Chapter 10: Biochemistry of The molds Genome

1. Describe how Hämmerling used single celled Algae to find that genetic information was located in the nucleus.

Joachim Hämmerling used Acetabularia, a single-celled alga, to show that genetic info is stored in the nucleus. He cut off either the cap or the foot of the cells. When he removed the cap, it grew back, but when he took off the foot, no new foot grew. This pointed to the foot, which holds the nucleus, as the source of the genetic material. In other experiments, he switched the stalks between two different species and found that the cap shape was always determined by the foot's nucleus, confirming that the nucleus controls the cell’s traits.

2. How did Beadle and Tatum’s experiments with mold spores result in their one gene–one enzyme hypothesis.

Beadle and Tatum's experiments with mold spores led to the "one gene–one enzyme" hypothesis by showing how mutations in specific genes affected the mold's ability to produce certain enzymes. They exposed Neurospora crassa spores to X-rays to cause mutations, then grew them on different types of media. Mutants that couldn't grow on minimal medium but could grow on complete medium (with added vitamins and amino acids) were identified. By adding individual amino acids to the minimal medium, they found that each mutant was missing the ability to produce a specific enzyme in the arginine biosynthesis pathway. This showed that each gene is responsible for making a specific enzyme, which led to their hypothesis that one gene encodes one enzyme.

3. How did the Griffith experiments show transformation of Streptococcus cells?

Griffith's experiments with Streptococcus pneumoniae demonstrated the process of transformation by showing how harmless bacteria could become deadly. He worked with two strains: the rough (R) strain, which is nonpathogenic and lacks a capsule, making its colonies appear rough on plates, and the smooth (S) strain, which is pathogenic and has a capsule that helps it evade the immune system. The capsule gives the S strain a smooth appearance on plates. In his experiments, Griffith injected mice with different combinations of these strains. When mice were injected with the live S strain, they died because the bacteria were virulent. Mice injected with either the live R strain or heat-killed S strain survived, as neither was harmful. However, when he injected mice with a mixture of live R strain and heat-killed S strain, the mice died. From the dead mice, Griffith recovered only live S strain bacteria. This meant something from the dead, heat-killed S strain had been transferred to the live R strain, transforming it into the deadly S strain. He called this unknown factor the "transforming principle," which later helped scientists understand that DNA carries genetic information.

4. How did Avery et al determine that DNA, and not the other organic polymers, was the transforming factor?

Avery and his colleagues determined that DNA was the transforming factor through a series of experiments where they selectively destroyed different organic molecules in the heat-killed Streptococcus pneumoniae S strain. First, they extracted a mixture of organic materials, including proteins, lipids, carbohydrates, and nucleic acids, from the heat-killed S strain, which had been shown to transform the harmless R strain into the pathogenic S strain. They then treated the mixture with enzymes that specifically broke down one type of organic molecule at a time: protease for proteins, lipase for lipids, amylase for carbohydrates, ribonuclease (RNase) for RNA, and deoxyribonuclease (DNase) for DNA. After each treatment, they tested whether the remaining material could still transform the R strain. They found that destroying proteins, lipids, carbohydrates, or RNA did not stop the transformation, but when DNA was destroyed with DNase, the transformation did not occur. This led them to conclude that DNA was the "transforming factor" responsible for passing genetic information, proving that DNA, not other molecules, carries hereditary material.

5. Describe Hershey and Chase’s experimental proof that DNA was the genetic material.

Hershey and Chase provided experimental proof that DNA is the genetic material through their work with bacteriophages, which are viruses that infect bacteria. In their classic experiment conducted in 1952, they prepared two batches of T2 phages. In the first batch, they labeled the DNA with radioactive phosphorus-32 (³²P), as DNA contains phosphorus but proteins do not. In the second batch, they labeled the proteins with radioactive sulfur-35 (³⁵S), since proteins contain sulfur but DNA does not. The labeled phages were then allowed to infect Escherichia coli (E. coli) bacteria. After the phages attached to the bacteria and injected their genetic material, the researchers used a blender to separate the phage protein coats from the bacterial cells. They then centrifuged the mixture to separate the heavier bacterial cells from the lighter phage coats, with the bacterial cells forming a pellet at the bottom and the remaining phage coats staying in the supernatant. Upon measuring the radioactivity in both the bacterial pellet and the supernatant, Hershey and Chase found that the radioactive phosphorus (³²P) was present in the bacterial pellet, indicating that DNA had entered the bacteria, while the radioactive sulfur (³⁵S) remained in the supernatant, showing that the protein did not enter the cells. This clear distinction demonstrated that DNA, not protein, was the genetic material responsible for carrying the instructions for producing new phages, providing strong evidence that DNA is the hereditary material and advancing the understanding of genetics.

6. Describe the structure of nucleotide monomers and polymers.

Nucleotides are the building blocks of nucleic acids like DNA and RNA. Each nucleotide consists of three components: a phosphate group, a five-carbon sugar (ribose in RNA and deoxyribose in DNA), and a nitrogenous base (adenine, thymine, cytosine, or guanine in DNA; adenine, uracil, cytosine, or guanine in RNA). 

In nucleic acid polymers, nucleotides are linked together by phosphodiester bonds, which form between the phosphate group of one nucleotide and the sugar of the next. This creates a sugar-phosphate backbone with nitrogenous bases extending from it. The sequence of these bases encodes genetic information.

1. How is DNA complementary and antiparallel?

DNA is composed of two strands that run in opposite directions, making them antiparallel. One strand runs in a 5' to 3' direction. 

While the complementary strand runs 3' to 5'. The strands are held together by hydrogen bonds between complementary nitrogenous bases: adenine pairs with thymine (A-T), and cytosine pairs with guanine (C-G). 

2. Describe the similarities and differences between RNA and DNA

Similarities: Both RNA and DNA are nucleic acids made up of nucleotide monomers. They both play crucial roles in storing and expressing genetic information. Each contains the bases adenine, cytosine, and guanine.

Differences: 

-Sugar: RNA contains ribose sugar, while DNA contains deoxyribose sugar (which lacks one oxygen atom). 

-Strands: DNA is typically double-stranded, forming a double helix, while RNA is usually single-stranded. 

-Nitrogenous Bases: DNA has thymine (T), whereas RNA has uracil (U) in place of thymine. 

-Function: DNA primarily serves as the genetic blueprint; DNA stores information for cell function and is passed to daughter cells through vertical gene transfer during replication. A cell duplicates its DNA before dividing, ensuring each new cell gets a copy. DNA can also be broken down for nucleosides and nucleotides but does not serve a structural role.

 RNA is involved in various functions related to protein synthesis (mRNA, rRNA, tRNA,) and gene expression.

3. Identify functions for various RNAs used in protein synthesis: mRNA, tRNA and rRNA.

-mRNA carries the genetic information from DNA to the ribosome, where proteins are synthesized. It serves as a template for translating the sequence of nucleotides into an amino acid sequence.

-tRNA is responsible for bringing the appropriate amino acids to the ribosome during protein synthesis. Each tRNA molecule is specific to one amino acid and has an anticodon that pairs with the corresponding codon on the mRNA

-rRNA is a key component of ribosomes, the cellular machinery where protein synthesis occurs. It helps catalyze the formation of peptide bonds between amino acids and ensures the proper alignment of mRNA and tRNA during translation.

7. Define gene, chromosome, genome and plasmid. Differentiate genotype from phenotype

A gene is a segment of DNA that contains the instructions for producing a specific protein or RNA molecule, influencing an organism's traits and functions. AKA Stretch of DNA that codes for a functional product.

A chromosome is a tightly coiled structure made of DNA and proteins that carries genetic information. Chromosomes are found in the nucleus of eukaryotic cells and in the cytoplasm of prokaryotic cells.

The genome is the complete set of genetic material, including all of the organism's genes and non-coding sequences, contained within its chromosomes. It represents the full hereditary information of an organism. AKA all genetic info in cells.

A plasmid is a small, circular piece of DNA that is separate from chromosomal DNA and can replicate independently. Plasmids are commonly found in bacteria and often carry genes that confer advantageous traits, such as antibiotic resistance.

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Genotype: The genetic makeup of an organism, specifically the versions of a gene it possesses. It represents the information encoded in the DNA.

Phenotype: The physical traits that can be seen and biochemical characteristics of an organism, resulting from the interaction between its genotype and the environment.

8. Compare prokaryotic and eukaryotic chromosome structure and packaging

Prokaryotic Cells: Have a single, circular chromosome located in the nucleoid region. This chromosome is not associated with histones and is relatively simple in structure.

The chromosome is tightly coiled to fit within the cell. DNA-binding proteins help organize the DNA within the nucleoid.

Eukaryotic Cells: Have multiple linear chromosomes located within a membrane-bound nucleus. Are complex and consist of DNA tightly coiled around histone proteins, forming a chromatin structure. Including plasmids, mitochondria/chloroplast, and viruses.

DNA is wrapped around histones, forming nucleosomes, which further coil and condense to create higher-order structures. This packaging allows for more efficient DNA management during cell division and gene expression regulation.