Lecture 01

Front 1

Charles Darwin: What is his Theory of Evolution? What is his theory of Natural Selection?

Back 1

All organisms are related in a family tree, which means all organisms are composed of the same types of chemical molecules.

Natural selection selects mutations to have an advantage to eventually take over populations.

Front 2

Genes: What are they? What is their function? What regions are in genes?

Back 2

Genes are hereditary units that make up DNA that ultimately define biological structure and maintain integration of cellular function. They encode proteins.

Genes contain at least a coding region (specifies AA sequence of a protein) and a regulatory region (which controls when and in which cells the protein is made).

Front 3

Proteins: What are they and their function?

Back 3

They are primary molecules that make up cell structures and carry out cellular activities. They play a huge role in regulating gene expression, which is the entire process where info encoded in DNA is decoded into proteins in the correct cells at the correct times in development.

Front 4

Mutations: What are they?

Back 4

They are alterations in the structure and organization of genes that provide the random variation in the biological structure and function. Some mutations can have no noticeable effect while others can lead to an evolutionary advantage.

Front 5

Central Dogma: What is it?

Back 5

It is the connection between DNA, RNA, and proteins. DNA holds genes that must be made into RNA through transcription in order to be expressed. RNA is then encoded into protein through translation.

Front 6

DNA: What is it? How do we know it is the transferable genetic material? Who discovered it? How is it built? Describe its structure and how it’s formed. Where is its genetic sequence?

Back 6

DNA is an informational molecule that contains in its nucleotide info required to build all proteins of an organism and hence the cells and tissues of that organism.

Through the Hershey-Chase Experiments using bacteriophages (viruses that infect bacteria) and labelling them differently, they were able to figure out that DNA was the material being transferred from the bacteriophage to E. Coli.

DNA is built as a double helix, which was found by Rosalind Franklin through X-ray diffraction study and Watson and Crick through a 3D model. Strands of it are composed of monomers called nucleotides (or bases due to cyclic organic bases in structure). Nucleotides are joined through phosphodiester bonds to form a DNA strand with base parts projecting inwards from backbone of strand and phosphate groups on the outside. The backbone of strand are made of repeating pentose-phosphate units from which the bases extend as side groups. The 5’ Carbon end of one strand usually has a phosphate or hydroxyl group. The 3’ Carbon usually has a hydroxyl group. Two strands bind together via the bases and twist to form the double helix in antiparallel fashion. The bases bind through complementary matching.

DNA has genetic info in its sequence. Genes are specific segments of DNA that carry instruction for making specific proteins.

Front 7

DNA vs. RNA: How are the two similar? How are the two different? What bases do the two have?

Back 7

Each chain has monomer units called nucleotides that have 3 parts to it: Phosphate group attached by phosphoester bond to carbon 5’ of a pentose sugar group, deoxyribose (DNA) or ribose (RNA) , which is linked to the nitrogen and carbon containing base at carbon 1’ that distinguishes the nucleotide. DNA is called deoxy because it has a proton instead of a hydroxyl group at the carbon 2’ position. RNA has the base uracil whereas DNA has the base thymine.

Both RNA and DNA have the bases adenine, guanine, and cytosine. RNA has uracil whereas DNA has thymine.

Front 8

Chargaff’s Rules: What is it?

Back 8

The base A pairs with T and G pairs with C, but the amount of A and T together does not equal G and C in DNA.

Front 9

Purines vs. Pyrimidines: What is the difference b/w the two?

Back 9

Purines have two ring structures (trick: purine is a two-syllable word) that include the bases A and G. Pyrimidines have single ring structures with the bases U, T, and C. Purines only base pair with pyrimidines and vice-versa.

Front 10

Transcription: What is it?

Back 10

It is the RNA synthesis process by which the coding region of a gene in DNA is copied (transcribed) into a single-stranded RNA through the enzyme RNA polymerase. In eukaryotic cells, RNA product is initially processed into a smaller messenger RNA molecule (mRNA) which moves out into the cytoplasm from the nucleus.

Front 11

Translation: What is it? What is a ribosome? What other proteins are involved in the process?

Back 11

It is the protein synthesis process. The ribosome (complex molecular machine made of RNA and protein) in the cytoplasm assembles and links together AA’s in the order dictated by the mRNA sequence. In the process, nucleotide sequence of mRNA is “read” by a type of RNA called transfer RNA (tRNA) with help of a third type of RNA, ribosomal RNA (rRNA). As tRNAs bring correct AA’s into sequence, peptide bonds link the AA’s together.

Front 12

Transcription Factors: What are they?

Back 12

They are DNA binding proteins, which bind to specific sequences of DNA and act as switches to activate or repress transcription of certain genes.

Front 13

Naming A Full Nucleotide: How do you do so?

Back 13

You look at the base and determine whether the nucleotide is a part of RNA or DNA. You then look at the phosphate group (mono, di, or tri). For RNA specifically, you use the world “ribose” in place of deoxy.

Front 14

Protein-DNA Interaction: How does protein read the bases? Which protein causes the conformational change?

Back 14

Proteins can see sequences to bind to. When initial protein binds to sequence, it causes distortion of DNA so that other bases are either hidden or more exposed that affects other proteins’ ability to bind. The TATA box-binding protein causes conformational change.

Front 15

Separation of DNA Strands: What binds the base pairs together? What holds the strands together? When do the strands separate? What is the melting temperature? How do you separate DNA strands or denature it? How do G-C pairs relate to DNA denaturation and melting temperature?

Back 15

Hydrogen bonds hold the base-pairs together (A-T pair makes two H bonds; G-C makes three H-bonds) along with some hydrophobic and van der Waals interactions between the stacked base pairs.

The strands separate during replication and transcription of DNA.

Melting temperature is the temperature at which half the pairs of a DNA strand are pulled apart or denatured to make single strands.

You can denature a DNA strand by using high temperatures, pH extremes, or helicase proteins (helicases are proteins in cells that unwind DNA).

Molecules that have more G-C pairs require higher temperatures to denature due to its 3 hydrogen bonds (1 more than A-T pairs). G-C pairs can be estimated from the melting temperature.

Front 16

Detection of DNA Denaturation: What can you use to detect DNA denaturation? What can melting temperature be related to?

Back 16

You can use light in the form of temperature. Electronic structure of bases absorb light when bases are in single stranded form, but absorbance is much higher when bases are paired in double stranded form. As you increase the temperature, DNA will increasingly absorb light as single strands are formed. As you decrease it, DNA will decreasingly absorb light as they form double strands again.