IB Biology Paper 2 Review

Emergent Properties of H2O

-Cohesion
-Moderation of Temperature
-Insulation of Large Bodies of Water
-The Solvent of Life

Cohesion

due to hydrogen bonds that hold water molecules together
-water moves up a tall tree from the roots to the leaves without the expenditure of energy by transpirational-pull cohesion tension (as one molecule of water is lost from the leaf by transpiration, another molecules is drawn in at the roots)
-capillary acton results from the combined forces of cohesion and adhesion
-surface tension allows insects to walk on water without breaking the surface

Moderation of Temperature

absorption of heat from the air (caused by kinetic energy); high specific heat, high heat of vaporization

Insulation of Large Bodies of Water

ice is less dense as a solid than as a liquid; water expands as it freezes

Solvent of Life

polar nature of water makes it well suited to dissolve other polar or ionic substances; composed of hydrogen (H+) and hydroxide (OH-) ions

Isomers

organic compounds that have the same molecular formula but different structures

Structural Isomers

differ in the arrangement of their atoms

Geometric Isomers

differ only in spatial arrangement around double bonds, which are not flexible like single bonds

Optical Isomers (Enantiomers)

molecules that are mirror images of each other

Carbohydrates

-consist of Carbon, Hydrogen, and Oxygen
-CH2O (generally some variation of that)
-the body uses carbohydrates for quick energy

Monosaccharides

-C6H12O6
-glucose/galactose/fructose (all isomers of each other)

Disaccharides

-C12H22O11
-consist of two monosaccharides joined together
-maltose: glucose + glucose
-lactose: glucose + galactose
-sucrose: glucose + fructose

Polysaccharides

-polymers of carbohydrates and are form as many monosaccharides join together by dehydration synthesis
-structural use: cellulose in plants (makes up plant walls), chitin in animals (makes up the exoskeleton in arthropods/cell walls in some fungi)
-storage use: starch in plants (usually found as amylose or amylopectin), glycogen in animals ("animal starch," stored in the liver and skeletal muscle for humans)

Condensation/Dehydration Synthesis

-the joining of two monomers by removing H2O

Hydrolysis

-the breakdown of a compound by adding H2O

Lipids

-diverse class of organic compounds that include fats, oils, waxes, and steroids
-all hydrophobic (not soluble in H2O)
-structurally, most lipids consist of 1 glycerol and 3 fatty acids

Glycerol

-an alcohol
-three hydrophilic hydroxyl groups (which will attach to fatty acids generally)

Fatty Acid

-a hydrocarbon chain with a carboxyl group at one end
-saturated: only single bonds within carbon backbone, generally come from animals, solid at room temperature
-unsaturated: at least one double bond formed by the removal of hydrogen atoms in the carbon skeleton, generally extracted from plants, liquid at room temperature, considered to be good dietary fats

Steroids

-instead of the general structure of lipids, composed of four fused rings

Lipid's Functions

-energy storage: one gram of any lipid will release 9 calories per gram
-structural: phospholipids (lipid + 1 phosphate group instead of fatty acid) are a major component of the cell membrane; cholesterol serves as an important component of the plasma membrane of the animal cell
-endocrine: some steroids are hormones

Proteins

-complex macromolecules that carry out many functions in the body
-consist of Sulfur, Phosphorous, Carbon, Oxygen, Hydrogen, and Nitrogen
-polymers (polypeptides) of amino acids (which are joined by peptide bonds)
-function determined by conformation (unique shape)

Functions of Proteins

-growth and repair
-signaling from one cell to another
-defense against invaders
-catalyzing chemical reactions

Amino Acid Structure

-carboxyl group
-amine group
-variable (R): differs with each amino acid
-all attached to a central asymmetric Carbon atom

Primary Structure

-the unique linear sequence of amino acids
(the slightest change in the amino acid sequence of a protein have dire consequences; sickle cell anemia caused by substitution of one amino acid for another in a molecule of hemoglobin)

Secondary Structure

-results from the hydrogen bonding within the polypeptide molecule
-refers to how the polypeptide coils or folds into two distinct shapes (alpha helix or beta pleated sheet)

Tertiary Structure

-the intricate three-dimensional shape or conformation of a protein that is superimposed on its secondary structure
-determines the protein's specificity
-affected by the following factors: Hydrogen bonding between R groups of amino acids; Ionic bonding between R groups (sensitive to changes in pH); hydrophobic interactions; Van der Waals interactions; disulfide bonds between cysteine amino acids

Quaternary Structure

-refers to proteins that consist of more than one polypeptide chain

The Protein Folding Problem

-scientists don't fully understand how proteins spontaneously fold into their unique shapes
-chaperone proteins assist in fold other proteins

Nucleic Acids

-ribonucleic acid (RNA) or deoxyribonucleic acid (DNA)
-polymers and carry all hereditary information
-consist of repeating units called nucleotides

Nucleotide

-consists of a phosphate, a 5-carbon sugar (deoxyribose or ribose), and a nitrogen base (Adenine, Cytosine, Guanine, Thymine, Uracil)

Laws of Thermodynamics

-Energy cannot be created or destroyed, only transferred (Law of Conservation of Energy)
-in the course of energy conversions, the universe becomes more disordered and entropy increases

Metabolism

-sum of all the chemical reactions that take place in cells
-takes place through pathways, controlled by enzymes and enables cells to carry out their chemical activities efficiently

Catabolism

-reactions that break down molecules

Anabolism

-reactions that build up molecules

Enzymes

-serves at catalytic proteins that speed up reactions by lowering the energy of activation (NOT the energy for the reaction)
-globular proteins that exhibit tertiary structure
-substrate specific
-unchanged in a reaction and are reused
-catalyze reactions in both directions
-may require assistance from cofactors (inorganic) or coenzymes (vitamins)

Induced-Fit Model

-as the substrate enters the active site, it induces the enzyme to alter its shape slightly so the substrate fits better

Efficiency of Enzyme

-affected by temperature and pH
-when temperature is too high, enzymes will begin to denature (since a quaternary structure), and lower their unique conformation and ability to function
-enzymes function at different pHs (gastric enzymes become active at low pH, when mixed with stomach acid, while intestinal amylase works best in an alkaline environment)

Inhibition of Enzyme

-Competitive Inhibition
-Noncompetitive Inhibition
-Allosteric Inhibition
-Cooperativity

Competitive Inhibition

-competitive inhibitors resemble the normal substrate molecule and compete for the same active site on the enzyme
-reduce the productivity of enzymes by preventing the substrate from combining with the enzyme

Noncompetitive Inhibition

-the enzyme contains more than one active site and the substrates do not resemble each other, however the binding of either substrate prevents the other one from binding to the enzyme
-which substrate binds to an enzyme is random and a function of the concentration of each substrate
-e.g. in the operon, the repressor binds to the operator on the DNA strand and blocks the binding site for RNA polymerase and no transcription can occur

Allosteric Inhibition

-involves two actives sites (one for a substrate and the other for an inhibitor)
-the enzyme oscillates between two conformations (one active and one inactive)
-when the inhibitor binds to the allosteric site, the enzyme undergoes conformational change, and the active site for the substrate is altered and the enzyme cannot catalyze the reaction
-e.g. in glycolysis, phosphofructokinase, which catalyzes step 3 in the production of pyruvic acid, is inhibited by ATP (feedback inhibition where a metabolic pathway is switched off by its end product)

Cooperativity

-sometimes substrates can stimulate an enzyme with quaternary structure (two or more subunits) to be more effective
-e.g. once hemoglobin (functioning LIKE an enzyme) binds to one oxygen atom, it can very rapidly bind to three more oxygen atoms

Theory of Endosymbiosis

-eukaryotic cells emerged when mitochondria and chloroplasts (once free-living prokaryotes) took up permanent residence inside other larger cells
-one and a half billion years ago (approximately)

Cell Theory

-all living things are composed of cells
-cells are the basic unit of all organisms
-all cells arise from preexisting cells

Prokaryotes

-no internal membranes (no nuclear membrane, endoplasmic reticulum, mitochondria, vacuoles, or other organelles)
-circular, naked DNA
-ribosomes are very small
-metabolism is anaerobic or aerobic
-cytoskeleton absent
-mainly unicellular
-cells are very small (1-10μm)

Eukaryotes

-contain distinct organelles
-DNA wrapped with histone proteins into chromosomes
-ribosomes are larger
-metabolism is aerobic
-cytoskeleton present
-mainly multicellular with differentiation of cell types
-cells are larger (10-100μm)

Cell Fractionation

-uses an ultracentrifuge to spin liquid samples at high speed, separating them into layers based on differences in density
-cells/tissue first mashed up in blender to form homogenate, then spun in centrifuge

Freeze Fracture

-multistep techniques used to prepare a detailed cast of the membrane
-tissue digested away, leaving only the cast of the tissue
-used to study membrane, separating phospholipid bilayer

Tissue Culture

-used to study the properties of specific cells in vitro
-cell lines can be grown in culture for years, and can be studied while growing

Nucleus

-contains chromosomes, wrapped with special proteins into a chromatin network
-surrounded by a selectively permeable membrane (envelope) that contains pores to allow for the transport of molecules (like messenger RNA), which are too large to diffuse directly through the envelope

Nucleolus

-a prominent region within the nucleus during interphase, where components of ribosomes are synthesized
-not membrane-bound structures, but rather a tangle of chromatin and unfinished ribosome precursors

Ribosomes

-the site of protein synthesis
-can be found free in cytoplasm or attached to endoplasmic reticulum

Endoplasmic Reticulum

-the membranous system of channels and flattened sacs that traverse the cytoplasm
-rough: the site of protein synthesis resulting from the attached ribosomes
-smooth: assists in the synthesis of steroid hormones and other lipids; connects rough ER to the Golgi Apparatus; carries out various detoxification processes

Golgi Apparatus

-lies near the nucleus and consists of flattened membranous sacs stacked next to one another and surrounded by vesicles
-packages substances produced in the rough endoplasmic reticulum and secrete them to other cell parts or to the cell surface for export

Lysosomes

-sacs of hydrolytic enzymes surrounded by a single membrane
-principal site of intracellular digestion
-programmed destruction of cells (apoptosis) by their own hydrolytic enzymes is a critical part of the development of multicellular organisms

Peroxisomes

-found in both plant and animal cells
-contain catalase, which converts hydrogen peroxide (H2O2), a waste of respiration, into water with the release of oxygen atoms
-detoxify alcohol in liver cells

Mitochondria

-the site of cellular respiration
-an outer double membrane and an inner series of membranes (cristae)
-contain own DNA

Vacuoles

-single, membrane-bound structures for storage
-vesicles: tiny vacuoles
-protista have contractile vacuoles that pump out excess water

Plastids

-double-membrane -found in plants and algae

1. Chloroplasts: the site of photosynthesis; own DNA, double outer membrane, as well as an inner membrane forming grana (consisting of thylakoids), surrounded by stroma

2. Leucoplasts: store starch and are found in roots like turnips or in tubers

3. Chromoplasts: store carotenoid pigments and are responsible for the red-orange-yellow of carrots, tomatoes, and daffodils

Cytoskeleton

-complex network of protein filaments that extends throughout the cytoplasm and gives the cell its shape, enables it to move, and anchors the organelles to the plasma membrane

Microtubules

-hollow tubes made of protein tubulin that make up cilia, flagella, and spindle fibers

Microfilaments

(also called actin filaments)
-help support the shape of the cell
-enable animal cells to form a cleavage furrow during cell division, amoeba to move by sending out pseudopods, and skeletal muscle to contract as they slide along myosin filaments

Centrioles/Centrosomes/Microtubule Organizing Centers (MTOCs)

-non-membranous structures that lie outside the nuclear membrane
-organize spindle fibers and give rise to the spindle apparatus required for cell division

Cell Wall

-NOT found in animal cells
-plants and algae have cell wall made of cellulose
-fungi have cell wall made of chitin
-prokaryotes have cell wall made of other polysaccharides and complex polymers
-composed of primary cell wall, secondary cell wall, and middle lamella

Primary Cell Wall

-immediately outside the plasma membrane

Secondary Cell Wall

-second cell wall outside of the primary cell wall

Middle Lamella

-a thin gluey layer formed between two cells

Plasma Membrane

-selectively permeable membrane that regulates the steady traffic that enters and leaves the cell
-phospholipid bilayer with proteins dispersed throughout the layers
-integral proteins have nonpolar regions that completely span the hydrophobic interior of the membrane
-cholesterol molecules are embedded in the interior of the bilayer to stabilize the membrane
-external surface of membrane also have carbohydrates attached to it, forming the glycocalyx (important for cell-to-cell recognition)

Functions of Membrane Proteins

-transport molecules, electrons, and ions through channels, pumps, carriers, and electron transport chains
-act as enzyme (one membrane-bound enzyme located within the cell membrane that synthesizes cyclic AMP (c-AMP) from ATP is adenylate cyclase)
-act as receptors for hormones, neurotransmitters, receptor-mediated endocytosis, and for cells of the immune system
-cell to cell attachments: desmosomes serve as anchors for filaments and rivet cells together

Tight Junctions

-belts around epithelial cells that line organs and serve as barrier to prevent leakage into or out of those organs
- in the urinary bladder, they prevent the urine from leaking out of the bladder into the surrounding body cavity

Desmosomes

-"spot welds" that rivet cells together
-consist of clusters of cytoskeletal filaments from adjacent cells that are looped together
-occur in tissues that are subjected to severe mechanical stress (such as skin epithelium or neck of the uterus)

Gap Junctions

-permit the passage of materials directly from the cytoplasm of one cell to the cytoplasm of the adjacent cell
-in the muscle tissue of the heart, the flow of ions through the gap junctions coordinates the contractions of the cardiac cells

Plasmodesmata

-connect one plant cell to the next (analogous to gap junctions in animal cells)

Signal Transduction Pathway

-relies on plasma membrane proteins in a multistep process in a which a small number of extracellular signal molecules produce a major cellular response
-reception: signal molecule (usually protein) binds to a specific receptor on the cell surface, causing the receptor molecule to undergo a change in conformation
-transduction: the conformation change causes a change in signal form, where the receptor relays a message to a secondary messenger
-response: this secondary messenger, such as cyclic AMP (cAMP) induces a response within the cell

Cell-to-Cell Recognition

-the cell's ability to distinguish one type of neighboring cell from another and is crucial to the functioning of a multicellular organism
-glycoalyx: consists of oligosaccharides attached to integral proteins within the plasma membrane, responsible for such phenomena as contact inhibition (the normal trait of cells to stop dividing when they become too crowded)

Chromosome

-consists of a highly coiled and condensed strand of DNA

Chromatid

-either of the two strands of a replicated chromosome, joined at the centromere

Kinetochore

-disc-shaped protein on the centromere that attaches the chromatid to the mitotic spindle during cell division

Ratio of the Cell Volume to Surface Area

-as cell grows, the area of the cell membrane increases as the square of the radius, while the volume of the cell increases as the cube of the radius
-therefore, as the cell grows larger, the volume increases at a faster rate than does the cell membrane
-since the cell depends on the cell membrane for exchange of nutrients and waste products, the ratio of cell volume to membrane size is a major determinant of when the cell divides

Capacity of Nucleus

-the nucleus must be able to provide enough information to produce adequate quantities to meet the cell's needs
-large sophisticated cells like the paramecium have two nuclei that each control different cell functions
-human skeletal muscle cells are giant multinucleate cells

Interphase

-consists of G1/S/G2

G1 Phase

-period of intense growth and biochemical activity

S Phase

-synthesis or replication of DNA
-90% of the life of a cell
-chromatin is threadlike, not condensed

G2 Phase

-the phase when the cell continues to grow and to complete preparations for cell division

Mitosis

-continuous process
-prophase
-metaphase
-anaphase
-telophase

Prophase

-the nuclear membrane disintegrates
-the strands of chromosomes begin to condense into discrete observable structures
-nucleolus disappears
-mitotic spindle begins to form, ending from centrosome to another
-longest phase of mitosis

Metaphase

-chromosomes line up in a single file located on the equator or metaphase plate
-centrosomes are at opposite poles of the cell
-spindle fibers run from the centrosomes to the kinetochores in the centromeres

Anaphase

-centromeres of each chromosome separate as spindle fibers pull apart the sister chromosomes
-shortest phase of mitosis

Telophase

-chromosomes cluster at opposite ends of the cell, and the nuclear membrane reforms
-supercoiled chromosomes begin to unravel and to return to their normal, pre-cell division condition as long, threadlike strands
-once two individual nucleoli form, mitosis is complete

Cytokinesis

-consists of the dividing of the cytoplasm
-begins during mitosis, often during anaphase
-in animal cells, a cleavage furrow forms down the middle of the cell as actin and myosin microfilaments
-in plant cells, a cell plate forms during telophase

Anchorage Dependence

-to divide, a cell must be attached or anchored to some surface, such as a Petri dish (in vitro) or an extracellular membrane (in vivo)

Meiosis

-a form of cell division that produces gametes with the haploid chromosome number (n)
-Meiosis I (reduction division): process by which homologous chromosomes separate
-Meiosis II (like mitosis)

Prophase I

-synapsis: pairing of homologues
-crossing-over: the exchange of homologous bits of chromosomes
-chiasmata: the visible manifestations of the cross-over events

Metaphase I

-homologous pairs of chromosomes are lined up double file along hte metaphase plate
-spindle fibers from the poles of the cell are attached to the centromeres of eac pair of homologues

Anaphase I

-homologous chromosomes are separated as they are pulled by spindle fibers nad migrate to opposite poles

Telophase I

-homologous pairs continue to separate until they reach the poles of the cell (each pole has the haploid number of chromosomes)

Cytokinesis I

-occurs simultaneously with Telophase I

Meiosis II

-functionally the same as mitosis and consists of the same phases: prophase, metaphase, anaphase, telophase, and cytokinesis
-chromosome number remains haploid and daughter cells are genetically identical to parent cells

Genetic Variation

-Independent Assortment of Chromosomes: during meiosis, homologous pairs of chromosomes separate depending on the eandom way in which they line up on the metaphase plate during metaphase I
-Crossover: produces recombinant chromosomes that combine genes inherited from both parents
-Random Fertilization

Cell Cycle Control System

-regulates the rate at which cells divide
-G1 checkpoint: restriction point (if denied, nondividing cell arrest in G0 phase)
-timing of cell division controlled by cyclins and cyclin-dependent kinases (CDKs)