IB chemistry Biochem

compounds taking part in metabolism are called?

metabolites

reactions controlled in cycles within an organism are called...

metabolic pathways

what happens in catabolism and what type of reaction is it in the body?

• break down

• hydrolysis

• exothermic

• e.g. respiration

what happens in anabolism and what type of reaction is it in the body?

• synthesis of larger molecules from small reactant molecules called precursors

• condensation polymerisation

• endothermic

• e.g. photosynthesis

Difference between larger and smaller molecules in terms of energy

larger molecules are energy rich, small molecules are energy poor

What is energy coupling?

Energy from catabolic reactions is used to drive anabolic reactions and involved an intermediary energy carrier called ATP

biomolecules (molecules present in living things) that are present in small amounts are called?

trace elements

condensation polymerisation vs condensation reaction

reaction is when only one water molecule removed, polymerisation is when many are removed

What is needed in the condensation polymerisation of biomolecules?

• each monomer must have two functional groups so they can link with other monomers on both sides

• enzymes often known as polymerases

the activity of biological molecules depends on...

their structures and shapes

What can you say about the environment where metabolic reactions take place?

highly controlled aqueous environments (temp, pH, chemical conc)

Respiration (3)

• a complex set of metabolic processes

• exothermic

• first step: glycolysis

Glycolysis (6)

• first stage of respiration

• common to all cells

• does not use oxygen, similar to incomplete combustion

• only small proportion of energy in glucose is released

• if no oxygen available, no more energy generated from the glucose

• this is enough energy to keep cells alive temporarily and even permanently in the case of some bacteria

reactants in aerobic respiration are called:

cytochromes

order of redox in aerobic respiration

A series of redox reactions where reactants (cytochromes) are first reduced and then re-oxidised.

In aerobic respiration oxygen acts as..

• the terminal electron acceptor

• it completely oxidises glucose to CO2 and H2O, when it becomes reduced to water.

Difference between aerobic and anaerobic in terms of oxidation and reduction.

Aerobic:

glucose is oxidised to pyruvate ions

pyruvate ions are converted to CO2 and water in the presence of oxygen

Anaerobic:

pyruvate ions are reduced to lactate ions

what are the two types of proteins called?

globular and fibrous

What determines the role of a protein?

it's three dimensional shape

fibrous proteins

elongated, insoluble, structural components, dominant secondary structure. e.g. keratin, collagen

globular proteins

compact and spherical, water-soluble proteins, dominant tertiary structure. Have a role in metabolic processes. e.g. insulin, haemoglobin

What is a zwitterion and what else are they referred to?

• a neutral molecule having separate positively and negatively charged groups.

• sometimes referred to as internal salts because the charges result from an internal acid-base reaction. H+ from acid -COOH transfers to basic -NH2

Amino acids are also called:

zwitterions or amphoteric

what does enzyme activity depend on?

conformation, changes in temperature, pH and presence of heavy metal ions

What are the four types of R groups? (focus on possible charges)

• non-polar/hydrophobic

• polar but uncharged

• basic (positively charged at pH 6-8)

• acidic (negatively charged at pH 6-8)

Chemical nature of R group (n°1)

• non polar/hydrophobic

• contains hydrocarbon

• e.g. alanine

Chemical nature of R group (n°2)

• polar but uncharged

• contains hydroxyl (-OH), sulfhydryl (-SH) or amide (-CONH2)

• e.g. serine

Chemical nature of R group (n°3)

• basic (positively charged at pH 6-8)

• contains amino (-NH2)

• e.g. lysine

Chemical nature of R group (n°4)

• acidic (negatively charged at pH 6-8)

• contains carboxylic acid (-COOH)

• e.g. aspartic acid

Properties of amino acids

• amino acids are crystalline compounds with high melting points, usually above 200°C

• more soluble in water than non-polar solvents

• move in an electric field

what are the three forms of amino acids

zwitterions, cations and anions

What happens to amino acids at high pH?

-NH3+ loses its H+ and the amino acid forms an anion

What happens to amino acids at low pH?

-COO- gains H+ and the amino acid forms a cation

What is the isoelectric point?

• The pH at which the amino acid is electrically neutral.

• With no net charge, amino acids will not move in an electric field.

• Molecules will have minimum repulsion and so be the least soluble

Why is the amphoteric nature of amino acids useful?

Amino acids can be used as pH buffers - resist changes due to small amounts of acid or alkali

What is the primary structure of a protein?

The sequence of amino acids in the polypeptide chain, held together by peptide bonds it forms the covalent backbone of the molecule.

What is the secondary structure of a protein? What are the two main types?

• folding of polypeptide chain as a result of H-bonds that form between the carboxyl of one and the amino group of another

• The exact location of the H.bonds is determined by R groups

• two main types: α-helix and β-pleated sheet

β pleated sheet

• The polypeptide chain folds back and forth. Two regions of the chain lie parallel to each other and are held together by hydrogen bonds between atoms of the polypeptide backbone (not the side chains/R-groups).

• flexible but inelastic

• e.g. in spider silk

α-helix

• a coil held together by hydrogen bonding between every fourth amino acid

• flexible and elastic bc intra-chain hydrogen bonds easily break and re-form as molecule stretched

• e.g. in keratin

What is the tertiary structure of a protein?

• further folding of a polypeptide chain due to interactions between side chains (R-groups)

• the resulting structure is very compact and three-dimensional, known as the protein's conformation

• keeps globular proteins soluble as hydrophilic side chains move outside while hydrophobic remain inside

What interaction stabilise protein conformation (tertiary structure)?

• hydrophobic/LDF interactions between non-polar side chains

• H-bonds between polar side chains

• ionic bonding between side chains carrying a charge

• disulphide bridges btw the sulfur-containing amino acid cysteine

What is the quaternary structure of a protein?

• two or more polypeptide chains joined together, consisting of the same bonds as the tertiary structure.

• not all proteins have a quaternary structure

Give two examples of quaternary structures

• collagen is a triple helix of three polypeptide chains with inter-chain H-bonds btw them. helps to give a stable, rope-like structure and resistance to stretching

• haemoglobin has four polypeptide chains that fit together tightly.

Describe the structure and conformation of enzymes

• globular proteins

• compact spherical shapes

• well-defined tertiary structure essential for enzyme activity

Sometimes enzymes depend certain non-protein molecules for their catalytic functions, these molecules are called...

• co-factors

• these can be both organic, in which case they are called coenzymes, or inorganic such as metal ions or vitamins

What type of interaction between enzyme and substrate? (4)

hydrophobic (LDF), dipole-dipole attractions, hydrogen bonding and ionic attractions.

What facilitates the breaking and forming of bonds in a catalytic reaction?

The binding in the enzyme-substrate complex puts a strain on the substrate molecule which facilitates the process

The relationship between substrate concentration and rate for an enzyme-catalysed reaction

velocity increases slower and slower as concentration increases because fewer enzymes are available for substrates. We say the enzymes are saturated.