PART 5: Molecular Genetics1. Euchromatin: loose, uncoiled chromatin that is available for use in the nucleus.

2. Heterochromatin: chromatin that is packed into tight bundles by proteins called histores to form chromosomes that deactivate the genes (most commonly for cellular reproduction).

3. DNA (deoxyribonucleic acid): as briefly discussed in Part 1 (#17), DNA is a genetic blueprint for cells. DNA’s role is to direct the manufacturing of proteins, which regulate all functions of a living organism.

Double Helix: the shape of a DNA molecule, discovered in 1956 by Watson and Crick. A helix is shaped like a stretched spring; this double helix is when two helices twist parallel to each other, joined by “bars”; just like a long, stretched ladder that is twisted.

Nucleotides: the “bars” that link the helices of DNA; the order of sequences of nucleotides determine genetic information; they contain a phosphate group, a 5-carbon sugar, and a nitrogenous base (base paired with another), all linked together by phosphodiester bonds.

o Phosphate group: a group with a center phosphate and 4 oxygen molecules.

o 5-Carbon sugar: a carbohydrate with five carbons in it; in DNA, deoxyribose is the sugar, whereas ribose is in the nucleotides of RNA.

o Nitrogenous bases: the “coding” molecules of DNA and RNA. In DNA, there are four nitrogenous bases (and each has another it will ALWAYS pair with from an opposite helix).

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o Base pair: one of the pairs of chemical bases joined by hydrogen bonds that connect the complementary strands of a DNA molecule or of an RNA molecule

Adenine: purine (double-ringed); opposite thymine Guanine: purine (double-ringed); opposite cytosine Cytosine: pyrimidine (single-ringed); opposite guanine Thymine: pyrimidine (single-ringed); opposite adenine

o Phosphodiester bonds: bonds that join nucleotides together.

4. DNA Replication: DNA replicates itself into exact copies for cell reproduction. This task is completed by a number of enzymes:

Helicase: an enzyme that breaks the hydrogen bonds of DNA nucleotides, splitting the DNA’s helices.

DNA topoisomerase: an enzyme that keeps the split strands from tangling.

DNA polymerase: an enzyme that adds complementary nucleotides to the open DNA strands in order to replicate the DNA.

RNA primase: an enzyme that adds starter nucleotides to the S’ end of the split DNA to allow replication to occur. This happens because DNA nucleotides can only attach to a 3’ end, and the RNA molecules temporarily added here by this enzyme mimics the 3’ end.

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Leading strand: the strand of split DNA that already has a 3’ end. Here, replication is continuous.

Lagging strand: the strand of split DNA that has a 5’ end – it requires RNA primase, and is replicated in segments.

o Okazaki fragments: the fragments of replicated DNA on the lagging strand.

o DNA ligase: an enzyme that joins the Okazaki fragments together. Semi-conservative: DNA is semi-conservative because it does not create an

entirely new molecule. Rather, it splits the molecule in half and fills in the missing space. The final product is half new and half of the original.

5. RNA (ribonucleic acid): a single strand of nucleotides attached to the 5-carbon sugar ribose. RNA differs from DNA not only in the structure (single strand versus double helix) and in the sugar (ribose versus deoxyribose) but also in one of the nucleotides – uracil (pyramidine single-ring nitrogen base) takes the place of thymine in RNA sequences as the new complement to adenine. There are three types of RNA:

mRNA (Messenger): copies and delivers information stored in DNA. rRNA (Ribosomal): builds ribosomes (the sites of protein synthesis [Part 2]

in the nucleolus). tRNA (Transfer): transports amino acids (the building blocks of proteins) to

mRNA and ribosomes for protein synthesis. They have an anti-codon of nucleotides in order to match mRNA in the right order to build a protein.

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mRNA rRNA tRNA

6. Protein synthesis: the building of proteins; there are three steps – transcription, RNA processing, and translation.

Transcription: the copying of a specific part of the genetic code from DNA to mRNA. Takes place in the nucleus. There are three steps: initiation, elongation, and termination.

o Initiation: DNA is split by the helicase enzyme, and the promoter (a sequence of DNA that marks where transcription should begin) is found on the sense strand (strand of DNA being used as a template) while the antisense strand (DNA strand not being used) lies dormant.

o Elongation: the addition of RNA nucleotides to each other to form a strand. An RNA polymerase enzyme is used to attach these nucleotides together – for every adenine RNA adds uracil, for every thymine adds adenine, for every guanine a cytosine, and for every cytosine a guanine.

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o Termination: similar to a promoter, there is a short series of nucleotides that code for the elongation to cease, release the RNA, and return the DNA to its double helix formation.

RNA processing: the subtraction and addition of substances to mRNA in order to regulate what sequences are to be translated. This takes place in the nucleus.

o Splicing: process (using an RNA-protein complex called a spliceosome) that removes introns (sequences not wanted for translation) and joins exons (sequences left that are wanted for translation) together.

o Poly (A) tail: a molecule added to the 3’ end of the spliced RNA.

o 5’ Cap: a molecule added to the 5’ end of the spliced RNA.

Translation : the final mRNA after processing finds a ribosome to begin an amino acid. Every three bases on this mRNA is called a codon, and every codon matches an anticodon (with the relationships between the nucleotides); anticodons are found at the bottom of every tRNA which carry amino acids. This is how polypeptides are built, as specific anticodons match specific amino acids. It’s important to note that ribosomes have three binding sites: A (attachment) site, P (polypeptide) site, and E (exit) site. There are three steps to translation (similar to transcription): initiation, elongation, and termination.

o Initiation: an initiation tRNA with anti-codon U-A-C attaches to the mRNA sequence A-U-G in the A site to commence the movement of the mRNA through the ribosome. The amino acid attached to this tRNA in order to start the building of the amino acid is methionine.

o Elongation: as the first tRNA moves to the P site, another tRNA joins at the A site to match another codon for a specific amino acid joining that amino acid. The system then continues to slide to allow the joining of more tRNA to the A site. As they enter the E site, the tRNAs disconnect from the ribosome and leave to pick up more amino acids.

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o Termination: once the polypeptide is complete, a stop codon (code of U-A-A, U-A-G or U-G-A) slides into the A site, causing the ribosome to break apart and the polypeptide is released.

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7. Protein structure: as proteins join and form structures, there are four distinct levels of structure:

Primary structure: a sequence of amino acids that forms a polypeptide chain.

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Secondary structure: when a polypeptide uses hydrogen bonds to form a basic structure either as a helix or as a pleated sheet.

Tertiary structure: the folding of polypeptides into 32 structures with the help of chaperonins.

Quaternary structure: when two or more polypeptides get together.

8. Mutations: an unintentional change in the genetic code. There are two types: substitutions and rearrangements.

Base substitution: when one base is in the place of another.o Nonsense: terminates protein synthesis early.o Missense: produces the wrong amino acids in protein synthesis.

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o Silent: no visible effect.

Gene Rearrangements: sequences that have deletions, insertions, duplications, inversions, translocations, and/or disjunction.

o Deletion: loss of a gene, multiple genes, or a single base.

o Insertion: addition of a gene, multiple genes or a single base.

o Duplications: caused by unequal crossing over (Part 6), genes can be copied more than once by accident.

o Inversion: when the orientation of chromosomal regions change.

o Translocation: when part of a chromosome breaks off and rejoins somewhere else on itself, or onto another chromosome. The segments of DNA that can rejoin in other areas are called transposons and are, fortunately, easily repaired by special enzymes.

o Nondisjunction: will be discussed in Part 6.

9. Gene expression: how genes visibly affect an organism (e.g., hair color, illness from mutations, etc.).

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10. Genetic engineering: the branch of technology that produces new organisms or products by transferring genes between cells.

Recombinant DNA: hybrid of DNA from two or more sources. Restriction enzyme: an enzyme that cuts DNA at specific sequences into

short fragments. These fragments all contain one sticky end that allows hydrogen bonding.

Cloning: the copying of DNA using genetic engineering. The sticky end of the desired fragment creates a hydrogen bond to the sticky end of a plasmid (AKA: cloning vector; DNA [usually of bacteria] that joins the fragments and then undergoes DNA replication).

o Transformation: the process of reproducing human genes in the circular DNA (plasmids) of bacteria. This is used to study gene expression as well as to mass produce proteins (e.g., insulin) needed for medicine.

Recombinant DNA is transformed into bacterium in order to clone a gene of interest (ex., this is used to mass produce insulin).

Gel electrophoresis: the visual separation of DNA fragments according to their molecular weight. A special gel is set in the shape of a block with small wells at one end. Dyed DNA samples are placed in the wells, and the block is placed into an electrical field (small charged box). Once the power is turned on, fragments (which are negatively charged) run to the positive end of the electric field, leaving a specific pattern. Fragments here are now called RFLP (Restriction Fragment Length Polymorphisms).

o DNA fingerprinting: when the RFLPs from one source are compared to those of another. If their patterns match, it is from the same person. This is often used to compare DNA found at crime scenes to the DNA of suspects.

Polymerase chain reaction (PCR): the process of DNA replication at a much faster speed for scientific use, done by mixing DNA, primers, polymerase

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and lots of nucleotides into a PCR tube (called a thermocycler). This tube is heated and cooled many times. The steps are as follows:

Heated; hydrogen bonds break Cooled; primers attach to DNA Heated; polymerase adds nucleotides And the process is repeated.

11. Human Genome Project: from 1990-2001, scientists all over the world participated, successfully mapping the exact genetic code of the entire human genome.

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