Module 2: Nucleic Acids

Nucleotides:

Polymers made up of many repeating units called nucleotides.

Pentose sugar:

A sugar with 5 carbon atoms.

DNA nucleotide components:

A deoxyribose sugar with hydrogen at the 2' position, a phosphate group, and one of four nitrogenous bases - adenine (A), cytosine (C), guanine (G), or thymine (T).

RNA nucleotide components:

A ribose sugar with a hydroxyl (OH) group at the 2' position, a phosphate group, and one of four nitrogenous bases - adenine (A), cytosine (C), guanine (G), or uracil (U).

Hydroxyl group:

A functional group consisting of an oxygen atom bonded to a hydrogen atom (OH).

Purines:

Nitrogenous bases with a double ring structure, specifically adenine and guanine.

Pyrimidines:

Nitrogenous bases with no double ring structure, specifically thymine and cytocine

Deoxyribose sugar:

A sugar component of DNA nucleotides that lacks one oxygen atom compared to ribose.

Ribose sugar:

A sugar component of RNA nucleotides that contains a hydroxyl (OH) group at the 2' position.

Thymine:

A nitrogenous base found in DNA nucleotides but not in RNA nucleotides.

Uracil:

A nitrogenous base found in RNA nucleotides that replaces thymine.

Molecular lifespan of RNA:

RNA has a shorter molecular lifespan compared to DNA due to the presence of the 2' hydroxyl group.

DNA as storage molecule:

DNA serves as the storage molecule for genetic information.

RNA as transport molecule:

RNA serves as the transport molecule for genetic information.

Key differences between DNA and RNA nucleotides:

RNA nucleotides contain ribose sugar and uracil, while DNA nucleotides contain deoxyribose sugar and thymine.

Nucleotide structure:

Each nucleotide consists of a pentose sugar, a nitrogenous base, and a phosphate group.

Nitrogenous bases in DNA:

A, T, C, G are the nitrogenous bases found in DNA.

Nitrogenous bases in RNA:

A, U, C, G are the nitrogenous bases found in RNA.

Double ring structure:

The structural configuration of purines.

Single ring structure:

The structural configuration of pyrimidines.

Phosphate group:

A component of nucleotides that links nucleotides together in a nucleic acid.

Nucleotide comparison:

DNA and RNA nucleotides are similar but differ in the type of sugar and nitrogenous bases they contain.

Phosphodiester Bond:

A bond formed between the phosphate group of one nucleotide and the pentose sugar of the next nucleotide through a condensation reaction.

Sugar-Phosphate Backbone:

The chain of alternating phosphate groups and pentose sugars produced as a result of many phosphodiester bonds in DNA or RNA.

Condensation Reaction:

A chemical reaction where two molecules combine to form a larger molecule, releasing a molecule of water.

Hydrolysis Reaction:

A chemical reaction where a larger molecule is broken down into smaller molecules by the addition of water.

Phosphorylated Nucleotides:

Nucleotides that contain one or more phosphate groups, such as ATP, ADP, and AMP.

Adenosine Triphosphate (ATP):

The energy-carrying molecule that provides energy to drive many processes inside living cells.

Adenosine Monophosphate (AMP):

A nucleotide consisting of adenosine and one phosphate group.

Adenosine Diphosphate (ADP):

A nucleotide consisting of adenosine and two phosphate groups.

Nucleotide:

The monomer of nucleic acids, consisting of a phosphate group, a pentose sugar, and a nitrogenous base.

Polynucleotide:

A polymer made up of many nucleotides joined together in long chains.

Antiparallel Strands:

The orientation of the two polynucleotide strands in DNA, running in opposite directions.

Nitrogenous Base:

A component of nucleotides that can be adenine, thymine, cytosine, or guanine in DNA.

Energy Currency:

A term used to describe ATP as it is used to transfer energy in all energy-requiring processes in cells.

Muscle Contraction:

A process that requires energy for coordinating movement at the whole-organism level.

Conduction of Nerve Impulses:

A process in animals that requires energy to transmit signals through the nervous system.

Nucleoside:

A molecule consisting of a nitrogenous base attached to a pentose sugar.

Phosphodiester bonds:

Specifically, a phosphate group links the 3' carbon of one sugar molecule to the 5' carbon of another sugar molecule. 

3' end and 5' end:

Refers to the ends of a DNA polynucleotide strand, indicating which carbon on the pentose sugar could be bonded with another nucleotide.

Nitrogenous bases:

The components of each nucleotide that project out from the backbone towards the interior of the double-stranded DNA molecule.

Hydrogen bonds:

Bonds that hold together the two antiparallel DNA polynucleotide strands between the nitrogenous bases.

Complementary base pairing:

The process where adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C) in DNA.

Complementary base pairs:

Pairs of nitrogenous bases that are bonded together, specifically A with T (two hydrogen bonds) and G with C (three hydrogen bonds).

Double helix:

The three-dimensional shape formed by the twisting of the DNA molecule.

Number of hydrogen bonds between A and T:

Two hydrogen bonds are formed between adenine (A) and thymine (T).

Number of hydrogen bonds between G and C:

Three hydrogen bonds are formed between guanine (G) and cytosine (C).

Base pair ratio:

In a DNA molecule, the number of adenine (A) equals the number of thymine (T) and the number of cytosine (C) equals the number of guanine (G).

DNA Purification:

The process of isolating DNA from cells.

Lysing:

Breaking cells and disrupting nuclear membranes to release DNA.

Denaturing:

Using enzymes to remove proteins associated with DNA.

Precipitating:

Using an organic solvent, such as ethanol, to isolate DNA.

Example practical investigation:

Extracting DNA from onions.

Onions:

Good for DNA extraction due to relatively large amounts of DNA in their cells.

Fruits for DNA extraction:

Strawberries, bananas, and kiwis also contain relatively large amounts of DNA.

Equipment for DNA extraction:

Includes a plastic syringe (1 cm³), plastic funnel, 2 beakers (250 cm³), 2 test tubes, stirrer, chopping board, knife, onion, washing-up liquid (10 cm³), ice-cold ethanol (10 cm³), protease enzyme (2-3 drops), coffee filter paper, water bath (60 °C), ice-water bath, and blender.

Ethanol preparation:

Ethanol must be placed in a freezer 24 hours before starting the investigation.

Onion cutting size:

Cut the onion into small pieces measuring 5 mm × 5 mm.

Detergent function:

Washing-up liquid disrupts the phospholipid bilayer of cell membranes, releasing DNA.

Heat application:

Heating at 60 °C for 15 minutes denatures enzymes that could digest DNA.

Cooling process:

Cooling the mixture in an ice-water bath for 5 minutes prevents DNA breakdown.

Blending:

Blending the mixture for 5 seconds breaks down cell walls and membranes, releasing more DNA.

Filtering:

Filtering the mixture removes cell debris and membrane fragments.

Filtrate:

Filtering the mixture removes cell debris and membrane fra

Protease enzyme:

Added to the filtrate to denature and remove proteins, leaving just the DNA.

Ethanol addition:

Carefully adding ice-cold ethanol to the test tube causes DNA to precipitate.

DNA precipitate:

The white layer formed at the top of the test tube mixture after adding ethanol.

Result of DNA extraction:

The DNA in the resulting white precipitate can be extracted for analysis or further investigations.

Semi-conservative Replication:

A process where one original DNA strand is retained in each new DNA molecule, ensuring genetic continuity.

Parent Cell:

The original cell that divides to produce daughter cells, containing the DNA that needs to be copied.

Daughter Cells:

The two new cells produced after a parent cell divides, each receiving a full copy of the parental DNA.

DNA Molecule:

A structure made up of polynucleotide strands that carries genetic information.

Polynucleotide DNA Strand:

A single strand of nucleotides that forms part of a DNA molecule.

Genetic Continuity:

The preservation of genetic information between generations of cells.

Cell Division:

The process by which a parent cell divides into two daughter cell

Mitosis:

A type of cell division that results in two genetically identical daughter cells.

S Phase:

The phase of the cell cycle during which DNA replication occurs.

Interphase:

The phase of the cell cycle when the cell is not actively dividing.

Helicase:

An enzyme that unwinds the DNA double helix by breaking hydrogen bonds between base pairs.

Template Strand:

A single polynucleotide DNA strand that serves as a guide for the formation of a new strand.

Free Nucleotides:

Nucleotides available in the nucleus that participate in DNA replication.

Nucleoside Triphosphates:

Activated nucleotides containing three phosphate groups used in DNA replication.

DNA Polymerase:

An enzyme that synthesizes new DNA strands by catalyzing condensation reactions.

Base Pairing:

The specific pairing of nucleotide bases (adenine with thymine, and cytosine with guanine) in DNA.

Condensation Reactions:

Chemical reactions that join molecules together, releasing water as a byproduct.

Chromosomes:

Structures within cells that contain DNA and genetic information.

Genetically Identical:

Having the same genetic information as another cell or organism.

Cell Growth:

The process during which cells increase in size and replicate their DNA in preparation for division.

Mutations:

Occasional mistakes occur in the form of bases being inserted into the complementary strand in the wrong order, an extra base being inserted by accident, or a base being left out by accident.

Random mutations:

Mistakes in the process of semi-conservative replication of DNA result in the occurrence of random, spontaneous mutations (i.e. errors in the genetic code).

Gene:

A gene is a sequence of nucleotides that forms part of a DNA molecule and codes for the production of a specific polypeptide (protein).

Polypeptide:

A polypeptide is a specific protein molecule produced by the sequence of nucleotides in a gene.

Primary structure of protein:

The initial sequence of amino acids in a protein molecule that determines its shape and behavior.

Triplet code:

The sequence of DNA nucleotide bases found within a gene is determined by a triplet (three-letter) code.

Amino acids:

There are 20 different amino acids that cells use to make up different proteins.

Triplet of bases:

Each sequence of three bases in a gene codes for one amino acid.

Protein structure:

The genes in DNA molecules control protein structure and function as they determine the exact sequence in which the amino acids join together when proteins are synthesized in a cell.

Genetic Code:

A system of triplets of bases that tell the cell where individual genes start and stop.

Non-overlapping Genetic Code:

Each base is only read once in which codon it is part of.

Codons:

Triplets within the mRNA code.