B1.1 Carbohydrates and Lipid

B1.1.1—Chemical properties of a carbon atom allowing for the formation of diverse compounds upon which life is based.
A covalent bond is formed between two atoms which share a pair of electrons..
A carbon atom 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, such as hydrogen and oxygen. Examples include Carbon dioxide, water, glucose (single ring), sucrose (double ring), glycogen (branched chain), starch / amylose (unbranched), and cellulose.  molecules.

NOS: Scientific conventions are based on international agreement (SI metric units have prefixes “kilo”, “centi”, “milli”, “micro” and “nano” for example kilogram, ).

B1.1.2—Macromolecules, such as polysaccharides, polypeptides and nucleic acids are produced by condensation reactions that link monomers to form a polymer

B1.1.3—Polymers are digested into monomers by hydrolysis reactions. Water molecules are split to provide the -H and -OH groups that are incorporated into a specific bond to produce monomers. This role of water gives the reaction its name, "hydrolysis". Hydro - water, Lysis - splitting.

B1.1.4—Form and function of monosaccharides
Pentoses (e.g. ribose) and hexoses (e.g. glucose) can be recognised as monosaccharides from molecular diagrams by the number of carbon atoms and the shape of the ring structure. Glucose has high solubility, transportability, chemical stability and a high yield of energy from oxidation. This is a great example of the link between the properties of a monosaccharide and how it is used in cells, for respiration.

B1.1.5—Polysaccharides as energy storage compounds
The compact nature of molecules of starch in plants and glycogen in animals makes them very good storage molecules. This is due to coiling and branching during polymerization and the relative insolubility of these compounds (due to large molecular size). It is relatively easy to add or remove alpha-glucose monomers (by condensation and hydrolysis) to build or mobilize energy stores.

B1.1.6—The structure of cellulose is important to its function as a structural polysaccharide in plants
The alternating orientation of beta-glucose monomers gives straight chains that can be grouped
in bundles and and held together by cross-links made by hydrogen bonds. These long structures form cell walls.

B1.1.7—Another function of carbohydrates is seen in Glycoproteins, molecules which have a carbohydrate and a protein component.  The ABO antigens which give blood groups are glycoproteins found in cell membranes which allow cell to cell recognition.

B1.1.8—Hydrophobic properties of lipids
Lipids are substances in living organisms that dissolve in non-polar solvents but are only sparingly (slightly) soluble
in aqueous solvents. Lipids include fats, oils, waxes and steroids.

B1.1.9—Two other important lipids are triglycerides and phospholipids which are formed by condensation reactions that join fatty acids to glycerol, and phosphate to glycerol in phospholipids. One glycerol molecule can link three fatty acid molecules or two fatty acid molecules and one phosphate group.

B1.1.10—There is a wide range of fatty acids. They can be saturated if they have no double C=C bonds, monounsaturated if they have one C=C bond, and polyunsaturated fatty acids if they have two or more C=C bonds.
The number of double carbon (C=C) bonds they have affects melting point. Different types of fatty acids are found in oils and fats used for energy storage in plants and endotherms respectively.

B1.1.11—Triglycerides are used in adipose tissues for energy storage and thermal insulation
The properties of triglycerides make them suited to long-term energy storage functions.
The body temperature and habitat of an organism will affect the use of triglycerides as thermal insulation.

B1.1.12—The formation of phospholipid bilayers is a consequence of the hydrophobic properties of the fatty acid tails and the hydrophilic properties of the phosphate regions. The term “amphipathic” describes a molecule which has both a hydrophobic region and a hydrophilic region.

B1.1.13—Non-polar steroids (e.g. oestradiol and testosterone) can pass through the phospholipid bilayer.
Steroids can be identified from molecular diagrams because they consist of a skeleton of carbon atoms making four fused rings. Hydrogen atoms and other functional groups are attached to this skeleton.

B1.2 Protein Guiding questions

• What is the relationship between amino acid sequence and the diversity in form and function of proteins?

• How are protein molecules affected by their chemical and physical environments?

B1.2.1 - A diagram of a generalized amino acid should show the alpha carbon atom attached to an amine group, carboxyl group, R-group and hydrogen.

B1.2.2 - Condensation reactions form dipeptides and longer chains of amino acids.

The word equation for this reaction:
amino acid 1 + amino acid 2 → dipeptide + water

A drawing of a generalized dipeptide  (after modelling the reaction with molecular models.)

B1.2.3 - Essential amino acids must be obtained from food in the diet, they cannot be synthesised (made from other nutrients). Non-essential amino acids can be made from other amino acids.
Note: There is no need to learn examples of essential and non-essential amino acids.

Vegans have to take special care to ensure they consume all the essential amino acids. A diet rich in oats, legumes and seeds can help.

B1.2.4 - There is an infinite variety of possible peptide chains.

• The genes code for 20 different amino acids.

• genes can be any length, making peptide chains with any number of amino acids. from a few to thousands,

• amino acids can be in any order in the polypeptide chain.

Examples of polypeptides:

• the hormone Insulin
  (made of 2 polypeptides),

• the enzyme Amylase
  (a large single polypeptide),

• the structural protein Collagen
  (three polypeptide chains)

• or the membrane protein Aquaporin
  (four polypeptides).

B1.2.5 - Changes in pH and temperature can change protein structure.

The 3D shape of polypeptides and protein is held together by bonds, including hydrogen bonds, which can be broken by extremes of pH or high temperatures. These conditions change the shape.
Changes to polypeptide structure which stop the protein functioning is called "denaturation”.

B1.2.6 - The diversity in protein form and function comes from the chemical diversity of the R-groups of amino acids.

• R-groups determine the properties of chains of amino acids -       polypeptides.

• R-groups can be hydrophobic (non-polar) or hydrophilic (polar/charged) and some hydrophilic R-groups are acidic or basic.

B1.2.7 - The primary structure of a protein (the sequence of amino acids and the precise position of each amino acid)  determines the three-dimensional shape of proteins (conformation = shape).
Proteins therefore have precise, predictable and repeatable structures, despite their complexity.

B1.2.8 - The secondary structure of proteins involves the pleating and coiling of polypeptides.
Hydrogen bonding in regular positions stabilizes alpha helices and beta-pleated sheet structures.

B1.2.9 - The tertiary structure of proteins is the 3D shape of the polypeptide chain.
Tertiary structure is held together by: hydrogen bonds, ionic bonds, disulfide covalent bonds and hydrophobic interactions.

• pairs of the sulfur containing amino acid cysteine form disulfide bonds.   -S-S-

• amine and carboxyl groups in R-groups can become positively or negatively charged by binding or dissociation of hydrogen ions and that they can then participate in ionic bonding.

B1.2.10 - Polar (hydrophilic) and non-polar (hydrophobic) amino acids influence the tertiary structure of proteins.

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

• hydrophobic amino acids of integral membrane proteins are found in regions of the polypeptides embedded in the hydrophobic lipid bilayer of membranes.

B1.2.11 - The Quaternary structure is the arrangement of multiple polypeptides in a protein.

• Insulin and Collagen are examples of non-conjugated protein, made of polypeptides alone.

• Hemoglobin is a good example of a conjugated protein, it has a non-protein heme group associated with each of its four globin polypeptides. Glycoproteins are also conjugated proteins.

NOS: Cryogenic electron microscopy has allowed imaging of protein molecules and their interactions with other molecules. An example of how technology allows imaging of structures that would be impossible to observe with the unaided senses.

B1.2.12 Insulin and collagen to exemplify how form and function are related in globular and fibrous proteins

• Globular proteins have complex 3D rounded / more spherical shapes and are often soluble, like enzymes or hemoglobin.

• Fibrous proteins are long insoluble proteins like collagen, used to build structures like hair and skin.

D3.2.8 - Single-nucleotide polymorphisms (SNP 'snip') make new alleles and there are multiple alleles in gene pools
Understand that any number of alleles of a gene can exist in the gene pool but an individual only inherits two.

D3.2.9 - ABO blood groups is an example of multiple alleles. Use IA, IB and i to denote the alleles.

D3.2.10 - Understand codominance at the phenotypic level.

• In codominance, heterozygotes have a dual phenotype. Include the AB blood type (IAIB) as an example.

D3.2.1 - Production of haploid gametes in parents and their fusion to form a diploid zygote is the means of inheritance common to all eukaryotes with a sexual life cycle. A diploid cell has two copies of each autosomal gene.

D3.2.3 - Genotype is the combination of alleles inherited by an organism
Use and understand the terms “homozygous” and “heterozygous”, and correctly use terms "genes" and "alleles".

D3.2.4 - Phenotype is the observable traits of an organism resulting from genotype and environmental factors
Suggest examples of traits in humans due to genotype only (e.g. sickle cell disease, cystic fibrosis) and human traits due to environment only (e.g. tattoos, scars), and also traits due to interaction between genotype and environment (e.g. skin colour).

D3.2.5 - Effects of dominant and recessive alleles on phenotype
Both a homozygous-dominant genotype and a heterozygous genotype for a trait will produce the same phenotype.