IB Biology HL Y1 Quarter 3

Blue highlight = example / Green highlight = important info i think probably

Standards - A2.2, B2.2, A2.1, B2.3, A1.1, B1.1, B1.2

A2.2 Cell Structure

Cell theory - Cells are the smallest unit of life, all cells come from preexisting cells, all living things are made from cells

• All cells have DNA as genetic material (in nucleus or in the open), cytoplasm (water of the cell), phospholipid bilayer (plasma membrane)

Prokaryotic cell - bacteria or archaea, single celled

• Must have:

  • Naked DNA in a loop

  • 70s ribosomes

  • Peptidoglycan (cell wall)

  • Cytoplasm

  • Plasma membrane

• Can have:

  • Pili (attachment to other bacteria for HGT)

  • Flagella (movement)

  • Plasmid (transferred in HGT)

• No membrane bound organelles

Eukaryotic cell - protists, fungi, animals, plants; single or multi celled

• Plasma membrane

• Compartmentalized cytoplasm (membrane bound organelles)

• 80s ribosomes

• Nucleus with DNA bound to histones

• Mitochondria

• Endoplasmic reticulum

• Golgi apparatus

• Vesicles (vacuoles or lysosomes)

• Cytoskeleton of microtubules and microfilaments

Animal vs Plant vs Fungi Cells

Atypical Cell Structure

Functions of Life

• Homeostasis - maintaining internal conditions

• Metabolism - all enzyme catalyzed reactions

• Nutrition - obtain energy

• Movement - move or move things

• Excretion - get rid of waste 

• Growth - grow

• Response to stimuli 

• Reproduction - sexual or asexual

Types of Microscopes

Endosymbiotic Theory - A primitive eukaryote (ancestor of all eukaryotes w/ nucleus + reproduced sexually) engulfed a free living prokaryote that later became the mitochondria, happened twice for the chloroplast

• Evidence for mitochondria:

  • 70s ribosomes

  • Has naked circular DNA

  • Replicates on its own

  • Has a double membrane

  • Size of prokaryote

Cell Differentiation - Different cells can become different cell types through gene expression (all cells have the same DNA), which is triggered by environmental changes

Multicellularity - caused by convergent evolution, happened multiple times in different lineages

• Allows for larger body size and cell specialization

• Found in many fungi and eukaryotic algae as well as all plants and animals

B2.2 Organelles and compartmentalization

Organelles - discrete subunits of the cell that are adapted to perform specific functions

• Nuclei, vesicles, ribosomes, plasma membrane

• Cell wall, cytoskeleton, cytoplasm are NOT organelles

• Freeze fracturing allowed identification of organelles

Advantages of compartmentalization - allows for concentration of metabolites (substrates) and enzymes in one area, keeps chemical processes separate

• Lysosomes and phagocytic vacuoles digest things but only what you want since they are in a vesicle

Advantages of nucleus - separates transcription and translation processes, protects DNA, allows modification of RNA (only in eukaryotes)

Advantages of the double membrane of the nucleus - has pores, allows for vesicle formation, connection to endoplasmic reticulum, the nuclear envelope separates DNA from cytoplasm, can speed up mitosis

ER vs free ribosomes

• Ribosomes can be free floating or attached to rough endoplasmic reticulum

• Free floating create proteins for the cell (cytoplasm)

• Rough ER proteins can be sent to other organelles, embedded in the membrane, or transported to golgi apparatus for exocytosis

Golgi Apparatus - processing and secretion of proteins

Vesicles - help remove big molecules from cell by fusing with membrane

Clathrin - protein that causes formation of vesicles

A2.1 Origin of Life

Conditions on early Earth

• no free oxygen, no ozone, no protection from UV, increase in energy

• higher carbon dioxide and methane = higher temperatures

• may have allowed for carbon compounds to form (carbon is special, not formed by living organisms)

Challenges to explaining first cells

• Requirements

  • Catalysis - inorganic molecules to organic molecules

  • Self-assembly - organic molecules to larger organic molecules

  • Self-replication - ability to duplicate molecules 

  • Compartmentalization - membranes

• Challenges

  • cannot replicate early earth conditions 

  • no fossils of early life

Evidence for the origin of carbon compounds

• Miller-Urey Experiment (1952) - tried to recreate early earth conditions and got some organic matter

Membranes

• Once lipids are formed they will naturally start to form vesicles (membrane bound packages) 

• Allows for separation of internal and external environments to form concentration gradients

RNA and DNA

• RNA most likely formed first as it can self replicate (unlike DNA) and act as a catalyst (called a ribozyme)

• DNA would eventually become more common because it is more chemically stable

• Proteins eventually became catalysts

Last Universal Common Ancestor (LUCA)

• Split into all life we see now (shared genes across all organisms)

• Probably other organisms around the time but must have went extinct

• Arose between 2 to 4 billion years ago

  • Biosignature evidence - chemicals produced by cells appear 3.7 billion years ago in the sediment

  • Phylogenetic evidence - molecular clock across all domains, 355 genes present in all organisms

• Arose in hydrothermal vents

  • Genomic evidence - conserved genes are used in areas with hydrothermal vents

  • Fossilized evidence - bacteria byproducts found in ancient seafloor vent sediments

B2.3 Cell Specialization

Origin of Stem Cells

• Zygote - formed as a result of fertilization, start to make specialized cells

  • Gametes to zygote to blastocyst to embryo to fetus to infant

• Cell signaling - process by which info is transferred from cell surface to nucleus, essential in controlling gene expression and differentiation

• Morphogens - signal molecules that control cell differentiation, occur in gradients (areas of concentration differences) in different regions of early embryo (different gradient = different gene expressed)

Stem cells - cells that retain their ability to divide and differentiate endlessly into various cell types, results in all the cell types organisms possess

• Self-renewal - when stem cells divide to form a specific tissue, they also produce daughter cells that remain as stem cells

• They can recreate functional tissues

Stem cell niches - certain locations where stem cells are present in high numbers due to regular proliferation (rapid reproduction), demonstrate differentiation

• Bone marrow - production of blood cells to be transferred by blood vessels, renewal of stem cells

• Hair follicles - most stem cells found in the bottom, rounded area of follicle, involved with hair growth, skin and hair follicle regeneration, production of sebaceous (oil producing) glands

• More examples - central nervous system, intestinal system, muscle fiber bundles

Types of Stem Cells

• Totipotent - ability to produce any tissue in organism, very low numbers of cells are this, only exist in very early stages of embryo development, may form a complete organism

• Pluripotent - arise from totipotent cells, only in early stages, mature into almost all different cell types, cannot produce complete organism (no placenta)

• Multipotent - only forms a limited number of cells, later in development and present during remainder of life (ex: skin cells)

• Unipotent - only forms a single cell type (ex: sperm cells), form in late stages, exist in functioning organism

Treatments - bone marrow transplant, skin grafts for burn victims, blood stem cell repair, retinal/corneal repair (AMD, Stargardt’s), cancer regeneration after chemotherapy, boosting immune system (WBCs), repair tissue for type 1 diabetes, autoimmune disorders

Ethical Issues

• Blastocysts are destroyed during the process

• Issue of getting stem cells from a petri dish

• IVF is the main method, make a bunch of embryos but only use three while others are disposed + donated for research

• Accessibility due to money reasons

Surface area to volume ratio - exchange of materials across the surface relies on surface area while the volume describes how much is needed

• need a high surface area to volume ratio to effectively gain nutrients and remove waste

Adaptations for Higher Ratio

• Flat shape - increase surface area

• Villi - in small intestine and kidney cells (projections) microvilli on cell surface  

• Invagination - fold over to create pockets

Sizes of Cells

• Blood cells - small because they squeeze through capillaries

• Sperm - small with tail for journey 

• Neurons - small width, long length

• Striated muscles - fused cells

• Egg - huge with lots of nutrients

Pneumocytes

• Type I - alveolar cell - flattened for increased surface area for transmission

• Type II - lots of vesicles for secretion of surfactant to maintain membrane fluid

Striated Skeletal Muscle Fibres

• Comprised of long, cylindrical fibres formed from the fusion of individual cells that are packed together in unbranching strands (~2-3 cm) which collectively form a muscle bundle

• Have a single, continuous plasma membrane (sarcolemma) and are multinucleate (multiple nuclei)

• Debated whether they are actually cells due to how it’s formed by fusion, its large size, and its process of cell death (apoptosis)

Cardiac Muscle Cells

• Found in the heart

• Are short (~0.1 mm), narrow and fairly rectangular

• Not fused together - mononucleated

• Individual cells are connected by gap junctions at intercalated discs

• Are branched - faster signal propagation and contraction in three dimensions

• More mitochondria than striated muscle fibres - more reliant on aerobic respiration

A1.1 Water

Water - medium of life, first cells originated in water, most organisms are mostly water, processes of life occur in water

• Is a polar molecule (uneven charge distribution/sharing of electrons), causes hydrogen bonds (intermolecular force)

Cohesion - water molecules stick to other water molecules

• useful for transport of water in plants - creates a pull

• surface tension allows for organisms to walk on water

Adhesion - water sticks to other polar or charged molecules

• causes capillary action in soil and in plant cell walls

Solvent properties of water

• Hydrophilic (polar) molecules dissolve in water

• Allows for reactions to occur in cells (cells are made of water)

• Allows molecules to be transferred around the body through blood

Physical Properties

• Buoyancy - upward force of a fluid, high buoyant force

• Viscosity - resistance to flow (thickness), somewhat viscous

• Thermal conductivity - ability of material to transfer heat, relatively low conductivity

• Specific heat capacity - amount of energy it takes to change the temperature of the material, incredibly high heat capacity

Ringed Seal - lives in arctic marine environments, floats pretty easily, streamlined body to minimize drag, flippers to swim, thick blubber to stay warm, paddle-like feet

Black-throated Loon - lives near lakes and rivers, floats easily, webbed feet and streamlined body for swimming, feathers and waterproof coating to stay warm

Origin of water on earth - early earth was too hot for water, as it cooled asteroids left water, water held by gravity, temperature condensed to a liquid

Search for aliens - we look for it where we think there is water and if it is in the goldilocks zone

B1.1 Carbohydrates and Lipids

Carbon

• All organic compounds have carbon at their core - backbone of life

• Carbon can form four bonds to different atoms by sharing electrons (covalent bond)

• Can also form double bonds with different atoms

Monosaccharides

• Pentose/hextose rings

• High solubility, transportability, energy source, and is chemically stable

• Examples: glucose (alpha/beta), galactose, fructose, ribose

Polysaccharides

• Made of alpha-glucose monomers

• Energy storage

  • Compact and efficient due to coiling nature

  • Easy access by removing a glucose

• Is insoluble due to its large size

• Plants: Starch (amylose and amylopectin), Animals: Glycogen

  • Cellulose in plants as well

    • Made of beta-glucose monomers

    • Stacks in straight chains that then cross link with hydrogen bonds - rigid and strong

    • Forms plant cell walls

Glycoprotein - found in cell membranes and stick out into the extracellular space for cell to cell recognition (blood types)

Condensation Reactions - monomers to polymers (create macromolecules)

• Releases a water molecule in the process

• Forms polysaccharides, lipids, polypeptides and nucleic acids

Hydrolysis Reactions - polymers to monomers by digestion

• Water is split and incorporated into molecules to make monomers

Lipids

• They are nonpolar (hydrophobic), mostly insoluble in water, and soluble in nonpolar solvents

• Includes fats and oils (triglycerides), waxes (single chain), and steroids (rings)

Fatty Acids

• Must be in liquid state, organisms want most tightly packed fatty acids

• Saturated fatty acid - 32 degrees C melting point

  • No double bonds, full of hydrogens, straight chain

  • From animals, unhealthy, solid at room temperature, high melting point

  • Found in endotherms

• Unsaturated fatty acid - -5 degrees C melting point (cis)

  • Has double bonds, kinked/bent chains

    • Mono = one double bond (between carbon), Poly = multiple double bonds (between carbon)

  • Cis = hydrogens on same side, Trans = hydrogens on opposite sides

  • Liquid at room temperature, low melting point, primarily in plants and also in fish (omega)

  • Found in ectotherms

Triglycerides

• Formed by a condensation reaction between glycerol and three fatty acids

• Used for long term energy storage

  • Twice as energy dense as carbohydrates

  • More difficult to digest and transport - nonpolar

• Used for thermal insulation

  • Low thermal conductivity

  • Example: aquatic animals have lots of blubber

Phospolipid Bilayer

• Formed by a condensation reaction between phosphate and two fatty acids

• Is amphipathic - part hydrophilic part hydrophobic

  • Tails cluster together to avoid water

Steroids - oestradiol and testosterone - nonpolar

• can travel through plasma membrane and affect cell

B1.2 Proteins

Amino acids - make up proteins

20 Amino Acids = infinite number of peptide chains (primary)

• Humans can create proteins like insulin, collagen, keratin, rhodopsin

Dietary Requirements for Amino Acids

• Non-essential amino acids can be made from any amino acid

• Essential amino acids must be obtained from food

• There are nine essential amino acids (don’t need to be named)

• Vegans need to watch their diet to consume all, but can be done easily

Primary structure - sequence of amino acids and their position determines the eventual shape of the protein, formed via condensation reaction (forms dipeptide + water)

Secondary structure - hydrogen bonds between nonadjacent amino acids (carboxyl of one, amine of another), includes alpha helix and beta-pleated sheets, start of 3D structure

Tertiary structure - combines alpha helices and beta-pleated sheets into 3D shape, occurs due to hydrogen bonds, ionic bonds, disulfide covalent bonds, and hydrophobic interactions between different R groups

Quaternary structure - multiple polypeptide chains together (takes multiple genes to code for)

• Non-conjugated - just multiple polypeptide chains

  • Examples: insulin and collagen

• Conjugated - multiple polypeptide chains AND a prosthetic group (something extra like iron)

  • Examples: hemoglobin and catalase

Chemical Diversity of R Groups

• Different r groups interact differently

• Some are hydrophilic (can be acidic, basic, polar, charged) while others are hydrophobic

• Affects the 3D structure of protein

• Cysteine can form disulfide bridges between other cysteines to form tertiary structure

pH and Temperature on Proteins

• Causes proteins to denature (change shape) —> lose their function

• Each protein has an optimum pH and temperature that it works best at

Globular vs Fibrous Proteins

• Globular - soluble, spherical, typically enzymes or hormones, insulin

• Fibrous - insoluble, strands, structural, collagen

Polar vs Nonpolar Amino Acids

• Polar can be on the outside

• Nonpolar typically need to be on the inside of globular proteins

• Exception is protein channels - part touching tail must be nonpolar