Bio info

Binomial nomenclature

• the system of naming organisms using a two-part format consisting of the genus name followed by the species name.

• Each species has a unique two-part name.

  • Genus: Capitalized

  • Species Descriptor: Lowercase

  • Example: Amphiprion ocellaris (Ocellaris clownfish).

Four kingdom’s

• Protista: Diverse, mostly unicellular organisms.

• Plantae: Multicellular organisms that photosynthesize.

• Fungi: Decomposers with cell walls, not photosynthetic.

• Animalia: Multicellular, typically with nervous systems and locomotion.

Levels of biological organization

1. Atoms

2. Molecules

3. cells

4. Tissues

5. Organs

6. Organisms

7. Population

8. Community

9. Ecosystem

10. Biosphere

Mitochondria

• Part of semiautonomous organelles

• tiny structures inside cells that produce energy

• have their own DNA and can make some of their own parts

• still need the cell to help them function

• often called the cell's "powerhouses" because they create most of the cell’s energy

• responsible for generating adenosine triphosphate (ATP) through cellular respiration.

Descent with modification

• Part of Darwins theory

• All species share common ancestry

• Changes occur through

  natural selection

Modification of structures

• Part of Darwins theory

• Existing structures adapt for new functions

• (e.g., limbs evolving into wings or flippers).

Scientific method

• a systematic approach to investigating phenomena, acquiring new knowledge, or correcting and integrating previous knowledge, involving observation, hypothesis formation, experimentation, and analysis.

1. observations & question

2. hypothesis

3. experimental design

4. data collection

5. data analysis

6. results

7. conclusion

Decondense

• The process of chromosomes relaxing and becoming less compact after mitosis or meiosis.

Three mechanisms contribute to genetic variation

• crossing over

• independent assortment of chromosomes

• random fertilization.

Evolutionary history

• Life began on Earth as primitive cells between 3.5 to 4 billion years ago

• Evolutionary change involves modificationsof pre-existing characteristics

  • Structures may be modified to serve new purposes
  

How does a single organism produce different types of cells?

• The DNA is identical in each cell of an organism

• However, the cells have different proteomes

Father of modern taxonomy

• Carolus Linnaeus (1707-78)

How Organisms are Classified

• A species is placed into progressively smaller groups that are more closely related

• Emphasizes the unity and diversity of different species

• Example:Clownfish (Amphiprion ocellaris)

Theory of Spontaneous Generation

• Redi’s Experiment challenged the idea of Spontaneous Generation by trying to prove that:

• Flies came from maggots – Maggots came from eggs – Eggs came from flies

When Forming a Hypothesis

• List possible explanations

• This includes alternative hypotheses

• based on your previous experience (what you already know); and on research you have done

• All of the hypotheses must be testable

Define the concepts of genes and alleles.

Genes are segments of DNA that contain the instructions for producing proteins, which determine traits and biological functions in an organism. Alleles are different versions or variations of a gene that can result in different traits, such as eye color or blood type, depending on which allele is inherited.

What r the outline phases of the eukaryotic cell cycle?

The eukaryotic cell cycle consists of four main phases:

1. G1 phase (Gap 1): The cell grows, carries out normal functions, and prepares for DNA replication.

2. S phase (Synthesis): The cell replicates its DNA, producing two copies of each chromosome.

3. G2 phase (Gap 2): The cell continues to grow and prepares for mitosis, ensuring that all DNA has been accurately replicated.

4. M phase (Mitosis): The cell undergoes mitosis (nuclear division) followed by cytokinesis (cytoplasmic division), resulting in two daughter cells.

Additionally, the cell may enter a resting phase called G0, where it temporarily or permanently stops dividing.

Mitosis

1. Prophase:

   • Chromosomes condense and become visible.

   • The mitotic spindle begins to form from the centrosomes.

   • The nuclear envelope starts to break down.

2. Prometaphase:

   • The nuclear envelope fully disintegrates.

   • Spindle fibers attach to kinetochores on the centromeres of chromosomes.

   • Chromosomes begin to move toward the cell’s center.

3. Metaphase:

   • Chromosomes align at the metaphase plate (the cell’s equator).

   • Each chromosome is attached to spindle fibers from opposite poles.

4. Anaphase:

   • Sister chromatids are pulled apart as the spindle fibers shorten, moving them toward opposite poles.

   • The cell elongates as the polar microtubules push against each other.

5. Telophase:

   • Chromosomes reach the poles and begin to decondense.

   • Nuclear envelopes re-form around each set of chromosomes.

   • The spindle apparatus disassembles.

Cytokinesis (not technically part of mitosis but closely associated) occurs after telophase, where the cytoplasm divides, resulting in two genetically identical daughter cells.

Describe the processes of synapsis and crossing over.

• Synapsis is the process during prophase I of meiosis in which homologous chromosomes (one from each parent) pair up closely along their lengths, forming a structure called a bivalent or tetrad. This pairing allows for precise alignment of homologous genes.

• Crossing over occurs during synapsis when non-sister chromatids of homologous chromosomes exchange segments of genetic material. This exchange happens at points called chiasmata and results in new combinations of alleles on the chromatids, contributing to genetic variation in the offspring.

Meiosis l & ll

Meiosis I (Reduction Division):

1. Prophase I:

• Chromosomes condense, and homologous chromosomes pair up in a process called synapsis.

• Crossing over occurs between non-sister chromatids, leading to genetic recombination.

• The nuclear envelope breaks down, and the spindle apparatus forms.

2. Metaphase I:

• Homologous chromosome pairs (bivalents) align at the metaphase plate.

• Spindle fibers from opposite poles attach to the kinetochores of each homolog.

3. Anaphase I:

• Homologous chromosomes are separated and pulled toward opposite poles of the cell (sister chromatids remain attached).

• This reduces the chromosome number by half (from diploid to haploid).

4. Telophase I:

• Chromosomes reach the poles, and the nuclear envelope may re-form.

• The cell undergoes cytokinesis, resulting in two haploid daughter cells.

Meiosis II (Equational Division):

1. Prophase II:

• Chromosomes condense again if they had decondensed, and the spindle apparatus reforms in each haploid cell.

• The nuclear envelope breaks down (if it had re-formed).

2. Metaphase II:

• Chromosomes (now consisting of sister chromatids) align at the metaphase plate in each cell.

3. Anaphase II:

• Sister chromatids are separated and pulled toward opposite poles, similar to mitosis.

4. Telophase II:

• Chromatids reach the poles, and the nuclear envelope re-forms around each set of chromosomes.

• Cytokinesis occurs, producing four genetically distinct haploid daughter cells.

Result:

• Meiosis produces four non-identical haploid cells (e.g., sperm or egg cells), each with half the original number of chromosomes.

Mitosis

Prophase

Prometaphase

Metaphase

Anaphase

Telophase

Cytokinesis

Mitosis metaphase

Chromosomes line up at the metaphase plate (the center of the cell). Spindle fibers ensure that each chromosome is attached to both poles of the spindle apparatus.

Mitosis Anaphase

Sister chromatids are pulled apart towards opposite poles of the cell by the spindle fibers.

Mitosis telophase

Chromatids reach the poles, and the nuclear envelope re-forms around each set of chromosomes. Chromosomes begin to de-condense.

Mitosis cytokinesis

The cytoplasm divides, resulting in two genetically identical daughter cells.

Meiosis l

Prophase I

Prometaphase I

Metaphase I

Anaphase I

Telophase I

Cytokinesis I

Meiosis l prophase l

Chromosomes condense, and homologous chromosomes pair up (synapsis) to form tetrads. Crossing over occurs, exchanging genetic material between homologous chromosomes. The nuclear envelope breaks down, and spindle fibers form.

Meiosis l prometaphase l

Chromosomes condense, and homologous chromosomes pair up (synapsis) to form tetrads. Crossing over occurs, exchanging genetic material between homologous chromosomes. The nuclear envelope breaks down, and spindle fibers form.

Meiosis l metaphase l

Tetrads align along the metaphase plate. Each homologous chromosome is connected to spindle fibers from opposite poles.

Meiosis l anaphase l

Homologous chromosomes are pulled apart to opposite poles, but sister chromatids remain attached.

Meiosis l telophase l

Chromosomes reach the poles, and the nuclear envelope may reform around each set. Chromosomes may de-condense slightly.

Meiosis l cytokinesis l

The cell divides into two haploid cells, each with half the number of chromosomes but with sister chromatids still joined.

Meiosis ll

1. Prophase II

2. Prometaphase II

3. Metaphase II

4. Anaphase II

5. Telophase II:

6. Cytokinesis II:

Meiosis ll prophase ll

Chromosomes condense again, and the nuclear envelope breaks down. Spindle fibers form in each haploid cell.

Meiosis ll prometaphase ll

The nuclear envelope dissolves completely, and spindle fibers attach to the kinetochores of sister chromatids.

Meisosis ll metaphase ll

Chromosomes line up along the metaphase plate in each haploid cell.

Meiosis ll anaphase ll

Sister chromatids are finally separated and pulled to opposite poles.

Meisosis ll telophase ll

Chromatids reach the poles, and the nuclear envelope re-forms around each set of chromosomes. Chromosomes begin to de-condense.

Meiosis ll cytokinesis lol

Each of the two haploid cells divides, resulting in four genetically unique haploid daughter cells

Mitosis prophase

1. Prophase:

   • Chromosomes condense and become visible.

   • The mitotic spindle begins to form from the centrosomes.

   • The nuclear envelope starts to break down.

Mitosis prometaphase

1. Prometaphase:

   • The nuclear envelope fully disintegrates.

   • Spindle fibers attach to kinetochores on the centromeres of chromosomes.

   • Chromosomes begin to move toward the cell’s center.

Comparison in meiosis and mitosis

• Mitosis results in two identical diploid cells from one diploid cell.

• Meiosis results in four unique haploid cells from one diploid cell.

The key differences lie in the pairing of homologous chromosomes and crossing over during meiosis, which introduces genetic diversity, whereas mitosis is more about producing identical cells for growth and repair.

mitotic spindle

a structure made of microtubules that organizes and separates chromosomes during cell division, ensuring accurate distribution to daughter cells.

What are the levels of biological organization from smallest to largest?

Atoms, Molecules, Cells, Tissues, Organs, Organism, Population, Community, Ecosystem, Biosphere.

What are the main differences between prokaryotic and eukaryotic cells?

Prokaryotic cells lack a nucleus and are simpler (e.g., bacteria). Eukaryotic cells have a nucleus and internal membranes forming organelles (e.g., plants, animals).

What is the role of the nucleus in a eukaryotic cell?

The nucleus contains DNA, regulates gene expression, organizes chromosomes, and is the site for ribosome assembly.

Define biological evolution.

Biological evolution is the change in species over time through mechanisms like natural selection and descent with modification.

What are the three domains of life?

• Bacteria, Archaea, Eukarya.

• Describe the process of vertical descent in evolution.

• Vertical descent involves the progression of changes in a lineage, where new species evolve from pre-existing ones through accumulated mutations and natural selection.

• What is the difference between a genome and a proteome?

• The genome is the complete genetic material of an organism, while the proteome is the complete set of proteins expressed by an organism.

• Explain binomial nomenclature.

• Binomial nomenclature is the scientific naming system where each species is given a two-part name: the genus (capitalized) and the species descriptor (not capitalized), both italicized (e.g., Amphiprion ocellaris)

 What are the main components of the endomembrane system in eukaryotic cells?

• Nuclear envelope, Endoplasmic Reticulum, Golgi Apparatus, Lysosomes/Vacuoles, Peroxisomes, Plasma Membrane

What is the role of the mitochondria in a cell?

• Mitochondria are responsible for ATP production, synthesis and modification of organic molecules, and production of heat.

What are the two mechanisms of evolutionary change?

• Vertical descent with mutation and Horizontal gene transfer

What is the difference between genomics and proteomics?

• Genomics is the study of DNA sequences, while proteomics is the study of proteins.

 What is artificial selection?

• Artificial selection is the process by which humans selectively breed organisms for desired traits.

Name the three domains of life

•  Bacteria, Archaea, Eukarya

What are the four kingdoms of the domain Eukarya?

• Protista, Plantae, Fungi, Animalia

How is binomial nomenclature used in classification?

•  Binomial nomenclature gives each species a two-part name: the genus (capitalized) and the species descriptor (lowercase), both italicized.

1. What is the scientific method used for?

To test theories through observation, forming hypotheses, experimentation, data collection, and drawing conclusions.

1. What distinguishes a hypothesis from a theory?

A hypothesis is a testable explanation for a phenomenon, while a theory is a broad explanation supported by extensive evidence.

What is  Define discovery-based science.

Discovery-based science involves collecting and analyzing data without a preconceived hypothesis to gather information and often leads to hypothesis testing.

1. What are the key steps of the scientific method?

Observations, Questions, Hypothesis, Experimentation, Data Collection, Conclusion, Publication.

1. What was the main conclusion of Redi’s experiment?

Maggots appear only when flies come into contact with meat, disproving the idea of spontaneous generation.

1. What is an independent variable in an experiment?

The factor that is deliberately changed by the experimenter.

1. How does a good hypothesis differ from a bad one?

A good hypothesis is testable and based on scientific evidence, while a bad hypothesis is not scientifically testable or lacks evidence.

1. What are controlled variables in an experiment?

Factors that are kept constant to ensure that the test results are due to the manipulation of the independent variable alone.

1. What are the main phases of the eukaryotic cell cycle?

Interphase (G1, S, G2) and Mitotic Phase (Mitosis + Cytokinesis)

1. What occurs during the G1, S, and G2 phases of Interphase?

• G1: Cell growth and preparation for DNA synthesis.

• S: DNA replication; chromosomes duplicate into sister chromatids.

• G2: Preparation for mitosis; synthesis of proteins required for cell division.

1. List the phases of mitosis in order.

Prophase, Prometaphase, Metaphase, Anaphase, Telophase

1. How does cytokinesis differ between animal and plant cells?

• Animals: Cleavage furrow constricts to separate the cells.

• Plants: Cell plate forms to create a new cell wall between daughter cells.

1. What is the primary difference between Meiosis I and Meiosis II?

• Meiosis I: Homologous chromosomes separate, reducing chromosome number by half.

• Meiosis II: Sister chromatids separate, similar to mitosis but without an intervening S phase.

1. What is crossing over and when does it occur?

• Crossing over is the exchange of genetic material between homologous chromosomes during Prophase I of meiosis.

1. What mechanisms contribute to genetic variation in sexual reproduction?

Independent assortment, crossing over, and random fertilization.

1. How many chromosomes do humans have in total and how are they divided?

Humans have 46 chromosomes (23 pairs), including 22 pairs of autosomes and 1 pair of sex chromosomes (XX or XY).

1.  What are the three main checkpoints in the cell cycle?

 G1 checkpoint, G2 checkpoint, Metaphase checkpoint.

1. What is the difference between diploid and haploid cells?

Diploid (2n): Cells with two sets of chromosomes (e.g., somatic cells).

• Haploid (n): Cells with one set of chromosomes (e.g., gametes).

What is resource partitioning?

The differentiation of niches, in both space and time, that allows similar species to coexist.

What is character displacement?

The tendency for species to evolve distinct traits in sympatric populations to minimize competition.

What is the difference between a fundamental and realized niche?

A fundamental niche is the full range of conditions under which a species can survive, while a realized niche is the actual range limited by competition.

Q: Give two examples of anti-predator strategies.

Camouflage and chemical defense.

What is Müllerian mimicry?

A: When two harmful species resemble each other to reinforce avoidance by predators.

what is Batesian mimicry?

When a harmless species mimics a harmful one to avoid predation.

Q: Describe the Bottom-Up Control hypothesis.

A: Population size is controlled by the availability of resources and energy from lower trophic levels.

Q: Describe the Top-Down Control hypothesis.

A: Population sizes are controlled by predators and natural enemies that regulate prey populations.

Q: What is parasitism?

A: A relationship where one organism (the parasite) feeds off another (the host) without killing it outright.

Q: What is mutualism?

A: A close relationship where both species benefit.

Q: What is commensalism?

A: A relationship where one species benefits while the other is unaffected.

Q: What is an example of resource-based mutualism?

A: Both species receiving benefits in the form of resources, like plants and their pollinators.

Q: What are plant mechanical defenses?

A: Physical structures like thorns or tough leaves to deter herbivores.

Q: What is population density?

A: The number of organisms in a given unit area or volume.

Q: What is the mark-recapture technique?

A: A method for estimating population size by marking animals and recognizing them when captured again.

Q: What are the limitations of the mark-recapture technique?

A: Animals may learn to avoid traps (leading to overestimation) or become "trap-happy" (leading to underestimation).

Q: What are the three types of dispersion patterns?

A: Clumped (most common), uniform, and random (rarest).

Q: What is semelparity?

A: A reproductive strategy where organisms produce all offspring in a single reproductive event and then die.

Q: What is iteroparity?

A: A reproductive strategy where organisms reproduce multiple times throughout their life cycle.

Q: What are the three types of survivorship curves?

• Type I: Low juvenile mortality, most die later in life (e.g., humans).

• Type II: Uniform death rate (e.g., birds).

• Type III: High juvenile mortality, low mortality for survivors (e.g., fish).

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Q: What is the net reproductive rate (R₀)?

A: A measure of population growth; R₀ > 1 means the population is growing, R₀ < 1 means it is declining, and R₀ = 1 means it is stable.

Q: What is exponential growth?

A: Population growth without limits, resulting in a J-shaped curve.

Q: What is logistic growth?

A: Population growth that slows as it approaches carrying capacity (K), resulting in an S-shaped curve.