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Nucleic Acids: DNA and RNA - Comprehensive Study Notes
Structure of the Nucleus
Found in both plant and animal cells.
Typically located in the center of animal cells.
In plant cells, it is usually pushed to the side due to the large vacuole.
The vacuole can occupy up to 30-80% of the cell volume in mature plant cells, exerting pressure on the nucleus.
Components of the Nucleus
Nuclear Membrane (Nuclear Envelope): A double membrane surrounding the nucleus, connected to the endoplasmic reticulum. Contains pores. The nuclear membrane is composed of an inner and outer lipid bilayer, and the space between them is called the perinuclear space. This membrane controls the movement of substances into and out of the nucleus.
Nuclear pores are large protein complexes that span both the inner and outer nuclear membranes, regulating the traffic of molecules between the nucleus and the cytoplasm.
Nucleoplasm (Nuclear Sap): The ground substance inside the nuclear envelope. It is a gel-like matrix comprising water, ions, enzymes, nucleotides, and chromatin.
The nucleoplasm provides a medium for biochemical reactions necessary for the maintenance and function of the nucleus.
Nucleolus: Located within the nucleoplasm; responsible for making and containing RNA. The nucleolus is a non-membrane bound structure mainly involved in the assembly of ribosomes. It is made up of proteins and RNA.
The nucleolus organizes the synthesis of ribosomal RNA (rRNA) and the assembly of ribosomes, which are essential for protein synthesis.
Chromatin Network: A tangled mass of thread-like structures. Each thread-like structure is a chromosome, composed of two chromatids held together by a centromere. Contains sections of DNA called genes. Chromatin is the complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells.
During cell division, chromatin condenses into chromosomes to ensure accurate segregation of genetic material.
Function of the Nucleus
Controls all cell activities. This is achieved through the regulation of gene expression.
The nucleus controls cell functions by regulating which genes are transcribed into RNA, which in turn directs protein synthesis.
DNA within the nucleus is responsible for protein formation. The sequence of nucleotides in DNA determines the sequence of amino acids in proteins.
The process of protein synthesis begins with transcription in the nucleus, where mRNA is synthesized from a DNA template.
Hormones and enzymes, which are proteins, control metabolic reactions. Enzymes catalyze biochemical reactions, while hormones regulate various physiological processes by interacting with specific receptors.
Enzymes lower the activation energy of biochemical reactions, accelerating the rate of these reactions in the cell.
Transmits hereditary characteristics from parent to offspring. During cell division, chromosomes (composed of DNA) are passed on to daughter cells, ensuring the inheritance of genetic traits.
Each chromosome contains genes that encode specific traits, ensuring the continuity of genetic information from one generation to the next.
Nucleic Acids
RNA and DNA are nucleic acids; organic molecules that control protein synthesis. Nucleic acids are essential for all known forms of life.
Nucleic acids store and transmit genetic information, playing a crucial role in heredity and cell function.
Composed of monomers called nucleotides.
Structure of a Nucleotide
Each nucleotide consists of three parts:
Phosphate (P)
Sugar (S)
Nitrogen base (NB)
Terminology
Nucleotides: Monomers or building blocks of nucleic acids. DNA nucleotides contain deoxyribose sugar, while RNA nucleotides contain ribose sugar.
Nucleotides are linked together through phosphodiester bonds to form polynucleotide chains, which make up DNA and RNA molecules.
DNA (Deoxyribonucleic Acid)
Types of DNA:
Nuclear/Chromosomal DNA
Mitochondrial DNA
Chloroplastic DNA
Location of DNA
Nuclear DNA: Found within the nucleus.
Extra-nuclear DNA: Found outside the nucleus.
Chloroplastic DNA: Extra-nuclear DNA in the chloroplast.
Mitochondrial DNA (mtDNA): Extra-nuclear DNA in the mitochondrion.
Terminology
Nuclear DNA: DNA found within the nucleus; contains hereditary information.
Extra-nuclear DNA: DNA found outside the nucleus; chloroplastic DNA is an example.
Discovery of DNA
James Watson and Francis Crick researched at the University of Cambridge, England.
Rosalind Franklin and Maurice Wilkins at King’s College London took an X-ray photograph of DNA in 1952.
Franklin hypothesized DNA had a helix shape.
Wilkins showed the photograph to Crick without permission.
On April 25, 1953, Watson and Crick formulated the double helix structure of DNA.
Further Discoveries
Watson and Crick discovered:
DNA has similar amounts of cytosine and guanine.
DNA has similar amounts of adenine and thymine.
This led to the concept of complementary base pairs. Complementary base pairing is fundamental to DNA replication and transcription.
A = T and G = C
This led to the idea that DNA can make exact copies of itself. DNA replication ensures the faithful transmission of genetic information during cell division.
Each strand serves as a template for creating a new, identical DNA molecule.
Later Events
In 1958, Rosalind Franklin died of cancer.
In 1962, Watson, Crick, and Wilkins received a Nobel Prize for their work.
Further research in the 1960s focused on DNA replication, RNA, and protein synthesis. These areas of research significantly advanced our understanding of molecular biology.
Researchers elucidated the mechanisms of transcription and translation, unraveling the central dogma of molecular biology.
DNA Structure
DNA is made of nucleotides.
Each nucleotide has:
Phosphate
Deoxyribose (sugar)
Nitrogen base
Nitrogen bases in DNA:
Adenine
Guanine
Cytosine
Thymine
Two types of nitrogen bases:
Purines (larger): Adenine, Guanine
Pyrimidines (smaller): Thymine, Cytosine
Nucleotide Bonding
Nucleotides connect: the sugar of one nucleotide bonds to the phosphate of another.
This forms a sugar-phosphate backbone. The sugar-phosphate backbone provides structural support to the DNA molecule.
These bonds create long, ladder-like strands.
Base Pairing
Nitrogen bases are held together by weak hydrogen bonds.
Specific base pairing:
Adenine pairs with Thymine (2 hydrogen bonds)
Guanine pairs with Cytosine (3 hydrogen bonds)
These pairs are complementary base pairs and are always in equal numbers.
Terminology
Complementary base pairs: Nitrogen bases that always pair with each other; adenine and thymine are an example.
Complementary base pairing ensures accurate replication and transcription of genetic information.
DNA Structure
The DNA molecule is double-stranded (like a ladder).
This "ladder" twists to form a double helix.
Terminology
Double Helix: Shape of the DNA molecule. DNA is made up of 2 strands of nucleotides that are joined together and then twists to form a double spiral shape.
The double helix structure provides stability and protection to the genetic information encoded in DNA.
DNA's Role – Genes
DNA carries hereditary information in genes.
A gene is a short segment of DNA with a specific base sequence.
DNA carries the genetic code for protein synthesis. The genetic code is a set of rules used by living cells to translate information encoded within genetic material into proteins.
This code determines the amino acid sequence and the protein that will be made. The order of amino acids dictates the structure and function of the protein.
DNA's Role - Non-Coding DNA
Only 2% of DNA codes for proteins.
The rest (98%) is non-coding DNA.
Non-coding DNA is different for each individual and is used in DNA profiling/ DNA finger printing. Non-coding DNA includes regions such as introns, regulatory sequences, and repetitive sequences.
Terminology
Gene: A small portion of DNA that carries genetic code for the formation of a particular trait or characteristic; can also carry the code for the formation of a protein.
Non-coding DNA: Portions of DNA that do not carry any codes.
Non-coding DNA can regulate gene expression.
Mitochondrial DNA (mtDNA)
mtDNA is not related to nuclear DNA.
It is shorter and circular.
mtDNA codes for enzymes that control respiration in the mitochondria. These enzymes are essential for the electron transport chain and ATP production.
mtDNA is inherited only from the mother. This is because the egg cell contributes the cytoplasm (and thus mitochondria) to the developing embryo, while the sperm cell contributes primarily nuclear DNA.
It is used to trace maternal lineages because it has few changes or mutations. The relatively slow mutation rate of mtDNA makes it useful in evolutionary studies and tracing ancestry.
Functions of Nuclear DNA
Controls the synthesis of proteins.
Transmits hereditary characteristics from parent to offspring.
RNA (Ribonucleic acid)
Types of RNA:
Ribosomal RNA (rRNA)
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Location of RNA
Ribosomal RNA (rRNA) is found in the cytoplasm. rRNA is a component of ribosomes, the protein synthesis machinery.
Messenger RNA (mRNA) is found in the nucleus and attached to ribosomes in the cytoplasm. mRNA carries genetic information from DNA to the ribosomes.
Transfer RNA (tRNA) is found in the cytoplasm. tRNA is involved in bringing amino acids to the ribosome for protein synthesis.
Structure of RNA
RNA is made of nucleotides.
Each nucleotide has:
A sugar
A phosphate
A nitrogen base
The sugar in RNA is ribose.
RNA has 4 nitrogen bases:
Cytosine
Guanine
Adenine
Uracil (Uracil replaces thymine)
RNA Structure (Differences from DNA)
RNA is single-stranded.
RNA strands are shorter than DNA strands.
RNA strands are not coiled around histone proteins. Histones are proteins around which DNA is wrapped in eukaryotic chromosomes.
The bases in RNA occur in any number and ratio.
Functions of RNA
RNA plays a role in protein synthesis.
mRNA carries the genetic code from DNA to ribosomes.
tRNA picks up amino acids and takes them to ribosomes.
Differences between DNA and RNA
DNA | RNA | |
|---|---|---|
Strands | Double-stranded | Single-stranded |
Sugar | Deoxyribose | Ribose |
Nitrogen bases | Adenine, Guanine, Cytosine, Thymine | Adenine, Guanine, Cytosine, Uracil |
Location | Nucleus, Mitochondria, Chloroplasts | Nucleus, Cytoplasm |
Function | Stores genetic information | Involved in protein synthesis |
DNA Replication
Unwinding and Unzipping:
An enzyme (helicase) breaks the weak hydrogen bonds between base pairs, separating the two strands of the DNA molecule of the parent cell. Helicase moves along the DNA, unwinding the double helix structure.
Helicase requires energy in the form of ATP to break the hydrogen bonds.
Template Formation:
Each strand acts as a template for the formation of a new complementary strand of DNA, forming two sets of DNA. The original DNA strands serve as templates for the synthesis of new strands.
Nucleotide Pairing:
Free nucleotides in the nucleus pair up with the bases on the exposed single DNA strands.
An enzyme, DNA polymerase, matches the bases on the template with the free nucleotides through complementary nitrogenous base pairing. DNA polymerase adds nucleotides to the 3' end of the newly forming strand.
DNA polymerase proofreads the new strand to ensure accuracy.
Base Pairing:
Pyrimidine bases (thymine and cytosine) pair with purine bases (adenine, guanine).
Helix Formation:
There are now two identical molecules of DNA, both of which are double-stranded.
Each one twists to form a helix. The two new DNA molecules are identical to the original DNA molecule.
The Process
The DNA double helix unwinds.
The weak hydrogen bonds between the nitrogenous bases are broken, causing the DNA strands to separate (unzip).
Each original DNA strand serves as a template on which its complement is built.
Free nucleotides build a DNA strand onto each of the original DNA strands, attaching their complementary nitrogenous bases (A to T and C to G).
This results in two identical DNA molecules. Each molecule consists of one original strand and one new strand.
Significance
DNA replication is important for cell division, particularly mitosis. It ensures that each daughter cell receives an identical copy of the genetic material.
Accurate DNA replication prevents mutations that could lead to disease.
It allows each chromosome to be copied so that each new identical daughter cell produced contains the same number and type of chromosomes. This is crucial for maintaining genetic stability and ensuring proper cellular function.
Additional Notes
DNA replication makes an exact copy of itself. High fidelity is essential to prevent mutations.
Histones (proteins) also duplicate during this process. Histone duplication is coordinated with DNA replication to maintain chromatin structure.
DNA replication occurs during Interphase, before cell division. Specifically, it occurs during the S phase of interphase.
It happens at the start of mitosis and meiosis, during interphase.
The Process in Detail
The original DNA is called parent DNA.
The double helix DNA molecule unwinds.
This forms a ladder-like structure.
Unzipping
The weak hydrogen bonds between nitrogen bases break with the help of the enzyme Helicase.
The DNA strands unzip, forming 2 single strands.
These single strands are templates for new DNA strands.
Nucleotides and Enzymes
Free-floating nucleotides are in the nucleoplasm.
These nucleotides attach to complementary bases.
DNA polymerase enzymes control this process. DNA ligase also plays a role in joining Okazaki fragments on the lagging strand.
Okazaki fragments are short DNA fragments synthesized on the lagging strand during DNA replication.
Daughter Strands
Two new identical DNA molecules are formed.
The new strands are called daughter strands.
Each new DNA has one original strand and one new strand. This is known as semi-conservative replication.
Significance of DNA Replication
DNA replication makes an exact copy of DNA.
This creates identical copies of chromosomes in the cell.
DNA replication ensures identical cells are produced at the end of mitosis.
It also ensures these cells are identical to the parent cell.
Terminology
DNA Replication: The process by which DNA makes an exact copy of itself. At the end of DNA replication, there are 2 copies of DNA that are identical to each other.
DNA Fingerprinting/Profiling
DNA is extracted from cells to make a barcode.
The barcode's pattern shows the person's inherited base pair sequence.
This barcode is a DNA profile/fingerprint.
DNA Profile Uniqueness
Non-coding DNA is used to determine this profile because it is highly variable amongst individuals, except for twins. Short tandem repeats (STRs) are commonly used regions.
Each person (except identical twins) has a unique DNA profile.
DNA is used as forensic evidence from crime scenes. DNA evidence can link suspects to a crime scene or exonerate innocent individuals.
DNA profiling process
Collect DNA: Obtain biological sample. Common sources include blood, saliva, hair, and skin cells.
Proper collection and storage techniques are essential to prevent contamination and degradation of DNA samples.
Extract DNA: Isolate DNA from cells. Various methods can be used, such as phenol-chloroform extraction or commercially available kits.
DNA extraction methods must effectively remove cellular debris and contaminants while preserving the integrity of the DNA.
Amplify DNA (PCR): Make many copies of specific DNA regions (STRs). PCR amplifies specific regions of DNA, allowing for easier analysis.
PCR involves repeated cycles of denaturation, annealing, and extension to amplify specific DNA regions.
Separate Fragments (Electrophoresis): Separate DNA fragments by size in a gel. Shorter fragments migrate faster through the gel than longer fragments.
Electrophoresis is typically performed using agarose or polyacrylamide gels, depending on the size range of the DNA fragments.
Visualize & Analyze: View banding patterns and compare between samples. The banding patterns are compared to determine if there is a match between the samples.
DNA fragments are visualized using staining techniques, such as ethidium bromide or silver staining.
PCR (Polymerase Chain Reaction)
Polymerase Chain Reaction (PCR) multiplies small amounts of DNA into millions of copies.
PCR replicates DNA.
This ensures enough DNA for testing. PCR is a sensitive technique that can amplify even small amounts of DNA.
PCR is widely used in molecular biology, genetics, and diagnostics.
Steps in the process of DNA fingerprinting
Cell sample
Extracted DNA
Cleavage of DNA by restriction enzyme
Binding of radioactive DNA probe to specific DNA fragments
Transfer to a membrane (Southern blot)
Separation of DNA fragments by electrophoresis
Membrane washed free of excess probe
X-ray film used to detect radioactive pattern
DNA comparison
Uses of DNA Profiling
Identify crime suspects
Proof of paternity
Determine genetic disorders/defects
Trace missing people
Identifying dead persons
Establish tissue compatibility for organ/tissue transplant
Fighting illegal trade
Reliability Concerns
A small DNA piece used might not be unique. This can lead to false positives.
Private labs may not follow standards, questioning results. Lack of standardization can compromise the accuracy and reliability of DNA profiling.
Human error can occur in result interpretation. Subjectivity in interpreting banding patterns can lead to errors.
Ethical Issues
DNA profiling is expensive, limiting some suspects' defense. This can create disparities in the justice system.
DNA analysis can reveal personal information, which can be misused. Genetic information can be used to discriminate against individuals.
Potential for abuse of DNA by criminals or government. DNA databases could be used for surveillance or coercion.
Discrimination based on genetic information.
Debates about ownership of DNA databases. Ethical concerns arise regarding who controls and has access to genetic information.
Ethics of Obtaining DNA Samples
DNA samples cannot be taken without consent. Forced DNA collection violates individual rights.
It can violate the right of privacy by being able to access individuals' information. Genetic information is highly personal and sensitive.
Abuse of DNA by criminals or government.
Discrimination can occur due to genetic information.
Debated ownership of the DNA database. Issues include who has the right to collect, store, and use DNA samples.
Terminology
DNA fingerprint / DNA profile: Black bars that are left behind on x-ray film when an extract of DNA undergoes a biochemical process; useful in identifying suspects in criminal investigations.
DNA fingerprinting/DNA profiling: Process of identifying an individual by comparing his DNA with that of another known DNA; used by forensic scientists to identify siblings.
Nucleotide: A monomer or building block of nucleic acids.
Nuclear DNA: DNA found within the nucleus.
Extra-nuclear DNA: DNA found outside the nucleus