IB Biology - Theme B

B1.1.1—Describe the nature of a covalent bond.

When two atoms share electrons with each other.

"B1.1.1—Give examples of the diversity of carbon compounds.

Include among the diversity of carbon compounds examples of molecules with branched or unbranched chains and single or multiple rings.

Examples are methane (CH4), ethane (C2H6), ethene which has a carbon to carbon double bond (C2H4), cycloproene which has a double bond and cyclical nature (C3H4),

"

"B1.1.1—What are the chemical properties of a carbon atom which allowing for the formation of diverse compounds upon which life is based

A carbon atom has a valency of four. This means it can form up to four single bonds or a combination of single and double bonds with other carbon atoms or atoms of other non-metallic elements.

Include among the diversity of carbon compounds examples of molecules with branched or unbranched chains and single or multiple rings.

"

"B1.1.1—What do the following scientific conventions which are based on international agreement mean - SI metric unit prefixes "kilo", "centi", "milli", "micro" and "nano".

kilo - 10^3

centi - 10^-2

milli - 10^-3

micro - 10^-6

nano - 10^-9

"

"B1.1.2—Describe the production of disaccarides and polysaccharides using word equations.

glucose + galactose --> lactose + water

glucose (many) ---> starch + water (many)

"

"B1.1.2—Describe the production of polypeptides using a word equation.

amino acids (many) ---> polypeptide + water (many)

The -OH group from the acid and the -H group from the amino group are released to form a water molecule and a peptide bond is formed.

"

B1.1.2—in general, what type of chemical reaction produces macromolecules?

Macromoelcules are produced by condensation reactions that link monomers to form a polymer

B1.1.2—What is a condensation reaction?

A water molecule is always formed as part of the reaction.

B1.1.2—What is a hydrolysis reaction?

A water molecule is split split to provide the -H and -OH groups that are incorporated to produce monomers.

B1.1.2—What is the word equation for the production of nucleic acids.

nucleotides (many) ---> nucleic acids + water (many)

"B1.1.3—Digestion of polymers into monomers by hydrolysis reactions

Water molecules are split to provide the -H and -OH groups that are incorporated to produce monomers, hence the name of this type of reaction.

e.g. lactose + water --> galactose + glucose

"

"B1.1.4—Using glucose as an example, link the form and function of monosaccharides

Glucose has 5 hydroyxl groups. Hydroxyl groups, as water, have polar covalant bonds and so glucose is a polar molecule

Molecular stability - Stable covalent bonds

High solubility - Polar nature

Easily transportable - it is soluble and can circulate in blood and fluids between cells.

High yield of energy from oxidation - covalent bonds contain a lot of energy and so when they are broken they release a lot of energy.

"

"B1.1.5—Give three reasons why the structure of polysaccharides helps them function as energy storage compounds

1. Compact nature of starch in plants and glycogen in animals due to coiling and branching during polymerization

2. Relative insolubility of these compounds due to large molecular size so they do not affect the osmotic balance in living tissues, whereas glucose is soluble and would.

3. Eelative ease of adding or removing alpha-glucose monomers by condensation and hydrolysis to build or mobilize energy stores.

"

B1.1.6—Describe the structure of cellulose and relate this to its function as a structural polysaccharide in plants

Cellulose is made of beta-glucose monomers arrange with the alternating orientation. This gives straight chains that can be grouped in bundles and cross-linked with hydrogen bonds between hydroxyl groups (-OH). This makes it very strong and stable molecule, it is insoluble and the fibres allow water to pass through them easily.

B1.1.6—Why can cellulose not be used as an energy storage molecule?

Very few organisms produce the enzyme cellulase which is needed to digest cellulose.

B1.1.7—Describe the role of glycoproteins in cell-cell recognition

There are glycoproteins on the surface of red blood cells which determine and person's ABO blood type. These glycoproteins are called antigens. They can be A, B, AB and there can be none.

B1.1.7—Give three examples of conjugated molecules.

Lipoprotein, glycolipid, glycoprotein.

B1.1.7—What do we call a molecule that can trigger an immune response?

Antigen

B1.1.8—Describe the solubility properties of lipids.

Lipids are substances in living organisms that dissolve in non-polar solvents but are only sparingly soluble in aqueous solvents. They are hydrophobic.

B1.1.8—Name four types of lipids.

Lipids include fats, oils, waxes and steroids.

"B1.1.9—Name the type of reaction that forms of triglycerides and phospholipids. State the molecules needed to make each.

Condensation reactions are needed to make triglycerides and phospholipids.

One glycerol molecule can link three fatty acid molecules --> triglyceride

two fatty acid molecules and one phosphate group --> phospholipid

"

"B1.1.10—Difference between the function of saturated, monounsaturated and polyunsaturated fatty acids

Saturated (fats e.g. butter, animal fat) - have high melting points, are solid at room temperature, are used by animals particularly endotherms) to store excess energy.

Monounsaturated - have lower melting points, are liquid at room temperature, some animals and plants store energy in this form.

Polyunsaturated fatty acids - have relatively low melting points, are liquid at room temperature, many plants store energy in this form

"

"B1.1.10—Difference between the structure of saturated, monounsaturated and polyunsaturated fatty acids

Saturated - have no double carbon (C=C) bonds, they are saturated with hydrogens.

Monounsaturated - have one carbon (C=C) bonds

Polyunsaturated fatty acids - have many carbon (C=C) bonds

"

"B1.1.11—Give three reasons why tiglycerides in adipose tissues are suited for energy storage and thermal insulation

Triglycerides make them suited to long-term energy storage functions.

1. Insoluble - so don't move from the storage location, and act as thermal insulators to body temperature and habitat.

2. Undergo hydrolysis to release glycerol and fatty acids which can be used to release energy in respiration.

3. They contain twice as much energy per gram as carbohydrates.

"

B1.1.11—In what type of animals do we find a thick later of adipose tissue?

Endotherms such as birds and mammals. The adipose tissue traps heat energy made by the animals.

B1.1.11—What do we call the type of tissue made of cells that store fat in the form of triglycerides in their vacuoles

Adipose tissue

B1.1.12—What do we call molecules which have both hydrophobic and hydrophillic regions?

Amphipathic

B1.1.12—Why do phospholipids spontaneously form bilayers in water?

Phosphlipids have hydrophobic tails (fatty acids) and hydrophilic regions (phosphate group). They are amphipathic. The tails extend towards each other to exclude the water, the heads face the water.

"B1.1.13—Name two steroids, and describe their structure.

Oestradiol - Has hydroxyl group

Testosterone - Has carbonyl group

Both are made from cholesterol, both have the same 17-carbon ring system

"

B1.1.13—What ability do non-polar steroids have regarding the the phospholipid bilayer

They can diffuse directly across it, and the nuclear membrane to where they influence transcription.

B1.2.1—Name and draw the structure of an amino acid

There is a central alpha carbon atom with amine group, carboxyl group, R-group and hydrogen attached.

"B1.2.2—Name and write the word equation for the type of reaction that forms dipeptides and longer chains of amino acids

Condensation reaction. Amino acid 1 + amino acid 2 --> dipeptide + water

Be able to draw a dipeptide

"

B1.2.3—What is the difference between essential and non-essential amino acids?

Essential amino acids cannot be synthesized and must be obtained from food. Non-essential amino acids can be made from other amino acids.

B1.2.3—What kind of diet requires care to get sufficient essential amino acids?

Vegan

B1.2.4—Explain why there is an infinite variety of possible peptide chains

Include the ideas that 20 amino acids are coded for in the genetic code, that peptide chains can have any number of amino acids, from a few to thousands, and that amino acids can be in any order. Students should be familiar with examples of polypeptides.

B1.2.4—Give examples of polypeptides

Haemoglobin, keratin, lipase, collagen, histones, insulin.

"B1.2.5—Describe and explain the effect of pH on protein structure

Extremes of pH will flood the plasma or cytoplasm with H+ or OH- ions. These interfere with the hydrogen bonding and again change the shape and function.

We say the enzyme has been denatured, has undergone denaturation.

"

"B1.2.5—Describe and explain the effect of temperature on protein structure

High temperatures increases molecular motion to such an extent that the hydrogen bonds holding together the 3D shape can break, changing the shape and function.

We say the enzyme has been denatured, has undergone denaturation.

"

B1.2.5—How is the precise 3D shape of proteins (especially enzymes) achieved.

Intramolecular bonds between amino acids e.g. hydrogen bonds, which fold the protein into a complex globular protein.

"B1.2.6—Describe the chemical diversity in the R-groups of amino acids as a basis for the immense diversity in protein form and function

R- groups are hydrophobic or hydrophilic and that hydrophilic R-groups are polar or charged, acidic or basic.

R-groups determine the properties of assembled polypeptides.

"

"B1.2.7—What is the impact of primary structure on the conformation of proteins

The sequence of amino acids and the precise position of each amino acid within a structure determines the three-dimensional shape of proteins because the sequence determines the intermolecular bonds that can form and therefore the shape. Sequences different in number and type of amino acid.

Proteins therefore have precise, predictable and repeatable structures, despite their complexity.

"

B1.2.8—Describe the nature of bonding and the possible secondary structures in proteins

Hydrogen bonds between peptide bonds stabilize alpha helices and beta-pleated sheets.

"B1.2.9—Name the four types of bonds that bring about tertiary structure.

a) Ionic bonds - amine (+ve charge) and carboxyl groups (-ve) in R-groups become positively or negatively charged by binding or dissociation of hydrogen ions and that they can then participate in ionic bonding.

b) Hydrophobic interactions - between non-polar amino acids

c) Disulphide bond - a covalent bond that forms between pairs of cysteines

d) Hydrogen bonds - form between polar amino acids

"

"B1.2.10—Effect of polar and non-polar amino acids on tertiary structure of proteins

In proteins that are soluble in water, hydrophobic amino acids are clustered in the core of globular proteins.

Integral proteins have regions with hydrophobic amino acids, helping them to embed in membranes.

"

"B1.2.11—Quaternary structure of non-conjugated and conjugated proteins

Include insulin and collagen as examples of non-conjugated proteins and haemoglobin as an example of a conjugated protein.

NOS: Technology allows imaging of structures that would be impossible to observe with the unaided senses. For example, cryogenic electron microscopy has allowed imaging of single-protein molecules and their interactions with other molecules.

"

"B1.2.12—Relationship of form and function in globular and fibrous proteins

Proteins can be globular (e.g. enzymes, hormones) and fibrous proteins (e.g. structural)

Use insulin and collagen to exemplify how form and function are related.

"

"B2.1.1—What molecules are the core basis of cell membranes

Lipid bilayers.

Phospholipids and other amphipathic lipids naturally form continuous sheet-like bilayers in water.

"

B2.1.2—Why do lipid bilayers function as barriers

The hydrophobic hydrocarbon chains that form the core of a membrane have low permeability to large molecules and hydrophilic particles, including ions and polar molecules, so membranes function as effective barriers between aqueous solutions.

B2.1.3—Name two moelcules which can do simple diffusion across membranes

Oxygen and carbon dioxide molecules - because they are small and uncharged.

"B2.1.4—Name two groups of proteins based on their location in the membrane. Explain how they are attached to the membrane.

Integral proteins are embedded in one or both of the lipid layers of a membrane. They have an amphipathic nature.

Peripheral proteins are attached to one or other surface of the bilayer, often to a integral protein.

Emphasize that membrane proteins have diverse structures, locations and functions.

"

"B2.1.5—How does water move across the membrane. Explain the nature of the movement and how the concentration gradients arise.

By osmosis. This is the passive movement of water molecules across a cell membrane from higher to lower water concentration. It is passive because it occurs without energy and simply as a result of the random movement of particles. The movement of water largely occurs by faciliated diffusion through channel proteins called aquaporins.

High and low water concentrations arise due to the impermeability of membranes to solutes and differences in solute concentration.

"

"B2.1.6—Explain how facilitated diffusion takes place across the cell membrane.

When diffusion takes place through carrier proteins and channel proteins.

The structure of channel proteins makes membranes selectively permeable by allowing specific ions to diffuse through when channels are open but not when they are closed.

"

B2.1.7—Name the type of proteins involved in active transport, and how these function.

Protein pumps. They use energy from adenosine triphosphate (ATP) to transfer specific particles across membranes and therefore that they can move particles against a concentration gradient.

"B2.1.8—How is selectivity in membrane permeability achieved?

Facilitated diffusion and active transport allow selective permeability in membranes.

Permeability by simple diffusion is not selective and depends only on the size and hydrophilic or hydrophobic properties of particles.

"

"B.2.1.9—Describe the structure, location and function of glycoproteins and glycolipids

Glycolipids are phospholipids with carbohyrates chains attached

Glycoproteins are membrane proteins with carbohyrates chains attached.

In both cases carbohydrate chains are only found on the extracellular side of membranes, they have roles in cell adhesion (cells sticking to each other) and cell recognition (idenitification of self and non-self).

"

B2.1.10—Draw a 2D representatio of the fluid mosaic model of membrane structure with hydrophobic and hydrophillic regions.

Students should be able to draw a two-dimensional representation of the model and include peripheral and integral proteins, glycoproteins, phospholipids and cholesterol. They should also be able to indicate hydrophobic and hydrophilic regions.

B2.1.11—Describe the relationships between fatty acid composition of lipid bilayers and their fluidity

Unsaturated fatty acids are less straight, this means that they do not pack together as tightly in lipid bilayers, and therefore have lower melting points, are more fluid and more flexible. At higher temperatures there are more saturated fatty acids, which are straighter, pack more closely, have higher melting points and make membranes stronger at higher temperatures. Unlike multicellular organisms, unicellular bacteria experience extreme changes in temperature. Some have fatty acid desaturase enzymes in their cell membrane to speed up reactions to increase the number of double bonds.

B2.1.12—Describe the position of cholesterol in membranes and how it affects membrane fluidity in animal cells

Cholesterol molecules are found closely associated with fatty acid tails. Cholesterol acts as a modulator (adjustor) of membrane fluidity, stabilizing membranes at higher temperatures and preventing stiffening at lower temperatures. Plant membranes don't have cholesterol, they have cell walls to compensate.

B2.1.13—Describe how endo and exocytosis are involved in the modification and secretion of proteins.

After protein synthesis the protein is packaged into a vesicle, the vesicle is then taken to the golgi apparatus where post translational modifications take place, the vesicle fuses with the cis side of the golgi apparatus - the proteins enter the lumen and are modified - then trans side of the golgi apparatus membrane then surrounds the modified protein and "pinches" off into a new vesicle by exocytosis. In this manner it passes through the golgi apparatus and then evenually is secreted from the cell.

"B2.1.13—Examples of endocytosis.

Amoeba engulfs its food through the process of endocytosis with the help of pseudopodia.

Pathogens are removed by white blood cells such as neutrophils and monocytes by the process of phagocytosis

"

"B2.1.13—Examples of exocytosis.

The secretion of insulin into the bloodstream by pancreatic cells.

The release of neurotransmitters into synpases in the nervous system.

"

"B2.1.13—Explain how membrane fluidity allows large molecules to enter and exit a cell.

The fluidity of the cell membrane allows changes in shape of the membrane to produce vesicles which can take in or remove macromolecule.

Endocytosis - takes macromolecules into the cell/organelle through the formation of vesicles, the membrane surrounds the matter to be taken into the cell and then ""pinches"" off into a vesicle. The ends of the membrane in both the vesicle and the membrane join together due to amphipathic nature of the phospholipids and their behaviour in an aqueous environment.

Exocytosis - takes macromolecules out of the cell/organelle through the fusion of vesicles, the vesicle fuses with the membrane allowing the proteins to enter the organelle or exit the cell.

"

B2.1.14—Describe the role of neurotranmitter-gated ion channels in neurons

Neurons have nicotinic acetylcholine receptors as an example of a neurotransmitter-gated ion channel. When the neurotransmitter acetylcholine diffuses across the synapse it binds to a nicotinic acetylcholine receptor, the associated channel opens and positive ions such as K+, Na+ and Ca2+ move into the neuron, changing the membrane potential so a nerve impulse can be generated.

B2.1.14—Describe the role of voltage-gated ion channels in neurons

Neurons have voltage-gated sodium and potassium channels. These open, for a brief period of time, in response to changes in membrane polarity, also known as an electrical stimulus. Na+ channels open first, the ions move into the cell, depolarising the membrane. Later, the K+ channels open, these move ions out of the cell, repolarising it again and reestablishing the membrane potential.

B2.1.14—What do we call the two types of channels that can be opened or closed as a result of stimuli?

Neurotransmitter-gated, voltage-gated.

"B2.1.15—Explain how the sodium-potassum pump functions as an exchange transporter to generate membrane potentials.

It moves 3 Na+ out and 2 K+ into a cell against the concentration gradient. This also makes the outside more positive and and the inside more negative, chasing a difference in charge across the membrane. We call this the membrane potential and we say the cell is polarised.

1. Pump has ATP attached and binds 3 IC Na+ ions.

2. Binding of Na+ causes the ATP to split leaving one phosphate attached to the pump (phosphorylation of the pump).

3. The phosphorylation changes the shape of the pump, decreasing affinity for and releasing Na+ out of the cell, and increasing the affinity for K+.

4. K+ ions bind, causing dephosphorylation of the pump.

5. The pump changes shape releasing K+ into the cell.

"

B2.1.15—What do we call the difference in charge across a cell membrane in animal cells, which is created by the sodium potassium pump.

Resting membrane potential.

B2.1.15—What kind of transport protein is the sodium-potassium pump.

Active transport (uses ATP to move ions against their concentration gradient). They are also known as an exchange transporter.

"B2.1.16—Describe an example of indirect active transport.

Sodium-dependent glucose cotransporters are an example of indirect active transport.

Both sodium and glucose bind to the extracellular surface of the cotransporter. Sodium moves down the concentration gradient into the cell, this energy is used to move glucose into the cell against the concentration gradient.

These cotransporters are used in glucose absorption by cells in the small intestine and glucose reabsorption by cells in the nephron.

"

B2.1.16—What do we call the type of transporter which uses the energy produced by the movement of one molecule down a concentration gradient to transport another molecule against a concentration gradient.

Indirect active transport.

"B2.1.17—Describe two types of CAMs and the types of organisms these are found in.

Different forms of CAM are used for different types of cell-cell junction.

Desmosomes - join cells in heart, stomach and bladder.

Plasmodesmata - join plant cells. They are tubes connecting the cytoplasm of adjecent cells allowing exchange of materials.

Students are not required to have detailed knowledge of the different CAMs or junctions.

"

B2.1.17—Name the structures needed to join cells together at cell-cell junctions to form tissues

Cell-adhesion molecules (CAMs).

"B2.2.1—Give four examples of structures considered organelles, and three that are not.

Nuclei, vesicles, ribosomes and the plasma membrane are organelles.

The cell wall, cytoskeleton and cytoplasm are not considered organelles.

"

"B2.2.1—Name a tool, other than microscopy which has been invested and used to study the function of individual organelles.

NOS: Students should recognize that progress in science often follows development of new techniques.

Ultracentrifuges spin a sample at high speed, separating the componets by size and shape. Larger and heavier components move to the bottom of the tube, lighter move to the top.

This process is called centrifugation or cell fractionation.

"

B2.2.1—What do we call the discrete subunits of cells that are adapted to perform specific functions

Organelles

"B2.2.2—What is the major advantage of the separation of the nucleus and cytoplasm into separate compartments in eukaryotes.

Separation of the activities of gene transcription and translation

With separation, post-transcriptional modification of mRNA can happen before the mRNA meets ribosomes in the cytoplasm. In prokaryotes this is not possible—mRNA may immediately meet ribosomes.

"

"B2.2.3—Advantages of compartmentalization in the cytoplasm of cells

1. Concentration of metabolites and enzymes

2. Separation of incompatible biochemical processes.

Include lysosomes and phagocytic vacuoles as examples.

"

"B2.2.3—Name two compartmentalized structures in white blood cells, and explain how they function to demonstrate the advantages of compartmentalization.

Lysosomes (contain desctructive enzymes which could otherwise damange the cell) and phagocytic vacuoles (contain the engulfed material protecting the rest of cell from damage).

They only fuse when the phagocytic vacuole is present.

"

"B2.2.4—Name three adaptations of the mitochondrion for production of ATP by aerobic cell respiration

1. Double membrane with a small volume of intermembrane space - maintains a reservoir (a high concentration of) hydrogen ions.

2. Large surface area of cristae - increase the surface area for reactions that take place at the end of respiration called oxidative phosphorylation.

3. Compartmentalization of enzymes and substrates of the Krebs cycle in the matrix - Contains the enzymes for the link reaction and Kreb cycle).

"

B2.2.5—Inside a chloroplast, there are stacks of flattened membrane sacs filled with chlorophyll. Name the flattened sacs and the stacks.

Sacs are thylakoids, stacks are grana

B2.2.5—Inside the double membrane of a chloroplast there is a fluid with enzymes and chemicals similar to a cell cytoplasm. What is this called.

Stroma

"B2.2.5—Name three adaptations of the chloroplast for photosynthesis

1. Large surface area of thylakoid membranes with photosystems

2. Small volumes of fluid inside thylakoids

3. Compartmentalization of enzymes and substrates of the Calvin cycle in the stroma.

"

"B2.2.6—Name two functional benefits of the double membrane of the nucleus

The double membrane separates the activities of the DNA so they are unaffected by the other processes in the cell.

1. The need for pores in the nuclear membrane - to allow small molecules, mRNA, protein-RNA complezes into and out of the nucleus

2. The nucleus membrane to break into vesicles during mitosis and meiosis, these can then re-join and reform the nuclear membranes at the end of mitosis and meiosis.

"

B2.2.6—What is the nucleolus, and its function?

A region of the nucleus where RNA-protein complexes are formed which leave the nucleus by pores to make ribosomes.

"B2.2.7—Descibe the two locations and functions of the ribosomes.

Free ribosomes - synthesise proteins for retention in the cell.

Membrane-bound ribosomes - synthesise proteins on the rough endoplasmic reticulum of proteins for transport within the cell and secretion.

"

B2.2.8—Name the organelle which consists of flattended sacs of membrane called cisternae.

Golgi apparatus

B2.2.8—Name which side of the of the Golgi apparatus faces the ER?

cis side

"B2.2.8—What is the function of the Golgi apparatus

The processing (post-translational modifications and secretion of protein.

The protein are modified so they can carry out the specific function needed at that time, and the chemical signal that determines the destination of the product.

"

B2.2.9—Name four types and functions of vesicles

Peroxisomes (contain enzymes to break down fatty acids), lysosomes (contain enzymes to digest cells and defective organelles), transport vesicles (transport materials around cell), secretory vesicles (to take materials to be removed from the cell e.g. neurotransmitters and insulin).

B2.2.9—What do we call small membrane-bound sacs in which various substances are transported or stored in the cell.

Vesicles

"B2.2.9—What is the role of clathrin?

They are involved in the production of vesicles in receptor-mediated endocytosis.

They are proteins in the cell membrane that line coated pits They anchor other proteins like receptors. When the receptors have sufficiently occupied, the pits deepen an form a vesicle.

"

"B2.3.1—Explain how morphogens direct gene expression in an early-stage embryo

The concentration of the morphogen directs the development of cells into head and tail structures.

The concentration results in different genes being expressed, resulting in different types of cells in different parts of the embryo and so the development of structures like head and tail.

"

B2.3.1—Following fertilization name the types of cells produced.

First, unspecialized cells are produced, later the cells of the embryo start to differentiate and produce specialised cells

B2.3.1—Name the process which produces specialised cells as the result of the expression of some genes but not others.

Differentiation.

B2.3.1—Name the signal molecules which occur in gradients in different regions of the early embryo

Morphogens

B2.3.2— Name two types of cells that can be produced by stem cells.

Replacement stem cells (self-renewal) or differentiated cells.

B2.3.2— What do we call the cell which retain the capacity to divide endlessly and differentiate along different pathways.

Stem cells

B2.3.3—Name two locations and functions of stem cell niches in adult humans

Bone marrow and hair follicles.

B2.3.3—What do we call locations where stem cells are present in high numbers due to proliferation, but they also demonstrate differentiation.

Stem cell niches e.g. bone marrow, hair follicles.

"B2.3.4—Differences between totipotent, pluripotent and multipotent stem cells

Totipotent - cells in very early-stage animal embryos - can make any tissue in the organism.

Pluripotent - cells in early-stage animal embryos - can make almost all the different types of cells but not the whole organism.

Multipotent - cells in adult tissue such as bone marrow are multipotent -only form a limited number of cell types.