DNA and Nucleic Acids

3.1 DNA

• DNA stands for deoxyribonucleic acid.
• DNA composes chromosomes and stores hereditary data.

Nucleic Acids

• There are two types of nucleic acids: DNA and RNA.
• DNA and RNA are polymers of nucleotides.
• Nucleotides make up genetic material, chromosomes, and participate in protein synthesis.
• DNA presents as a double helix composed of repeating nucleotide units.
• Nucleotides consist of phosphoric acid (phosphate group), a 5-carbon sugar (deoxyribose), and one of four nitrogenous bases.

Purines and Pyrimidines

• Purines and pyrimidines are nitrogenous bases within DNA nucleotides.
• Adenine and guanine are two-carbon nitrogen ring bases classified as purines.
• Thymine and cytosine are one-carbon nitrogen ring bases categorized as pyrimidines.
• Bases bond together to form the "rungs" in the DNA ladder in a specific pattern.
• Deoxyribose sugar and phosphates make up the rails (backbone).
• Adenine always bonds to thymine, using two hydrogen bonds.
• Guanine always bonds to cytosine, using three hydrogen bonds.
• Complementary base pairing does not allow other bases to bond together, as two purines would overlap, and two pyrimidines would be too short.
• Hydrogen bonds hold the double strand in place between the bases.
• The number, order, and type of bases determine the type of organism that will develop.

DNA Replication

• DNA replicates, duplicates, itself so each new cell has a complete and identical copy.
• DNA controls cell activities by producing proteins.
• The combination of proteins determines the characteristics or phenotype of each living organism.
• Occasional mutations occur in DNA through mistakes in replication, accounting for a variety of living things.

Steps in DNA Replication

• The DNA molecule becomes untwisted using enzymes that breaks the bonds.
• The two strands making up the DNA become "unzipped", and each side acts as a template.
• Helicase unzips the weak hydrogen bonds between the nitrogenous base pairs.
• New complementary nucleotides move into place, pairing with complementary bases on the exposed strands.
• DNA polymerase is involved with complementary base pairing, A joins T, and C joins G.
• Ligase joins the adjacent nucleotides together by their sugar-phosphate components, forming the alternating sugar-phosphate backbone.
• Two complete DNA molecules are present at the end of the process, identical to each other and to the original molecule.
• Both new DNA strands wind back up into their helical shape.
• DNA replication is called semiconservative as each new double helix comprises an old (parental) strand and a new (daughter) strand.
• Enzymes assist the unwinding, joining, and rewinding processes.
• A mutation can arise when errors occur in replication.

Recombinant DNA

• Recombinant DNA has genes from 2 different organisms.
• Recombinant DNA is produced in the laboratory by introducing foreign genes into a bacterial plasmid.
• A vector is used to introduce recombinant DNA.
• A plasmid is the most common vector, small rings of DNA found in bacteria.
• A restriction enzyme breaks the plasmid DNA when removed from the bacteria to have a foreign gene inserted.
• The new foreign DNA can now be attached to the plasmid.
• Ligase acts to connect the foreign DNA to the plasmid to make it whole again.
• The plasmid DNA is then placed back into the bacteria to produce a plasmid with the foreign gene.
• After time there are many genes of the foreign gene.
• Viral DNA can be used as a vector to carry recombinant DNA into a cell.
• Viral vectors allows cloning of a particular gene.
• Viral vectors are also used to create genomic libraries.
• A Genomic Library represents a collection of engineered viruses carrying genes of a species.
• Segments of DNA (particular genes) can be inserted into bacteria which produce those genes.
• Protein hormones such as insulin can be created using yeast cells.
• Interferon, a protein used in cancer treatments, can be mass-produced.

Uses of Recombinant DNA

• Generate a DNA library, which will catalogue all the base sequences of known genes.
• Identify specific genes (e.g. genes that cause prostate cancer).
• Produce synthetic copies of genes to mass produce chemicals such as insulin.
• Insert genetic material into chromosomes that will help regulate cell function to make the organism genetically "better" (gene therapy).

DNA vs RNA

• DNA and RNA are nucleic acids which are polymers of nucleotide monomers.
• Nucleotides have a phosphoric acid, a 5 carbon sugar and four nitrogen bases.
• G always pairs with C, while A always pairs with T.
• If a DNA strand contains 34% adenine bases then it must also contain 34% thymine bases.
• DNA replication results in the formation of two identical daughter strands of DNA.
• Cells could loose important genetic information leading to errors, diseases, or failure of cell function without DNA replication.
• Because DNA replication results in two identical double helices it is termed semiconservative.

DNA Replication Steps

• Unwinding- the enzyme helicase unzips the double-stranded DNA by breaking the weak hydrogen bonds between the base pairs in the nucleus creating two single strands that serve as templates for new DNA.
• Matching- the enzyme DNA polymerase adds new nucleotides to each exposed strand, making sure they pair correctly: A with T and C with G.
• Joining- the enzyme ligase helps glue the sugar-phosphate backbone together, connecting the new nucleotides into a continuous strand.
• Two identical DNA molecules are produced each with one strand and one new strand.

DNA and RNA

DNA Replication and Protein Synthesis

• DNA replication is the process of making an identical strand of DNA and occurs in the nucleus.
• Protein synthesis refers to the process of using the information encoded in DNA to make proteins and involves two steps
  • Transcription: DNA is used as a template to make mRNA.
  • Translation: mRNA is used to direct the synthesis of proteins.

Protein Synthesis

• DNA replication produces an identical DNA strand.
• Protein synthesis uses DNA to produce proteins.
• It uses DNA to produce proteins.
• Proteins are structural and functional elements.
• DNA never leaves the nucleus.
• Messenger RNA (mRNA) transports a copy of the DNA.
• The process of making messenger RNA (mRNA) from a DNA template is called transcription.
• The newly synthesized mRNA molecule then travels into the cytoplasm where it is translated into proteins.
• Nitrogenous bases in DNA contain the instructions for making proteins.
• Every 3 bases in a DNA strand code for one amino acid.
• The code for protein synthesis is transcribed from a DNA template into an mRNA molecule.
• Once the code is transcribed each set of 3 bases on the mRNA strand is called a codon.
• Nitrogenous bases in DNA contain the instructions for making proteins.
• Every 3 bases in a DNA strand code for one amino acid.
• Many amino acids make up a protein.
• Once the code is transcribed, each set of 3 bases on the mRNA strand is called a codon.
• There are 64 possible codon combinations, but there are only about 21 amino acids.
• Amino acids often have more than 1 codon and only differ in the last phase e.g CAA and CAG which both codons for Glutamine.
• Duplicate codons may be a way of protecting/reducing the effects of mutations.
• The duplication of codons is called degeneracy.
• If a DNA strand contains 34% adenine bases then it must also contain 34% thymine bases.

Genetic Code

• Is basically "Universal "where the same codons stand for the same A.A.
• It suggests that all living things came from a common ancestor.
• AUG which is methionine is a start codon whereas UAA and UAG are stop codons.
• A the end of each mRNA strand there are long chains of Adenine bases (Adenine tail).
• It tells the body that this particular mRNA is no longer needed.
• The cell will then digest the no longer functional mRNA using lysosomes .

Transcription

• A. The gene in DNA is selected, isolated and uncoiled by the enzymes RNA polymerase.
• The gene codes for the protein that will eventually be produced.
• Free-Hoaring nucleotides join complementary to the selected gene on the DNA template and RMA polymerase assists with this.
• There is no Thymine in RNA.
• *** Vravil always joins to Adenine when forming the mRNA.
• DNA strand is called the template.
• C. The enzyme ligase gives the alternating sugar-phosphate baumbone together
• D. Enzymes break the hydrogen bond and the MRMA is released from the DNA template.
• E. The DNA molecule joins back together and after the mRNA.

Translation

• mRNA becomes associated with a ribosome in the cytoplasm
• The ribosome is made of ribosomal RNA and protein.
• The mRNA comes near the two ribosomal subunits, the large subunit attaches to the mRNA strand.
• the small subunit then attaches.
• One both subunits are attached a functional complete is formed.
• A second tRNA comes in complementary to codon and binds to the messenger cell strand.
• Ribosome assists in the transferring amino acid from the first tRNA to the amino acid on the second tRNA forming a peptide bond forming a chain.
• The ribosome then moves down the mRNA by one codon (now empty).
• It can then pick up another amino ecid.
• The ribosome continues to read / translate the mRNA and polypeptide chain grows until a terminator code is reached.
• mRNA will then read by more ribosomes and many ribosomes together is a polyribosome.

Mutations

• A gene mutation is a permanent alteration in the DNA sequence and is different to what is found in most people.
• A range in size and can affect everything from one DNA building block to multiple genes.

Types of Mutations

• Hereditary mutations are inherited from a parent.
• Acquired mutations occur at some point during a person's life and are present only in certain cells.

Chromosomal Mutation Types

• Deletion-Chromosomal aberration in which a portion of a chromosome is missing or deleted.
• Duplication-a chromosome abnormality in which a region of DNA has been duplicated, increasing the number of genes located in that region.
• Inversion-A chromosome rearrangement in which a segment of a chromosome is reversed end to end.
• Translocation (Insertion)-A broken piece attaches to a nonhomologous chromosome.
• Nondisjunction- a pair of chromosomes fail to separate during cell division.
• Point mutations- a change in a single nitrogen base in DNA.
• Frame-shift mutations- the addition or deletion of a nitrogen base, causing the gene sequence to read out of sequence

Environmental Mutagens

1. Chemical
   • Food additives
   • Certain drugs
   • Pesticides Fertilizers
   • Industrial chemicals
2. Radiation
   • (non visible short wavelength from electromagnetic spectrum)

• Mutagens that lead to an increased chance of cancer are called carcinogens

Chromosomal Translocation

• Down' Syndrome a part of chromosome #21 becomes attached to another chromosome e.g #'s 12, 14, 15, or 22 and also have 2 normal chromosome #21.

Other Mutations

• Sickle-Cell Anemia substitution of a base to produce a different amino acid that results in abnormal hemoglobin molecules and casues decreased ability for the blood to carry oxygen
• CANCER-a Somatic mutation (affects an individual's body cells)results in uncontrolled growth of abnormal body cells and often occurs in body cells
• HEMOPHILIA- a germ cell mutation (a mutation of the original sex cells)passed on to the individual from a previous generation..

3.3: PROTEIN SYNTHESIS

1. Why is the genetic code considered "universal"?
   • the same codous stand for the same A.A. in all living things
2. Please complete the following table. Replication has been filled out as an example.

translation and provide a brief description of each step.

1. The tRNA molecule binds with the first mRNA amino acid in a process called translation.

2. A second mRNA codon is added and bonded together forming a chain.

3. the translation continues until it reaches a stop codon then the chain is released

4. If an enzyme is composed of 687 amino acids, how many bases would the mature mRNA that encoded for it have?2061

5. The codon table allows you to determine the amino acid sequence of a polypeptide based on the MRMA sequence.

6. A mutagen leads to changes in DNA and may have serious effects.

3.4 Introduction to Enzymes

• an enzyme is a protein that speeds up chemical reactions and are called catalysts.
• Apoenzyme is a protein portion and the coenzyme is a non protein portion.
• Substrates are changed into a new molecule.
• The reactants must be brought close so that a new reaction occurs .
• Reactions will not start until the activation energy starts

enzymes

• governs the rate that cells consume oxygen, thus having an overall impact on enzyme activity and the body's metabolism.
• can be exhausted and impacts your energy, your heart, digestion, and fertility.
• more exhausted than usual, or jittery and anxious.

Enzymes

• Substrates bond to the active site on the enzyme together
• reaction occurs and enzyme goes back to its normal position
• The product must have a key shape so the enzymatic energy can increase the activity of the cell.
• the active must interact with the enzyme shape so a chemical reaction occurs

Factors Affecting Enzyme Activity

• Enzyme molecules or called enzymes or metals, such as heavy metals e.g lead or mercury.
• Metals that get bonded called non competitive inhibition