in DNA?

Adenine from one of the strands always forms two hydrogen bonds with Thymine from the other strand. Similarly, cytosine from one backbone always forms three hydrogen bonds with guanine from another backbone. This is referred to as complimentary base pairing as the link between the bases are very specific.

DNA replication process?

DNA replication occurs at many different places/ regions on the DNA strand called the origins of replication. The DNA strand is unwound and the 2 strands are separated by an enzyme called helicase. This is accomplished by breaking the hydrogen bonds between the base pairs. DNA gyrase relieves strain of the strand as it is unwound by the helicase. Single-stranded binding proteins bind to the open strands and keep the strands apart long enough to prevent the strands from recoiling before the strands are copied. DNA replication begins at the different origins in the 5' to 3' direction at the replication fork. Each of the 2 separated strands act as template for building the new DNA strands.

There are free nucleotides present inside the nucleus of the cell. DNA polymerase III adds free nucleotides found in the nucleus in the 5' to 3' direction in the direction of the replication fork. These nucleotides when added are actually deoxynucleoside triphosphates (dNTP), which means the nucleotide contains 3 connection phosphate groups. As dNTP's are added, two phosphates are lost and the energy released is used to bind the nucleotides together on the growing strand. This strand is called the leading strand because replication is continuous on this strand.

DNA replication on lagging strand?

Because DNA polymerase III can only add nucleotides in the 5' to 3' direction, the other strand is replicated in the opposite direction. This strand is called the lagging strand to allow replication in the opposite direction to the leading strand. Replication in this direction is discontinuous. The lagging strand is therefore made as a series of fragments called Okazaki fragments. DNA primase adds a small primer on the lagging strand of DNA. DNA polymerase III adds nucleotides again in the 5' to 3' direction which is in the opposite direction of the leading strand because the stands are antiparallel. After the fragment is created, DNA polymerase I replaces the RNA primer with DNA. As the strand continues to open, a new RNA primer is added and a new fragment of DNA is created away from the replication fork. As these fragments are made, little gaps are created between the fragments. DNA ligase finally forms a covalent bond between 3' OH on the growing strand and the 5' phosphate on the next fragment and seals the spaces between the phosphates and the sugars.

What are DNA Base Sequences?

DNA Base Sequences are the sequence of nucleotide bases, which make up DNA.

What is the function of coding sequences in DNA?

The coding sequences in DNA contain the genetic information that is used to create polypeptides during transcription and translation.

What are non-coding sequences in DNA?

Non-coding sequences in DNA do not code for proteins but have other important functions.

What is the function of enhancers in DNA?

Enhancers are short DNA sequences that regulatory proteins bind to, to activate transcription.

What are repressors in DNA and what is their function?

Repressors are DNA sequences that bind regulatory proteins, which prevent RNA polymerase from binding to the promoter site and, thereby, prevent transcription.

What are introns in DNA?

Introns are the non-coding regions of mRNA that are coded for by DNA in eukaryotes, and they are removed before the mRNA leaves the nucleus.

What are telomeres in DNA and what is their function?

Telomeres are repetitive sequences present at the end of chromosomes that protect the DNA during replication.

What are tRNA and rRNA, and how are they produced?

tRNA and rRNA are specific types of RNA molecules used in protein synthesis, and their production is mediated by specific sequences of DNA.

What is Sanger Sequencing?

Sanger Sequencing is a method used for determining the sequence of bases in an unknown DNA fragment.

How does Sanger Sequencing work?

DNA replication is allowed to happen with normal bases and a small amount of "dideo" base (missing OH on carbon atom 3 so additional nucleotides cannot connect) 'A'. Fragments of different lengths are produced whenever a dideo "A" base is reached. The process is repeated with "dideo" bases of each remaining type to create different fragments. The data is pieced together using gel electrophoresis and automated 'dye' analysis to determine the sequence.

What are Tandem Repeats?

Tandem Repeats are sequences of DNA with repeating patterns found in human (and other species) genomes.

What is the length of Tandem Repeats?

The repeats can be 2 to 60 or more bases.

Why are Tandem Repeats useful for DNA profiling?

The number of repeats varies between individuals (no two individuals are likely to have the exact same repeats), which creates a variable number of tandem repeats. This feature is used for DNA profiling (DNA fingerprinting) in forensic science and paternity tests.

What is the process of formation of mRNA from DNA called?

Transcription.

Where does transcription occur in eukaryotic cells?

Transcription occurs in the nucleus.

What is the specific sequence of DNA that RNA polymerase responds to called in prokaryotic cells?

The promoter.

What does the promoter signal RNA polymerase to do during transcription?

It signals RNA polymerase where to begin the transcription process.

What is the first step of transcription initiated by?

It is initiated by the binding of RNA polymerase to the promoter site.

What does RNA polymerase do during transcription to separate the two strands of DNA?

It uncoils the DNA and creates a transcription bubble.

Which strand does mRNA resemble after transcription is finished?

It resembles the sense strand.

Which strand of DNA acts as the template strand for transcription?

Only one of the strands acts as the template strand (anti-sense strand).

Are free RNA nucleoside triphosphates present in the nucleus during transcription?

Yes, they are present in the nucleus.

In which direction does the RNA polymerase use free nucleoside triphosphates to build mRNA?

It builds mRNA in a 5'→3' direction.

What do the free nucleoside triphosphates bond to during transcription?

They bond to their complementary base pairs on the template strand (except that U binds to A).

What do the nucleoside triphosphates become as they bind to the template strand during transcription?

They become nucleotides by losing two phosphate groups and release energy.

What pairs with adenine in RNA during transcription?

Uracil pairs up with adenine instead of thymine.

What type of bonds does RNA polymerase create between nucleotides during transcription?

It creates covalent bonds (phosphodiester bonds) between these nucleotides.

What happens to the RNA polymerase during transcription when it reaches a sequence of DNA called the terminator?

It stops transcription when it reaches the terminator.

What happens to the newly created mRNA after the RNA polymerase is released from the DNA during transcription?

The newly created mRNA separates from the template DNA strand.

Is transcribed RNA modified before leaving the nucleus?

Yes, it is modified (introns removed).

Where does the newly synthesized mRNA strand go after leaving the nucleus?

It enters the cytoplasm.

What happens to the DNA after transcription is complete?

The DNA rewinds back to its original double helical structure.

What is a promoter?

A DNA sequence that initiates the process of transcription.

Is the promoter region transcribed?

No, it is an example of non-coding DNA that plays a role in gene expression.

Where is the promoter sequence located?

Near the starting site of transcription.

What is the function of RNA polymerase in transcription?

It binds to the promoter in order for transcription to take place.

What is the role of repressor proteins in transcription?

Repressor proteins can bind to the promoter to prevent transcription.

How do transcription factors affect transcription in eukaryotes?

Extra proteins called transcription factors need to bind first to the promoter, then RNA polymerase can bind.

Are transcription factors always sufficient to initiate transcription?

No, oftentimes several of these are needed and may need to be activated themselves before they can bind.

What is the sense strand in DNA?

The sense strand is the DNA strand which has the same base sequence as the newly synthesized mRNA strand with thymine instead of uracil.

What is the role of the sense strand in transcription?

The sense strand does not take part in transcription and acts as a non-template strand.

What is the antisense strand in DNA?

The antisense strand is the template DNA strand which is transcribed.

What is the base sequence of the antisense strand in DNA?

The base sequence of the antisense strand in DNA is complementary to that of the mRNA strand.

What is gene expression?

Gene expression is the process by which genetic information is used to synthesize proteins, involving transcription of a gene to produce mRNA, followed by translation of the mRNA to produce polypeptides.

How is gene expression regulated?

Gene expression is regulated by specific proteins that bind to DNA sequences, including enhancers, silencers, and promoter elements. Environmental factors such as temperature and light can also affect gene expression.

What are enhancers and silencers?

Enhancers and silencers are regulatory proteins that can increase or decrease the amount of transcription of a particular gene, respectively.

Are regulatory proteins unique to a particular gene?

Yes, regulatory proteins that bind to specific DNA sequences to regulate gene expression are unique to a particular gene.

How does gene expression differ between prokaryotes and eukaryotes?

In prokaryotes, translation can begin immediately after transcription, while in eukaryotes, transcription occurs in the nucleus, mRNA is modified before exiting through nuclear pores into the cytoplasm, and then translated in the cytoplasm.

What are some external conditions that can affect gene expression?

Some external conditions that can affect gene expression in certain organisms include temperature and light.

How can the internal environment of an organism impact gene expression?

The internal environment of an organism, including factors such as its hormones and metabolism, can impact gene expression.