Cell Structure and Organization

Cell Structure & Organization

• Cells are the basic, functional units of life and the smallest independent component that we find when breaking down an organism.
• Cells are the smallest, basic unit of life responsible for all of life's processes.

Types of Cells

• Prokaryotic cells lack a nucleus, possess a nucleoid region where genetic material is suspended, and are single-celled microorganisms.
• Examples of prokaryotes: archaea, bacteria, and cyanobacteria.
• Eukaryotic cells possess a true nucleus and includes plants, fungi, protozoans, and animals.

Cell Structure

• Cell structures consist of individual components with specific functions essential for carrying out life's processes.
• Cell structure components include: cell wall, cell membrane, cytoplasm, nucleus, and cell organelles.

Organization of the Cell

• Cells: The building blocks and basic units of life in living organisms by regulating biological processes.
• Tissues: Groups of cells performing a specific function.
• Animal tissue examples: connective, nervous, epithelial, and muscle tissues.
• Plant tissue examples: epidermal, vascular, and ground tissues.
• Organs: Groups of tissues perform specific functions; kidneys, heart, and lungs are examples of organs.
• Organ systems: Different organs combine to form systems such as the circulatory, digestive, and respiratory systems.

Function of Cellular Organelles in Animal Cells: The Nucleus

• The nucleus, the largest organelle in a eukaryotic cell, is the cell's control center.
• The nucleus contains most of the cell's DNA, which makes up chromosomes with genetic instructions for making proteins.
• The function of the nucleus is to regulate gene expression, including which proteins the cell makes.
• Nucleoplasm, a thick liquid similar to cytosol, is in the nucleus.
• While most eukaryotic cells contain a single nucleus, red blood cells, lack one.
• Muscle cells contains multiple nuclei.
• The nuclear envelope, which contains tiny perforations or pores, surrounds the nucleus.
• The nucleus contains a dense center called the nucleolus.
• The membrane enclosing the nucleus is a double membrane called the nuclear envelope, it isolates the nucleus contents from the cellular cytoplasm.
• Nuclear pores allow large molecules to pass through the nuclear envelope with the help of special proteins.
• Large proteins and RNA molecules pass through the nuclear envelope for protein synthesis in the cytoplasm and to maintain genetic material inside the nucleus.
• The nucleolus is mainly involved in the assembly of ribosomes.
• Ribosomes are exported to the cytoplasm after being produced in the nucleolusand are involved in protein synthesis.

Function of Cellular Organelles in Animal Cells: Mitochondria

• The mitochondrion makes energy available to the cell.
• Mitochondria uses energy from organic compounds such as glucose to make ATP (adenosine triphosphate).
• ATP is an energy-carrying molecule used universally inside cells for energy.
• Mitochondria are specialized to carry out aerobic respiration, and contains an inner membrane folded into cristae, forming the inner membrane space and the matrix.
• The Krebs Cycle occurs in the matrix.
• The electron transport chain is embedded in the inner membrane and uses both compartments to make ATP by chemiosmosis.
• Mitochondria has its own DNA and ribosomes.

Mitochondrial Compartments

• The double membrane nature of mitochondria results in five distinct compartments that plays a role in cellular respiration.
• The compartments: outer mitochondrial membrane, the intermembrane space, inner mitochondrial membrane, cristae, and the matrix.

Endoplasmic Reticulum (ER)

• The Endoplasmic Reticulum is a network of phospholipid membranes that form hollow tubes, flattened sheets, and round sacs called cisternae.
• There are two major functions of the ER: transport and synthesis.
• The transport function allows molecules, like proteins, to move from place to place inside the ER.
• The synthesis function allows ribosomes to attach to the ER and make proteins; lipids are also produced in the ER.
• The two types of endoplasmic reticulum are rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER).
• The rough endoplasmic reticulum is studded with ribosomes, and transport vesicles transport the proteins the ribosomes make.
• The transport vesicles pinch off the ends of the ER.
• The rough endoplasmic reticulum assists the Golgi apparatus to move new proteins to their proper destinations in the cell.
• The membrane of the RER is continuous with the outer layer of the nuclear envelope.
• SER does not have any ribosomes attached to it, giving it a smooth appearance.
• SER has lipid synthesis, calcium ion storage, and drug detoxification.
• The smooth endoplasmic reticulum is found in both animal and plant cells and serves different functions in each.
• SER is made up of tubules and vesicles that branch out to form a network.
• Some cells have dilated areas like the sacs of RER.
• Smooth endoplasmic reticulum and RER form an interconnected network.

Golgi Apparatus

• The Golgi apparatus processes proteins and prepares them for use both inside and outside the cell.
• The Golgi apparatus modifies, sorts, and packages different substances for secretion out of the cell or for use within the cell.
• It modifies proteins delivered in transport vesicles from the Rough Endoplasmic Reticulum
• The Golgi apparatus is also involved in the transport of lipids around the cell and assists the transport of molecules around the cell.
• The Golgi apparatus functions similarly to a post office because it packages and labels "items" and sends them to different parts of the cell.
• Cells that synthesize and secrete large quantities of materials have larger Golgi complexes, like the plasma B cells and the antibody-secreting cells of the immune system.
• It manipulates products from the Rough Endoplasmic Reticulum (ER) and also produces new organelles called lysosomes.
• Proteins and other products of the ER are sent to the Golgi apparatus, which organizes, modifies, packages, and tags them.
• Some are transported to other areas of the cell and some are exported from the cell through exocytosis.
• The Golgi apparatus packages enzymatic proteins as new lysosomes.
• The stack of cisternae has four functional regions: the cis-Golgi network, medial-Golgi, endo-Golgi, and trans-Golgi network.
• Vesicles from the ER fuse with the network and progress through the stack, where they are packaged and sent to their destination.
• Each cisterna includes special Golgi enzymes for modification or help proteins.

Vesicles and Vacuoles

• Vesicles and vacuoles are sac-like organelles for storing/transporting materials in the cell.
• Vesicles are much smaller than vacuoles and possess various functions.
• Vesicles pinch off from the membranes of the ER and Golgi apparatus and stores and transport protein and lipid molecules.
• Lysosomes is another type of vesicles that breaks down foreign matter and dead cells with enzymes.
• Peroxisomes is another type of vesicles that uses oxygen to break down poisons.
• Transport vesicles transports contents between organelle as well as between cell exterior and interior.

Centrioles

• Centrioles are organelles involved in cell division by helping to organize chromosomes.
• Centrioles are found only in animal cells and are located near the nucleus.
• Centrioles mainly consist of tubulin, a protein.
• Centrioles are cylindrical in shape and consist of microtubules.

Ribosomes

• Ribosomes are where proteins are made.
• Ribosomes are small structures that are not enclosed within a membrane.
• Each ribosome consists of two subunits made of proteins and RNA.
• RNA from the nucleus carries the genetic code, copied from DNA.
• At the ribosome, the genetic code in RNA is used to assemble and join amino acids to make proteins.
• Ribosomes can be found alone or in groups within the cytoplasm, as well as on the RER.

Characteristics and Classifications of Living Things

• Living things are organisms with the characteristics of life, one or more cells, a fixed life cycle, and the ability to exhibit movement, growth, reproduction, and response to stimuli.

Characteristics of Living Things

• All living organisms share characteristics that distinguish them from non-living things.

Cellular Organization

• Living things are composed of one or more cells, which perform all necessary biological functions.
• Organisms can be unicellular (e.g., bacteria) or multicellular (e.g., humans, plants).

Growth and Development

• Living things grow in size and complexity through cell division and enlargement.
• Development involves changes in form and function over time (e.g., metamorphosis in butterflies).

Metabolism

• Living things carry out biochemical reactions to obtain and use energy, including anabolism (building up complex molecules, e.g., photosynthesis) and catabolism (breaking down molecules to release energy, e.g., respiration).

Reproduction

• The ability to produce offspring ensures the survival of a species.
  • Asexual reproduction: offspring arise from a single parent (e.g., binary fission in bacteria).
  • Sexual reproduction: offspring result from the fusion of male and female gametes (e.g., humans, flowering plants).

Response to Stimuli (Irritability)

• Living things detect and respond to environmental changes (stimuli).
• Plants bending toward light (phototropism).
• Humans pulling their hands away from a hot surface (reflex action).

Homeostasis

• Ability to maintain a stable internal environment despite external changes: regulation of body temperature in humans and maintaining water balance in plants and animals.

Movement

• All living things exhibit some form of movement; animals use muscles, plants exhibit growth movements (e.g., roots toward water).

Adaptation

• Living organisms develop structural, behavioral, or physiological features that help them survive where they live.
• Examples of adaptation: Camouflage in chameleons and thick fur in polar bears for insulation.

Excretion

• Removing metabolic waste from the body.
• Metabolic wastes include ammonia, uric acid, and urea in animals.
• Humans excrete urea through urine.
• Carbon dioxide and oxygen are also examples of metabolic waste.
• Plants excrete oxygen as a by-product of photosynthesis.

Nutrition

• The process of obtaining and utilizing food for energy and growth.
• Autotrophic nutrition: organisms make their own food (e.g., plants via photosynthesis).
• Heterotrophic nutrition: organisms obtain food from other organisms (e.g., animals, fungi).
• Understanding the characteristics of living things can differentiate them from non-living matter.

Classification of Living Things

• Taxonomy is classifying living organisms based on shared characteristics to make their study easier.

Levels of Classification

• Living organisms are grouped into hierarchical categories:
  • Kingdom: Broadest classification (e.g., Animalia, Plantae).
  • Phylum: Groups organisms with similar body structures.
  • Class: Further division within a phylum.
  • Order: Groups organisms based on even more specific similarities.
  • Family: Closely related organisms.
  • Genus: Groups species with similar characteristics.
  • Species: The most specific level; organisms can interbreed to produce fertile offspring.
• Human Classification
• Kingdom: Animalia
• Phylum: Chordata
• Class: Mammalia
• Order: Primates
• Family: Hominidae
• Genus: Homo
• Species: Homo sapiens

Five Kingdom Classification

• The five kingdom is the most widely used classification system; organisms are grouped as:
  • Kingdom Monera (Prokaryotae): unicellular and lack a nucleus (prokaryotic); bacteria and archaea like Escherichia coli, Streptococcus spp.
  • Kingdom Protista: mostly unicellular with a nucleus (eukaryotic); autotrophic (e.g., algae) or heterotrophic (e.g., protozoa) like Amoeba, Paramecium, Euglena.
  • Kingdom Fungi: mostly multicellular (except yeast); absorb nutrients (heterotrophic) like mushrooms, yeasts, molds.
  • Kingdom Plantae: multicellular, autotrophic (photosynthetic) with cell walls made of cellulose, like mosses, ferns, flowering plants.
  • Kingdom Animalia: multicellular (like Kingdom Plantae) but heterotrophic, no cell walls, and highly mobile, like Insects, Fish, Mammals.

Three-Domain System (Modern Classification)

• Modern taxonomy classifies organisms into three domains based on genetic and molecular differences:
  • Bacteria: true bacteria and unicellular prokaryotes.
  • Archaea: prokaryotes in extreme environments.
  • Eukarya: protists, fungi, plants, and animals (all eukaryotic organisms).
• In summary, classification organizes biological diversity, making it easier to study and understand the relationships among organisms.

Reproduction

• Reproduction is a biological process where an organism gives rise to offspring similar to itself.

• Offspring grow, mature, and reproduce, creating a cycle of birth, growth, and death.

• Reproduction enables the continuity of species.

• Living things reproduce to produce similar offspring for survival.

• Inability to reproduce may lead to extinction.

• There are two types of reproduction depending on whether one or two organisms participate.

• When a single parent produces offspring without the involvement of gametes, it is asexual reproduction.

• When two parents produce offspring that involves fusion of male and female gametes, it is called sexual reproduction.

• There are also two types of fertilization:

  • Internal fertilization (insects, worms, reptiles, birds, mammals).
  • External fertilization (amphibians, fish, jellyfish, clams, starfish, corals).

Asexual Reproduction

• A single parent produces offspring.
• Offspring are identical to their parent and each other.
• There is no cell fertilization.
• Young offspring are clones because they are morphologically and genetically similar to their parents.
• Common in single-celled organisms, and in plants/animals with simple organizations.
• Types of asexual reproduction:

1. Binary fission: cell divides into two halves, each grows into an adult (e.g., Amoeba, Paramecium). Nucleus first divides into two, followed by cytoplasm, then the cell wall/membrane.
2. Budding: offspring grows out of the parent's body then breaks off; the offspring is smaller than the parent.
3. Regeneration: if a piece of a parent is detached, it can grow and develop into a new individual. Can be performed by starfish and salamanders

Benefits of Asexual Reproduction

• No mate is needed.
• Many offspring can be produced quickly, and externally.
• No parental care is required.
• Useful characteristics/genes/traits are retained.
• Offspring establish faster/shorter life cycle.

Disadvantages of Asexual Reproduction

• Lack of genetic variation leads to less diversity.
• Low resistance to disease and loss of hybrid potency.
• Competition for resources due to overpopulation.
• All individuals are affected which causes an inability to adapt to new environments.

Sexual Reproduction

• Formation of male and female gametes fuse to form a zygote, which develops into a new organism.
• Most multicellular organisms use sexual reproduction to increase their numbers.
• Two parents are involved where each reproduce sex cells called ganetes resulting in a variety in species.
• In animals, male gametes are sperm (produced in testes) and female gametes are eggs (produced in ovaries).
• The fusion of gametes (fertilization) form a zygote The types of fertilization are external and internal.

External fertilization

• Union of male/female gametes occurs outside the female's body.
• Found in amphibians and fish.
• Offspring are not identical to parents or each other.

Advantages of External Fertilization

• Large numbers of offspring produced per breeding season.
• Female does not suffer gestation stress.
• Mother does not need to care for the young (except in a few species).
• Survival is of the fittest

Disadvantages of External Fertilization

• Many predators can feed on the eggs before or after fertilization.
• Higher risk of fertilization not happenning which results in a lot of gametes being wasted
• Embryo development is at the mercy of the environment.
• Large numbers of female gametes are required causing the female to be exhausted.

Advantages of Internal Fertilization

• Increased chances of fertilization.
• Fertilized eggs are protected in female's body.
• Created stable internal environment.
• Fewer gametes are required.

Disadvantages of Internal Fertilization

• Less offspring.
• Prone to adapt less to sudden environmental changes.
• in mammals, females suffer gestation stress.

Interrelationships of Organisms

• Biological interaction: the relationship between two species in an ecosystem.

• It is the impact of two species living together in a community.

• Interactions can be intraspecific (same species) or interspecific (different species).

• Impacts can be short-term (pollination, predation) or longterm (extinction).

• Symbiosis: a long-term relationship.

• Mutualism (benefits both), and competition (destructive to both) are examples of symbioses.

• Five types of interactions: competition & predation, commensalism, parasitism, mutualism, and saprophytism.

Competition and Predation

• Competition is when populations or individuals compete for food resources.
• Exploitative or consumptive competition is typically considered the interaction of individuals that vie for a limited and common resource.
• Competition is the direct or indirect interaction of organisms that leads to a change in fitness when the organisms share the same resource.
• Negative effects are on the weaker competitors.
• Three major forms of competition: interference competition, exploitation competition, and apparent competition.
• Interference and exploitation competition are types of real competition.
• Interference competition is directly between individuals, and exploitation and apparent competition occur indirectly.
• Predation refers to one entity (predator) hunts another (its prey) to eat to satisfy their nutritional requirements.
• Occurs between species (inter specific): when it occurs within a species.
• Interspecific predation can become cannibalism
• Cannibalism is often when food resources causes same species to feed on each other.

Commensalism

• An imbalanced interaction where one individual benefits, and the other is unaffected.
• Orchids (epiphytes) grow on tropical rainforests.
• Commensalism is hard to identify because benefits may have indirect effects.
• Examples of commensal interactions: inquilinism, chemical commensalism, phoresy, and metabiosis.

Parasitism

• Parasitism occurs when one individual, the parasite, benefits while harming the other, the host, in the process.
• Parasites, found within (endoparasites) or outside (ectoparasites) feed on host tissue or fluids.
• Parasitism occurs when the host is killed.
• Ectoparasites (fleas, leeches) live on the host's surface.
• Endoparasites live inside the host and can be intracellular or intercellular parasites.
• Ticks are common ectoparasites on animals and humans.
• Parasites does not kill their hosts, but weaken them, which indirectly causing host fatality.
• Infected snails lose some of their characteristics and may stay on tops of rocks, causing them to be open for aquatic predators to feed.

Mutualism

• A symbiotic interaction where both or all individuals benefit.
• Mutualism can be obligate or facultative.
• If species involved in obligate mutualism cannot survive without the relationship, while facultative mutualistic species can survive individually.
• An obligate mutualistic relationship example is leafcutter ants, where the ant larvae eat only one kind of fungi.
• Examples of mutualistic patterns: facultative, obligate, and diffusive mutualism and have three purposes: defensive, trophic and dispersive mutualism.

Habitats

• Where an organism (plant and animal) normally/naturally lives.
• Habitat is the physical place means the home where an organism live while an ecologist studies habitats.
• Niche: It is the functional role of an organism in a community, its job or position.
• Potential niche: what organisms can do, and those with no competitiors and resource limitations.
• Realized niche: is the part of the fundamental niche that the species actually occupies in nature.

Types of Habitats

• There are three types of habitat: terrestrial, aquatic and arboreal.

Terrestrial Habitat

• Land-based habitat distributed around various geological zones:
• Forest habitat consists of plants, animals and microorganisms that coordinates with the abiotic factors of the environment and helps temperature by maintaing it while being the carbon sink.
• Grassland habitat vegetation is dominated by grasses and herbs.
• Temperate grasslands and savanna grasslands are examples of grassland ecosystems.
• Tundra habitat Trees are not present, and are found in cold climates or where rainfall is scarce.
• Found in the Arctic or mountain tops and covered with snow for most of the year. Desert habitats are found throughout the world, with very little rainfall.

Aquatic Habitat

• Habitats present in a body of water.
• Divided into freshwater and marine habitat:
• Freshwater habitats include lakes, ponds, rivers, streams and wetlands that contain no salt.
• Marine habitats habitat includes seas and oceans as has a more substantial salt content and greater biodiversity in comparison to the freshwater habitat.

Arboreal Habitat

• An environment where organisms primarily live in trees where organisms spend time; it may also the place where where organisms can live and eat. The arboreal include the roots of the trees, the tree canopy and the branches that have leaves and holes.

Heredity and Evolution: Introduction

• Genetics studies heredity and variation; heredity refers to the passing of traits from parents to offspring.
• Genes, the hereditary units transmitted from one generation to the next, contain coded information for protein production
• The genetic structure, physiology, bio-chemistry and behaviors are determined and passed on by chromosomes
• DNA is the genetic or hereditary material which determines the structure, physiology, biochemistry, and behavioral traits of offspring.

Heredity and Evolution: Basis of Heredity

• Heredity characteristics traits are determined by genes found in long molecules of DNA
• Chromosomes are in the nucleus of cells and are made of DNA and protein which forms nucleoprotien.
• Each gene occurs in alleles (alternative form) responsible for the expression of different forms of a trait.
• Gene locus is where genes are located on a specific position on a chromosome
• Chromosomes occur in pairs that bear alleles for a particular gene on the same loci.
• Homologous chromosomes are the alleles occurring in chromosome pairs bearing the same set of gens.

Total of Chromosomes

• The variable amount of chromosoems is 46 in humans, and 23 in sex chromosomes from XX (female) or XY (male).
• Chromosomes for somatic cells have diploid number of chromosomes.
• Gametic cells have haploid number of chromosomes.
• When the two copies of a gene are the same allele, the individual is said to be homozygous.
• If the two copies of alleles on homologous chromosomes at particular loci are different, the individual is said to be heterozygous.
• The description an allelic ( gene coding for the expression of a particular trait) combination in genes is a phenotype.
• The genetic constitution with respect to the alleles is known as its genotype
• Interactions of environmental occurs result in the observable characteristics of phenotype (AA, Aa, aa).

Gregor Mendel (1822-1884)

• Gregor Mendel, an Austrian monk, discovered the basic principles of genetics:
• Was born in 1822 and was derived the basic laws of gene transmission from Czrech Republic,
• He developed his theory of heredity working with the Pisum sativum garden peas because:
• Garden pea: was easy and available to reproduce pure breeding green peas and yellow peas, had reproductive structures, traits that are visible, and could easily cultivate.
• He introduced his findings in the 1866s, or serven years after Charles Darwin's publication.

Monohybrid Inheritance and the Law of Segregation

• Mendel introduced matings between individual garden peas based on the traits of the parents

• Mendal planted pure breeding peas for parental generation and crossed stigma with pollen

• Mendel used Yellow pea stigma with green pea pollens and made the reciprocal cross resulting in the (P) generation producing the first filial (F1) generation

• Menda self pollinated the F1 plants and generated the second filial (F2) generation

• Such test produces a ration of 3 Yellow and 1 Green to introduce an alleic factor that produces the expression of trait

• This allelic formation with sperm and egg result in parent alleles restoring two copies fo the gene or fertalizing the egg.

• As a result, only one of the two alleice copies result in a gamate due to seed and wrinkes, the allelic formation comes through transmission.

Law of Segregation - First law of Mendel

• The alleles are separate during meiosis, and each gamete receives one copy of each allele contained.

Dihybrid inheritance and the law of independent assortment

• Traits of YyRr result a dihybrid test for the progenics based on a ratio of 9:3:3:1
• In order to create two genes of traits resulting from parental lines, the gene undergoes gamete formation independently and results in a second law or principle

Law of independent assortment Second law of Mendel

• Genes that undergo gamate formation independently and is determined on how an individual segregates or merges
• With deviances, came a closer understanding that that traits linked in genes are inherited together and form an exception to the law.

Evolution

• Evolution means change with characteristics that are passed down biologically through generation.

• The observation of change that evolved from a common ancestor is a theory

• The fundamental evolution of human life can be traced in life, to discover more the origins and the diversity of living things.

• The following lists potential theroies of the origin of creation on earth.

• Theory of special creation states life was made by an supernatural creation

• Theory of spontaneous generation states Aristotle (384-322BC) proposed that life formed when particles merged and had what was needed to be a living organism.

• Theory of Steady state theory state species never originated, but have always existed

• Theory of Cosmozoan theory state Life arrived from another planet

• Theory of Biochemical evolution stated theory that life arose to to chemical and physical laws.