Biology Notes - Bacteria, Viruses, DNA, and More PDF

### Bacteria - **Feature** | **Archaea** | **Bacteria** - ---------------- | ------------- | ------------- - **Cell wall** | No peptidoglycan | Peptidoglycan - **Membrane Lipids** | Ether Linkages | Ester linkages - **Habitat** | Extreme environments (hot springs, salty lakes) | Commo...

### Bacteria - **Feature** | **Archaea** | **Bacteria** - ---------------- | ------------- | ------------- - **Cell wall** | No peptidoglycan | Peptidoglycan - **Membrane Lipids** | Ether Linkages | Ester linkages - **Habitat** | Extreme environments (hot springs, salty lakes) | Common in many environments (soil, water, human body) - **Pathogenicity** | Not known to cause diseases | Some bacteria are pathogenic - **Sensitivity to antibiotics** | Not typically affected by antibiotics | Affected by many antibiotics ### Shapes of Bacteria 1. **Cocci** (coccus) - round 2. **Bacillus** - rod-shaped 3. **Spirill** - spiral shaped 4. **Comma shaped** - vibrio ### Hans Christian Gram - He invented the gram staining. - **Gram (+)** - purple - thick peptidoglycan (double wall) - **Gram (-)** - pink - thin peptidoglycan (wall) - Is covered by an outer membrane - **Safranin** - will show the gram negative (pink) - **Ethanol** - will come to clean, remove the thin layer of the cell wall. ### Fimbricae and Pili: - Bacteria use fimbriae and pili to attach cell surfaces or to each other - **Sex pili** - help transmit DNA between bacteria ### Halophiles - loves salt ### Symbiosis ### Viruses that cause Cancer: - Some viruses can lead to cancer by integrating their genetic material into host DNA, disrupting normal cell regulation. - **Examples include:** - **Human Papillomavirus (HPV):** causes cervical cancer - **Hepatitis B virus:** linked to liver cancer - **Epstein-Barr Virus:** associated with Burkitt's lymphoma and nasopharyngeal cancer - **Human T-cell leukemia virus (HTLV-1):** causes adult T-cell leukemia ### DNA and RNA viruses 1. **DNA viruses:** - Contain DNA as their genetic material. - Replication: DNA is replicated in the host cell's nucleus using host enzymes. - Examples: Herpesviruses. 2. **RNA viruses:** - Contain RNA as their genetic material. - Replication: RNA is replicated in the host cell's cytoplasm. They rely on RNA-dependent RNA polymerase or undergo reverse transcription (in retroviruses). - Example: Influenza virus ### HIV (Human Immunodeficiency Virus) - HIV is a **retrovirus** with an RNA genome. - **Replication process:** 1. HIV enters the host cell and releases its RNA. 2. Reverse transcriptase converts viral RNA into double-stranded DNA (dsDNA) 3. The dsDNA is integrated into the host's DNA by **integrase.** 4. Host machinery produces new viral RNA and proteins 5. New HIV particles assemble and exit the cell by **budding**, taking part of the host membrane. ### Watson and Crick - In 1953, James Watson and Francis Crick proposed the **double-helix model** of DNA. - They showed that DNA has: - Two strands running antiparallel. - Complementary base pairing (A=T) (G=C) - The structure allows for both information storage and replication. ### Direction of Nucleotides: - **DNA synthesis** occurs in the **5' to 3' direction.** - DNA polymerase can only add nucleotides to the 3' hydroxyl group of an existing strand. - The 5' end has a phosphate group attached, while the 3' end has a hydroxyl group attached. ### Basic Units of DNA: - DNA is made of **nucleotides**, each consisting of: - Deoxyribose - Phosphate group - Nitrogenous base: adenine (A), thymine (T), guanine (G), cytosine (C). - Nucleotides are connected by **phosphodiester bonds** between the 3' carbon of one sugar and the 5' phosphate of the next. ### Okazaki fragments: - Okazaki fragments are short DNA segments synthesized on the **lagging strand** during replication. - They are created because **DNA polymerase** synthesizes DNA only in the **5' to 3' direction** - Each fragment begins with a **RNA primer**, which is later replaced with DNA and joined by **DNA ligase.** ### Chromosome, Chromatin, and Chromatid - **Chromatid:** One of two identical copies of a duplicated chromosome, held together at the centromere. - **Somatic cells:** Are the body's non-reproductive cells. They are **diploid**, meaning they contain 2 complete sets of chromosomes, and they reproduce through mitosis to create identical daughter cells. - **Sex cells (gamete):** Are specialized cells involved in reproduction. In humans, the sex cells are sperm and ova. Unlike somatic cells, sex cells are **haploid**, meaning they contain only half the number of chromosomes, which ensures that when fertilization occurs, the resulting offspring will have the correct number of chromosomes. - **Autosomal:** Refers to 22 pairs of chromosomes that are not involved in sex determination. They carry genes responsible for various traits and functions. Humans have 44 autosomal chromosomes and 2 sex chromosomes (XX or XY). They can be inherited in dominant or recessive patterns. ### Stages of Meiosis - **Meiosis I:** - Prophase I: Homologous chromosomes synapse and exchange segments by crossing over; nuclear envelope breaks down. - Metaphase I: Tetrads line up across the cell midplane. - Anaphase I: Homologous chromosomes separate and move to the opposite poles. - Telophase I: One chromosome of each pair is at each pole; cytokinesis occurs. - **Meiosis II:** - Prophase II: Chromosomes condense. - Metaphase II: Chromosomes line up at the midplane. - Anaphase II: Sister chromatids separate and move to the opposite poles. - Telophase II: Nuclei form at the poles of the cell, and cytokinesis occurs. - **Mitosis:** A parent cell transmits one copy of every chromosome to its 2 daughter cells. (nuclear process and DNA duplication) ### Difference between chromosome, chromatin, and chromatid - **Chromosome:** Highly packaged structure composed of DNA and proteins that becomes visible during cell division when chromatin condenses. Each species has a characteristic number of chromosomes, with humans having 46 chromosomes that contain the genetic info. - **Chromatin:** Is the extended and partially unraveled form of DNA that is present when the cell is not dividing. In this state, the DNA is wound around histones. ### Stages of Mitosis 1. **Prophase:** - Chromosomes become visible. - Sister chromatids held by centromeres which are held together by cohesion. - Attached to each centromere is a Kinetochore where the microtubules can bind - Chromatid condenses for the chromosomes to be able to attach the spindle fibers by Kinetochores. 2. **Prometaphase:** - Nuclear membrane breaks down. - Spindle microtubules - shorten or lengthen as they contact chromosomes. - Chromosomes start to move to the middle. 3. **Metaphase:** - Chromosomes line up in the middle. - Chromatids are very condensed - The cohesion dissociates completely - At this phase, we can tell if there is a certain abnormality by forming a karyotype - At this phase, the Kinetochores shorten while the non Kinetochores lengthen in order to maintain the chromosomes in the middle plate. - Pericentriolar, Kinetochores, and non Kinetochores maintain the structure 4. **Anaphase:** - Sister chromatids separate and move to opposite poles of the cell. - Kinetochores shorten to pull the chromosomes. 5. **Telophase:** - Chromosomes reach to the poles - Nuclear envelope will reappear - Nuclear envelope starts to be formed; spindle microtubules disappear. ### 3 Phases of Interphase 1. **G1 phase:** Cell will grow, increase in number increase in the activity of enzyme required and DNA synthesis 2. **S phase:** DNA replicates and histone proteins are synthesized 3. **G2 phase:** Protein synthesis increases in preparation for division (mitosis) ### M phase - **Mitosis and Cytokinesis:** - nuclear division that produces 2 nuclei containing chromosomes identical to the parental nucleus. - Division of cytoplasm into 2 separate cells. - This is unlike meiosis because of crossing over, they can't have identical chromosomes. ### Stages of Meiosis - **Meiosis I:** Partner homologous chromosomes pair, then separate and move into different nuclei. - **Meiosis II:** Sister chromatids separate and are distributed to 2 different nuclei. ### Gregor Mendel - The 2 fundamental laws of inheritance are: 1. **Law of segregation:** This law states that each organism has two alleles for each trait and these alleles separate during gamete formation. Each gamete receives one allele. During fertilization, offspring receive one allele from each parent. This was demonstrated through Mendel's pea plant experiments. 2. **Law of Independent Assortment:** This law states that alleles for different genes are distributed independently of one another during gamete formation. This means that the inheritance of one trait will not affect the inheritance of another trait as long as the genes are located on different chromosomes. - He conducted the scientific study of inheritance by breeding pea plants. He chose strains of pea plants representing several characters and observed how these traits were passed on. ### Mendel's Experiments - Mendel's principles come from experiments where he crossed plants from two true breeding lines with different phenotypes. - **Generations:** - **P generation:** Parental generation, consisting of genetically pure individuals. - **F1 generation:** The first generation of offspring all resembling one parent. - **F2 generation:** The second generation, showing a 3:1 ratio of dominant traits to recessive traits. ### Punnett Square/Codominance - Incomplete dominance - dominant - recessive. 1. **Punnett Square:** Is a grid arrangement that shows the possible combinations of alleles. - Example: Mating BB and bb: - F1 generation only Black (B). However, mating the two F1 offspring yields an F2 generation offspring in expected ratio 3 Black to 1 brown, indicating that F1 is heterozygous. 2. **Dominant - Recessive:** - *Dominant:* It is one that masks the expression of another trait. It is expressed when at least one dominant allele is present. - *Recessive:* It is one that is masked by a dominant trait. It is expressed only when 2 copies of the recessive allele are present. 3. **Codominance:** When two different alleles are fully expressed in the offspring. The phenotype shows distinct traits from both parents simultaneously. - Example: Black cow x white cow - offspring shows a blend of the traits from both parents with black and white spots. 4. **Incomplete dominance:** Offspring shows a blend of the traits from both parents. Neither allele is completely dominant, so the phenotype is an intermediate between the two - Example: Red x White → Pink. RR x WW → RW (pink) ### Types of Crosses 1. **Monohybrid Cross:** A cross between homozygous parents with different alleles leading to the law of segregation. Example: Purple flowered plant (PP) x white flowered plant (pp) 2. **Dihybrid Cross:** Two pairs of alleles called on non-homologous chromosomes are inherited independently, leading to the law of independent assortment. Example: Crossing guinea pigs with different for colors and for lengths, F2 offspring ratio 9:3:3:1 ratio in the phenotypes of the F2 generations. 3. **Test Cross:** Used to determine the genotype of an individual by crossing it with a recessive individual. ### His goals 1. Understand patterns of inheritance. 2. Identify dominant and recessive traits. 3. Formulate genetic laws. ### The 7 characters (criteria): 1. Stem height (tall x short) 2. Flower color (purple x white) 3. Flower position (axial x terminal) 4. Pod color (green x yellow) 5. Pod shape (inflated x pinched) 6. Seed color (yellow x green) 7. Seed shape (smooth x wrinkled)