HLTH1005 Week 1: The Tree of Life – Vocabulary Flashcards

Vocabulary flashcards covering key terms from HLTH1005 Week 1 lecture notes on the Tree of Life, taxonomy, and domains.

Levels of organisation

Organism → Systems → Organs → Tissues → Cells → Organelles/biomolecules; arranged from macro to micro.

Phylogeny

Evolutionary relationships among organisms.

Domain

Highest taxonomic rank; the three domains are Bacteria, Archaea, and Eukarya.

Prokaryote

Single-celled organisms that lack a nucleus and organelles; divide by binary fission; generally small.

Eukaryote

Organisms with a membrane-bound nucleus and organelles; typically larger; includes plants, animals, fungi, and protists.

Protista

types of eukaryotic unicellular and simple multicellular organisms like algae, amoebas.

Kingdom Fungi

Mostly multicellular; chitin cell walls; heterotrophic; spores; no chloroplasts; no embryonic stage.

Kingdom Plantae

Multicellular; photosynthetic autotrophs; cellulose cell walls; cannot move; classification includes seed formation.

Bacteria

Domain Bacteria: prokaryotic, unicellular, lacking a nucleus and membrane-bound organelles,

Archaea

Domain Archaea: diverse prokaryotes often in extreme environments; genetically distinct from bacteria; horizontal gene transfer occurs.

Eukarya (Eukarya/Eukaryota)

Domain containing organisms with a membrane-bound nucleus and organelles; includes Protista, Fungi, Plantae, and Animalia.

Nucleosome

DNA packaging unit in eukaryotes; not present in bacteria or archaea.

ribosomes in domains

70S ribosomes in Bacteria and Archaea; 80S ribosomes in Eukarya.

Chromosomes

Usually circular in Bacteria/Archaea; usually linear in Eukarya.

Introns

Genetic segments commonly found in Eukaryotes; rare in Bacteria/Archaea.

Promoters and transcription

Bacteria have promoters with -35 and -10 sequences; Eukaryotes use a TATA box.

Initiator tRNA

In Bacteria: formylmethionine; in Archaea and Eukaryota: methionine.

Cell membrane lipids

Ester-linked lipids in Bacteria and Eukarya; ether-linked lipids in Archaea.

Operons

Coordinated gene expression typical in Bacteria and Archaea; generally not present in Eukarya.

Horizontal gene transfer

Exchange of genetic material between organisms; common in prokaryotes.

Kingdom Animalia

Metazoa: eukaryotic, lack cell wall

– Most have specialised tissues

– Made up of cells with similar embryonic origin

• Heterotrophs

– Ingest food for growth

– Digest in internal cavity

• Most are motile

What do Hox genes determine in animal development?

Hox genes determine the animal body plan and are responsible for the similar appearance of many animal species during embryonic development. They contain homeoboxes, which can turn large numbers of genes on/off.

List the four key features of Phylum Chordata.

1. Notochord: Flexible, rod-shaped skeletal support, later replaced by the spine.
2. Dorsal hollow nerve cord: Develops into the brain and spinal cord.
3. Pharyngeal slits: Gill/jaw support in fish, modified into ear/tonsil parts in tetrapods.
4. Post-anal tail: Used for locomotion in fishes; reduced and non-functional in apes (including humans).

What distinguishes Class Mammalia from birds and reptiles?

Mammals are distinguished by:

1. Mammary glands

2. Hair or fur

3. Neocortex brain region

4. **Three middle ear bones).
   Humans are also part of the *Amniota* clade, characterized by an amnion, chorion, and allantois for embryonic protection and waste/gas exchange.

What adaptations for arborality are found in Order Primates?

Primates have hands and feet adapted for brachiation, including a rotating shoulder joint, separated big toe and thumb, and stereoscopic vision for depth perception.

Distinguish between Prosimians and Anthropoids.

• Prosimians: Nocturnal, smaller size, smaller brains.
• Anthropoids: Include monkeys, lesser apes, and great apes.

Which genera belong to the Great Apes (family Hominidae)?

Pan (chimpanzees), Gorilla, Pongo (orangutans), and Homo (humans). They are divided into two subfamilies: Ponginae (Asian apes like orangutan) and Homininae (humans and African apes like gorilla, chimpanzee, bonobo).

What is a Hominin, and when did humans and chimpanzees diverge?

Humans and chimpanzees diverged from a common hominoid ancestor approximately 6 million years ago (mya). A Hominin refers to species that evolved after this split, being more closely related to humans than chimpanzees.

What was the significance of bipedalism in the Hominini tribe?

Bipedalism freeing up hands for carrying and tool use, allowing quicker escape from predators, and adapting to changing landscapes (forest to savannah).

Describe the Genus Australopithecus.

Early hominins existing in Africa during the Pliocene and Early Pleistocene. Key species like A. afarensis ("Lucy") showed faster growth to adulthood than modern humans, but possessed the SRGAP2C gene which increased neuron number and migration in the brain.

What role did tool use play in the early Genus Homo?

Early ancestors like Homo habilis had a varied diet, and their stone tool use (e.g., for accessing bone marrow) is associated with early human brain development. Homo erectus was the longest-lived Homo species, with human-like proportions.

What is the "Out of Africa" theory and its molecular evidence?

The theory proposes modern humans (H. s. sapiens) migrated out of Africa in two waves. Molecular evidence from Mitochondrial DNA (mtDNA) suggests all modern humans share a common female ancestor ("Mitochondrial Eve") who lived in Africa ~160 thousand years ago (kya). Y-chromosome analysis supports a common male ancestor in Africa ~140 kya.

How has human activity impacted the environment over time?

While climate once drove human migration, permanent settlements and innovations like agriculture and metal use led to significant resource extraction, demonstrating a profound human impact on the environment.

What is a macromolecule?

Large molecules formed when individual, similar molecules (monomers) join to form chains (polymers) linked by covalent bonds, often via the loss of H_2O.

List the four main types of macromolecules.

Carbohydrates, Lipids, Nucleic acids, and Proteins.

Describe the Hydroxyl functional group.

Formula: --OH. Property: Polar. Found in: Carbohydrates, many cellular compounds.

Describe the Sulfhydryl functional group.

Formula: --SH. Property: Polar. Found in: Amino acids (cysteine, methionine).

Describe the Phosphate functional group.

Formula: --HPO_4^{2-}. Property: Polar. Found in: Nucleic acids.

Describe the Carboxyl functional group.

Formula: --COOH. Property: Acid. Found in: Organic acids (amino, fatty).

Amino functional group.

Formula: --NH_2. Property: Base. Found in: Amino acids (proteins), nitrogenous compounds.

What are Carbohydrates?

The most abundant biomolecules on Earth, containing carbon, hydrogen, and oxygen. They are important energy sources.

What is a saccharide?

'sugar', referring to carbohydrates.

What is the primary role of glucose?

Glucose is the preferred 6-carbon sugar fuel source for all living organisms and the starting molecule for yielding ATP.

What are disaccharides?

consisting of two monosaccharide units, at least one of which is glucose. They are digested by enzymes into monosaccharides.

What are polysaccharides?

Complex carbohydrates that are long chains (polymers) of the same or different monosaccharides

How do animals store excess glucose?

Animals store excess glucose in the liver and muscle as glycogen through a process called glycogenesis.

What are the structural roles of polysaccharides?

Polysaccharides provide structural support by forming strong, rigid components like plant cell walls (cellulose) and insect exoskeletons and fungi walls (chitin)

What are lipids?

Fatty or waxy substances that are insoluble in water and involved in a wide range of biological processes including energy storage, insulation, structural components, and signalling.

List types of lipids and their functions.

1. Triglycerides: Storage, insulation, fuel.
2. Phospholipids: Structural components of membranes.
3. Eicosanoids: Signalling molecules (e.g., prostaglandins).
4. Steroids: Hormones (e.g., testosterone, estrogen, corticosteroids).

What are essential fatty acids?

Polyunsaturated omega-3 and omega-6 fatty acids that humans cannot synthesize and must obtain from their diet (e.g., from marine animals, plants, nuts, seeds).

What are nucleic acids and their function?

Nucleic acids (DNA and RNA) carry genetic information, providing instructions for cell form and function, and ensuring the continuity of life.

Distinguish between DNA and RNA.

• DNA (Deoxyribonucleic acid): Contains information to make protein products, which can be turned on/off.
• RNA (Ribonucleic acid): Mostly involved in protein synthesis.

What are nucleotides?

The monomeric units that make up nucleic acid polymers. Each nucleotide consists of a nitrogenous base, a phosphate group, and a pentose sugar.

What are proteins?

Long chains of amino acids involved in numerous biological processes,

List the diverse functions of proteins.

• Structural: Collagen, keratin.
• Chemical reactions: Enzymes.
• Regulation: Hormones.
• Immune: Antibodies.
• Transport: Heme, channel proteins.
• Various cell signalling roles.

What is denaturation in proteins?

The loss of a protein's quaternary, tertiary, and secondary structures due to exposure to changes in pH, temperature, detergents, UV, or other chemicals, while the primary structure generally remains intact. A denatured protein usually loses its function.

Why is water considered the biological solvent?

its polar molecular structure allows it to dissolve a vast range of substances. which is essential for transporting nutrients, minerals, and waste throughout biological systems.

Describe the polarity of a water molecule.

In a water molecule (H_2O), the oxygen atom carries a partial negative charge, and the hydrogen atoms each carry a partial positive charge, making it a polar molecule.

What unique properties of water allow it to be an ideal biological solvent?

1. Hydrogen bonds:

2. Hydrophobic interactions:

3. Buffer action:

4. Dissociation of salts: transport medium

How does water act as a transport medium?

Salts dissociate when placed in water, forming electrolytes. The differing concentrations of these electrolytes inside and outside cells (e.g., more K^+ and proteins inside, most other electrolytes outside) facilitate transport and cellular functions.

What is osmosis?

The movement of water down a concentration gradient through a semipermeable membrane, contributing to tonicity. Osmotic pressure describes the force required to resist this movement.

What are the key differences between Prokaryotic and Eukaryotic cells?

Prokaryotic cells lack membrane-bound organelles, have genetic material in a nucleoid/plasmids, possess 70S ribosomes, contain peptidoglycan in their cell walls, and reproduce by binary fission. Eukaryotic cells have membrane-bound organelles with genetic material in a nucleus, and 80S ribosomes.

List the four main components of a Eukaryotic cell structure.

1. Cell membrane:

2. Intracellular fluid:

3. Cytoskeletal elements:

4. Membranous organelles:

Describe the structure and components of the cell membrane in eukaryotes.

The cell membrane is a phospholipid bilayer following a fluid mosaic model. It contains cholesterol, various proteins, and a carbohydrate glycocalyx on the extracellular side for cell type-specific recognition. Membrane proteins move laterally within this dynamic fluid structure.

What are the main types of cytoskeletal elements and their functions?

The main types are:

• Microtubules (\approx25 nm, tubulin)
• Actin filaments (\approx6 nm)
• Intermediate filaments (\approx10 nm, various subunits)

Their functions include structural support, cell shape, internal organization, assembly of cells into tissues, intracellular transport, and cell movement.

What is the function of the Nucleus and Nucleolus?

The Nucleus stores genetic information. The Nucleolus produces and assembles ribosomes.

Distinguish between the functions of Rough Endoplasmic Reticulum (RER) and Smooth Endoplasmic Reticulum (SER).

• Rough ER (with ribosomes) is involved in protein synthesis and modification for secretion or insertion into membranes.
• Smooth ER (without ribosomes) synthesizes lipids, metabolizes carbohydrates, and regulates \text{[Ca}^{2+}\text{]} (especially in muscle cells).

What are Ribosomes and their role in eukaryotes?

Ribosomes are made up of RNA and proteins, and they are responsible for protein synthesis. In eukaryotes, they are 80S in size (composed of 60S and 40S subunits) and can be free in the cytosol or attached to the RER.

Describe the function of the Golgi apparatus.

The Golgi apparatus sorts, modifies, packages, and ships proteins and lipids. It has a cis face (receives from ER) and a trans face (exports materials and recycles molecules from endocytic vesicles).

What are Lysosomes and Peroxisomes?

• Lysosomes: Contain enzymes for degradation of intracellular or extracellular waste.
• Peroxisomes: Contain enzymes for breaking down fatty acids and neutralizing free radicals.

What is the primary function and structure of Mitochondria?

Mitochondria are responsible for aerobic respiration and ATP production. They have an outer and an inner membrane forming folds called cristae, with an intermembrane space in between.

What are Chloroplasts and their function?

Chloroplasts allow for photosynthesis in plants and algae, primarily within their thylakoid membranes (which contain chlorophyll). They also contain accessory pigments like phycocyanins and carotenoids, and have their own DNA and ribosomes.

Explain the "Colonial theory" regarding multicellular organisms.

The "Colonial theory" suggests that multicellular organisms arose from the cooperation of many organisms of the same species, leading to a hierarchical organization of cells into tissues, organs, systems, and ultimately a whole body.

List and describe the three main functional groups of cell connections.

1. Occluding junctions: Seal cells together to prevent small molecules from leaking between them, forming a selectively permeable barrier.
2. Anchoring junctions: Provide mechanical attachment of the cytoskeleton to neighboring cells (adherens junctions) or to the extracellular matrix (integrins).
3. Communicating junctions (Gap junctions): Mediate the passage of chemical and electrical signals directly between cells.

What is a tissue in multicellular organisms, and how is it studied?

A tissue is a group of connected cells with a similar function that specializes in one or more functions essential to the organism's survival. Tissues are studied via histology to understand the structure and function of an organ.

List the four main types of animal tissues and their general roles.

1. Epithelium: Protect, exchange, transport; can be ciliated or secretory.
2. Muscle: Includes skeletal (striated), smooth, and cardiac muscle, responsible for movement.
3. Connective: Loose/dense, adipose, cartilage, bone, blood; provides support, binds, and protects.
4. Nervous: Neurons and glial cells; responsible for transmitting signals.

What does "stemness" refer to in cell development?

Stemness refers to the developmental potential of a cell. It describes a cell's ability to continually divide to regenerate (self-renewal) or to differentiate and specialize into various cell types. This potential decreases as a cell becomes more specialized.

What two sources of information guide cell migration and development?

Cell migration and development are guided by:

1. Intrinsic factors: Cell lineage.
2. Extrinsic factors: Cell-signaling from the environment.

Genes are selectively expressed through transcription factors based on these cues, determining a cell's function.

What is the function of a Vacuole?

Vacuoles are primarily involved in maintaining cell turgor and expansion, and they can also serve for protein storage in germinating seeds (especially in plants).

What is the Fluid Mosaic Model of the cell membrane?

The cell membrane is a phospholipid bilayer with interspersed cholesterol and various proteins. Its 'fluid' aspect means membrane proteins move laterally, and its 'mosaic' aspect refers to the diverse proteins embedded within it, aiding in cellular transport and communication.

Distinguish between Integral and Peripheral membrane proteins.

• Integral proteins: Permanently embedded within the lipid bilayer, often spanning the entire membrane (transmembrane) or attached from one side (monotopic). They are typically amphipathic and involved in transport, channels, and receptors.
• Peripheral proteins: Temporarily associated with either side of the membrane surface, not penetrating the lipid bilayer. They are generally hydrophilic and involved in cell signaling, maintaining cell shape, and anchoring.

What are the main types of cellular transport across membranes?

1. Passive transport: Movement of substances down their concentration gradient, without requiring cellular energy (e.g., facilitated diffusion, osmosis).
2. Active transport: Movement of substances against their concentration gradient, requiring energy (e.g., primary active, secondary active transport).
3. Vesicular transport: Movement of large molecules via membrane-bound vesicles (e.g., endocytosis, exocytosis).

Explain the role of Channels in facilitated diffusion.

Channels allow for the rapid movement of ions along their electrochemical gradients. They are highly selective and can be classified as voltage-gated, ligand-gated, or mechanically-gated, transitioning between closed, open, and inactivated states.

What are Aquaporins?

Aquaporins are specialized water channels that act as the cell's 'plumbing system,' allowing water to pass through the cell membrane rapidly while blocking ions and other solutes. They are crucial for water transport in organs like the gall bladder and kidneys, and help plants manage stress.

How do Carrier proteins function in cellular transport?

Carrier proteins bind to a specific target molecule on one side of the membrane, undergo a conformational change to transport the molecule across, and then release it on the other side. They are highly specific, slower than channels, and can become saturated at high substrate concentrations.

How are Carrier proteins classified based on transport coupling?

1. Uniporter: Transports a single solute down its concentration gradient (facilitated diffusion).
2. Symporter: Transports two different solutes in the same direction, with at least one moving against its gradient using the energy from the other moving down its gradient.
3. Antiporter: Transports two different solutes in opposite directions, similarly coupling movement against a gradient to movement down a gradient.

Explain Primary Active Transport using the Na^+/K^+ pump as an example.

Primary active transport uses energy directly from ATP hydrolysis to move substances against their concentration gradient. The Na^+/K^+ pump (or Na^+/K^+-ATPase) is an example, actively moving 3 Na^+ ions out of the cell and 2 K^+ ions into the cell, consuming one ATP molecule per cycle.

What is Secondary Active Transport?

Secondary active transport is a two-stage process where ions or solutes are moved into cells using the energy derived from the electrochemical gradient of another ion (often Na^+). This gradient was previously established by primary active transport, but the co-transporter itself does not directly hydrolyze ATP.

What is Membrane Potential and its role?

Membrane potential is the difference in electrical potential across a cell's membrane, typically between -80 and -60 mV in eukaryotic cells at rest. It is maintained primarily by the Na^+/K^+ pump and selective ion channels, creating a more negative charge inside the cell. It is essential for nerve impulse transmission and muscle contraction.

Describe Endocytosis.

Endocytosis is the process where small portions of the plasma membrane engulf substances from the extracellular environment, forming vesicles that enclose and import the substances into the cell. Types include:

• Phagocytosis: 'Cell eating,' for large particles (common in immune cells).
• Pinocytosis: 'Cell drinking,' for fluids and dissolved small molecules.
• Receptor-mediated endocytosis: Specific uptake of substances that bind to receptors on the cell surface.

Describe Exocytosis.

Exocytosis is the process where vesicles inside the cell fuse with the plasma membrane to export their contents to the extracellular environment. There are three main secretory pathways:

• Constitutive: Continuous release of materials without external signals.
• Regulated: Release triggered by specific signals (e.g., hormones) to export stored substances.
• Lysosomal: Lysosomes fuse with the plasma membrane to release waste or repair damage.

How do epithelial cells regulate transport?

Epithelial cells regulate the movement of substances between body compartments. They have distinct apical (lumen) and basolateral membranes with different transport proteins, and tight junctions that restrict movement between cells, forming a selectively permeable barrier.

Explain glucose transport in the intestine.

Glucose moves from the gut lumen to the blood against its gradient. This involves:

1. Na^+/glucose symporter (SGLT1) on the apical membrane, which uses the Na^+ gradient to co-transport glucose into the epithelial cell.
2. A glucose uniporter (GLUT2) on the basolateral membrane, which moves glucose from the epithelial cell into the bloodstream via facilitated diffusion.
3. The Na^+/K^+ ATPase on the basolateral membrane, which maintains the Na^+ gradient by pumping Na^+ out of the cell, using ATP.

What is Cystic Fibrosis (CF), and which transport protein is involved?

Cystic Fibrosis is a genetic disorder caused by mutations in the CFTR (Cystic Fibrosis Transmembrane conductance Regulator) gene. CFTR normally functions as a chloride ion channel. When defective, it leads to the production of thick, sticky mucus in the lungs and digestive tract, impairing normal organ function due to altered fluid balance.

What laboratory techniques are used to study membrane transport processes?

1. Patch clamp: Used to study the electrical activity of ion channels by isolating a small patch of membrane.
2. Fluorescence microscopy: Uses labeled molecules to visualize and track transport processes within cells.

What is cellular communication?

Cells communicate to coordinate growth, metabolism, and immune responses, allowing them to adapt to environmental changes (e.g., regulate temperature, pH, glucose levels). It is critical for tissue and organ function.

What are the key components of cellular communication?

Cellular communication involves a ligand, receptor, signal transduction, and a cellular response. It regulates gene expression, enzyme activity, and cell behavior.

List the four major types of cellular signaling.

1. Autocrine
2. Paracrine
3. Endocrine
4. Juxtacrine

Describe Autocrine signaling.

Cells release signals that bind to their own receptors, inducing a specific effect. It is involved in cell proliferation and differentiation, and is common in cancer to drive uncontrolled growth (e.g., white blood cells using cytokines, neural tube development).

Describe Paracrine signaling.

"Short-range signaling" where cells release signals that affect nearby cells, diffusing over short distances. Examples include neurotransmission at synapses and embryonic development regulated by growth factors.