IB Biology Unit 2: Biochemistry

A: Water

A1.1.1 Water as the medium for life

  • Life needs chemical reactions to take place to gain energy, grow, and get rid of waste.

  • Water is a liquid medium that allows the chemistry of life to take place.

  • The first cells on the planet probably originated in water (hydrothermal vents)

A1.1.2 Hydrogen bonds as a consequence of the polar covalent bonds within water molecules.

  • Water (H2O) is made up of two hydrogen atoms covalently bound to an oxygen atom

  • While this bonding involves the sharing of electrons, they are not shared equally

  • The number of protons in each atom is different; oxygen atoms have 8, whilst hydrogen atoms have just 1

  • Having more protons, the oxygen atoms attract the electrons more strongly

  • Thus, the oxygen atom becomes slightly negative and the hydrogen atoms become slightly positive (i.e., the oxygen has a higher electronegativity)

  • Covalently bonded molecules that have a slight potential charge are said to be polar

A1.1.3 Cohesion of water molecules due to hydrogen bonding and consequences for organisms.

  • Cohesion:

    • This property occurs as a result of the polarity of a water molecule and its ability to form hydrogen bonds

    • Although hydrogen bonds are weak, the large number of bonds present (each water molecule bonds to four others in a tetrahedral arrangement) gives cohesive forces great strength

    • Water molecules are strongly cohesive (they tend to stick to one another)

    • Water droplets form because the cohesive forces are trying to pull the water into the smallest possible volume, a sphere

A1.1.4 Adhesion of water to materials that are polar or charged and impacts for organisms

  • Result of the polarity of a water molecule and its ability to form hydrogen bonds

  • Water molecules tend to stick to other water molecules that are charged or polar for similar reasons that they stick to each other

  • Single hydrogen bonds are weak but a large number of bonds give adhesive forces a lot of strength

  • Capillary action

    • combination of adhesive forces that cause water to bond to a surface

    • Helpful in the movement of water during transpiration and when you drink using a straw

A1.1.5 Solvent properties of water linked to its role as a medium for metabolism and for transport in plants and animals

  • Properties of water molecules

    • Solvent

      • Water can dissolve many organic and inorganic substances that have charged or polar regions

      • Water is often wrongly referred to as being the universal solvent, it is good for many substances though

      • Metabolic reactions

        • Happen most readily in solutions of water - water in cells dissolves the reactants/substrates

      • Cells are mostly water so diffusion into and out of them happens most easily if the substance is in solution

      • Soluble substances such as sucrose can easily be transported around the plant in the phloem. Once dissolved in the water of the phloem, the sucrose can be moved to where it is needed by mass flow

    • Hydrophilic

      • Substances that are chemically attracted to water

      • All substances that dissolve in water are hydrophilic, including polar molecules like glucose, and particles with positive or negative charges like sodium and chloride ions

      • Substances that water adheres to are also hydrophilic

    • Hydrophobic

      • Substances that are insoluble in water

      • Molecules are hydrophobic if they DON’T have negative or positive charges and are nonpolar

      • All lipids are hydrophobic 

      • Hydrophobic molecules dissolve in other solvents like propanone

    • Transport of molecules in the blood

      • Blood plasma consists of mainly of water, plus dissolved substances which it transports

      • Glucose

        • Polar molecule=freely soluble

        • Carried by the blood plasma

    • Amino acids

      • Positive and negative charges = soluble in water

      • Carried by the blood plasma

    • Oxygen

      • Non-polar molecule

      • Barely soluble

      • Water becomes saturated with oxygen at relatively low concentrations

      • As temperature increases, the solubility decreases

      • Hemoglobin in red blood cells carry the majority of oxygen

    • Fats

      • Insoluble

      • Non-polar

      • Carried in blood inside lipoprotein complexes

    • Cholesterol

      • Insoluble

    • Lipoprotein complex

      • Fats also need to travel in the blood but they’re nonpolar

    • Sodium chloride

      • Freely soluble in water

      • carried in the blood plasma

A1.1.6 Physical properties of water and the consequences for animals in aquatic habitat

  • Thermal

    • Water has a high specific heat capacity

      • Water needs a lot of heat to warm up and cools down slowly because it can store a lot of energy.

    • Water has a high boiling point and latent heat of vaporization

      • It takes a lot of heat to boil and turn into steam

      • Latent heat is the extra energy needed to change from a liquid to a gas without changing its temperature

    • Water has a high heat of fusion

      • It takes a lot of heat to melt ice into water

  • Water as a coolant

    • High temperatures damage tissues and denature proteins

      • enzymes don’t work

    • It takes a lot of energy for water to change temperature

      • Heats and cools more slowly than air or land

      • Useful for animals in hot climates who can use water to cool off

    • When water evaporates it removes a lot of energy from the system

      • Cooling sensation

      • Helps aquatic animals remain at fairly constant temperatures in hot weather

  • Physical states of water

    • Water is less dense as a solid  because of hydrogen bonding

  • Seals

    • Buoyancy helps them stay afloat without using too much energy

    • Water has a greater thermal conductivity than air so the seal needs to insulate itself with blubber

B: Carbohydrates and Lipids

B1.1.1 Carbon atoms can form four covalent bonds allowing a diversity or stable compounds to exist

  • Carbon forms the backbone of every organic molecule

  • Carbon atoms form covalent bonds

    • Strongest type of bond between atoms

    • Stable molecules can be formed

  • Carbon atoms have 4 electrons in their outer shell 

    • Allows them to form 4 covalent bonds with 4 other different atoms

  • Carbohydrates

    • Have carbon, hydrogen and oxygen

    • They have a monomer (little molecules) and a polymer (a bunch of monomers chain up together that form a polymer)

    • Monomers are commonly ring shaped molecules

  • Lipids

    • Made up of fatty acids

    • Common lipids

      • Triglycerides

        • Glycerol + 3 fatty acids

      • Phospholipids

        • Phosphate + glycerol + 2 fatty acids

      • Steroids

        • 4 fused hydrocarbon rings

  • Proteins

    • Contain carbon, hydrogen, oxygen, and nitrogen

    • Large organic compounds made of amino acids

    • Arranged into one or more linear chains

    • Structural or part of the plasma membrane

  • Nucleic Acids

    • Contain carbon, hydrogen, oxygen, nitrogen, and phosphorus

    • Chains of subunits called nucleotides

      • Base, sugar, and phosphate groups covalently bonded together

B1.1.2 Carbon production of macromolecules by condensation reactions that link monomers to form a polymer

  • Condensation makes bonds

    • water releasing

    • Anabolic reactions are those which build molecules

  • Hydrolysis breaks bonds

    • water splitting

    • Catabolic reactions are those which break down molecules

  • Monosaccharides (sugars) are the monomers of polysaccharides (carbs)

B1.1.3 Digestion of polymers into monomers by hydrolysis reactions

B1.1.4 Form and functions of monosaccharides

  • Monosaccharide 1: Glucose

    • Forms a hexagonal ring

    • Form of sugar that fuels respiration

    • Forms base unit for many polymers

    • Highly soluble in water

  • Monosaccharide 2: Ribose

    • Forms a pentagonal ring

    • Backbone of RNA

    • Deoxyribose differs as shown in the diagram and forms backbone of DNA

B1.1.5 polysaccharides as energy storage compounds

  • Polysaccharides

    • Polymers with more than two molecules

    • Often long and may be branched

  • Cellulose

    • The tensile strength of cellulose (the basis of cell walls) prevents plant cells from bursting, even under very high (water) pressure.

  • Starch (amylopectin)

    • Contains hundreds of glucose molecules

  • Glycogen

    • Found in animals and some fungi

    • Stored in the liver and some muscles in humans

    • Short-term energy storage

    • Made up of repeating glucose subunits

    • Excess glucose is converted into glycogen

    • Doesn’t affect the osmotic balance of cells

      • The way the water moves in a cell

  • Energy storage by lipids and carbohydrates

    • Why is glycogen needed at all?

      • Fats in adipose tissue cannot be mobilized as rapidly

      • Easily transported by the blood

        • Adipose: fat storage tissue in mammals

B1.1.6 Structure of cellulose related to its function as a structural polysaccharide in plants

  • Polysaccharide 1: Cellulose

    • Hydrogen bonds link the molecules together

    • Straight chain - not curved

    • Basis of cell walls

      • Very strong to keep plant cells from bursting even under very high water pressure

  • Polysaccharide 2: Starch

    • Amylose and amylopectin

      • Forms of starch made from repeating glucose units

    • Curved molecule

    • Only made by plant cells

    • Hydrophilic but too large to be soluble in water

    • Easy to add or remove extra glucose molecules 

      • Short term energy storage

  • Polysaccharide 3: Glycogen

    • Polymer made from repeating glucose subunits

    • Made by animals and some fungi

    • Stored in the liver and some muscles in humans

    • Good for energy storage

B1.1.7 Role of glycoproteins in cell–cell recognition

  • Glycoprotein

    • Enable cells to recognize another cell as familiar or foreign 

      • Cell-cell recognition (labeling)

      • Naming of the cell

        • Liver cells, skin cells, etc. 

      • Carbohydrate tails

    • Ex. Blood antigens

      • A, B, O, AB

B.1.1.8 Hydrophobic properties of water

  • º1Substances that are insoluble in water

  • Molecules are hydrophobic if they DON’T have negative or positive charges and are NONPOLAR

  • All lipids are hydrophobic, including fats and oils

  • Hydrophobic molecules dissolve in other solvents such as propanone (acetone)

B1.1.9 Formation of triglycerides and phospholipids by condensation reaction

  • Triglycerides formation

    • Condensation reaction between glycerol and fatty acids

    • Glycerol + 3 fatty acids = triglyceride

  • Example of condensation

    • smaller molecules linking up to create a larger molecule

  • Lipids are glycerol combined with 1, 2, or 3 fatty acids

    • Triglycerides are lipids

B.1.1.10 Difference between saturated, monounsaturated and polyunsaturated fatty acids

  • Cis-isomers

    • Natural

    • Tend to be curved because the hydrogen atoms are on the same side of the two carbon atoms

    • loosely packed

    • Liquid at room temperature

  • Trans-isomers

    • Artificial

    • Tightly packed

    • Solid at room temp

    • Increased chance of heart disease

    • Straight

B.1.1.11 Triglycerides in adipose tissues for energy storage and thermal insulation

  • Functions of lipids

    • Structure: Phospholipids are a main component of cell membranes

    • Hormonal signaling: Chemical messengers, steroids are involved in hormonal signaling (estrogen, testosterone, etc)

    • Insulation: Fats in animals can serve as heat insulators while sphingolipids in the myelin sheath can serve as electrical insulators. Fat keeps them warm

    • Protection: Triglycerides form a tissue layer around many key internal organs and provide protection against physical injury. Cushioning. (The heart)

    • Storage of energy: Triglycerides can be used as a long-term energy storage source

B.1.1.12 Formation of phospholipid bilayers as a consequence of the hydrophobic and hydrophilic region

  • Cell membrane is made up of phospholipids

  • Phospholipids are amphipathic

    • Have a hydrophilic head

    • Have a hydrophobic tail 

    • Phospholipid bilayer is very stable, but also flexible

    • They form double layers (cell membrane)

Phospholipid

B.1.1.13 Ability of non-polar steroids to pass through the phospholipid bilayer

  • Hormones are chemical messengers that produce a response in the target cells of an organism

  • Lipid based hormones are called steroids

  • Steroids are nonpolar so they can pass freely through the cell membrane

  • Ex: Testosterone

C: Proteins

A

A.1.2.1 DNA as the genetic material of all living organisms

  • Universal code

    • Every living thing uses DNA as the way of storing information

  • Some viruses use RNA or DNA but never both as their genetic material but they are not considered to be living

    • Acellular

    • Can’t do any of the life stuff without invading a cell

A.1.2.2 Components of a nucleotide

A.1.2.3 Sugar- phosphate bonding and the sugar phosphate “backbone” of DNA and RNA

  • DNA nucleotides are linked together by covalent bonds formed in condensation reactions into a single strand

A.1.2.4 Bases in each nucleic acid that forms the basis of a code

  • State the names of the four bases in DNA

  • Purines

    • Adenine

      • Always bonds with the T

    • Guanine

  • Pyrimidines

    • Thymine

    • Cytosine

      • Always bonds with G

  • Purines need to go with pyrimidines because they need to balance out the lengths

A.1.2.5 RNA as a polymer formed by condensation of nucleotide monomers

  • Has Uracil instead of Thymine

  • Function of RNA

    • Protein synthesis

      • Making a gene into a trait

    • It takes a copy of DNA out of the nucleus because DNA is too big to leave the nuclear pores and functions as a working copy of DNA

  • Working copy of the DNA

    • Made through transcription

  • RNA can go to a ribosome and create a protein

A.1.2.6 DNA as a double helix made of two antiparallel strands of nucleotides with two strands linked by hydrogen bonding between complementary base pairs

  • Secondary structure of DNA is the double helix

    • Two strands of DNA

  • How is the double helix structure maintained?

    • Hydrogen bonds hold sections together

    • Hydrogen bonds hold complementary base pairs together

    • Complementary base pairing ensures that mistakes are not made when copying or transcribing DNA

    • Covalent bonds

      • Sugar to phosphate

      • Sugar to nitrogenous base

    • Hydrogen bonds   

      • Base pair to base pair

      • Each line to each line

      • Sections of the backbone to each other that makes it twirly

      • Nucleotides to nucleotides

  • DNA double helix is formed using complementary base pairing and hydrogen bonds

  • C and G have 3 hydrogen bonds

  • A and T have 2 hydrogen bonds

  • Sequence of bases on DNA make up genes

    • Genes are heritable factors that control specific characteristics

    • Nuclear DNA contains single-copy genes and regions of highly repetitive sequences

      • Coding DNA and non-coding DNA

A.1.2.7 Differences between DNA and RNA

A.1.2.9 Diversity of possible DNA base sequences and the limitless capacity of DNA for storing information

  • The human genome project which has decoded the case sequence for the whole 6 feet of the human genome requires a data warehouse to store the information electronically

  • Entirety of all the genes inside a living organism

  • Divided up the mapping of the human information code between many different universities

  • About 500,000 dvds worth of data in 1 gram of DNA

A.1.2.10 Conservation of the genetic code across all life forms as evidence of universal common ancestry

  • Strongest evidence in the theory of evolution is in the sharing of DNA across all life forms

  • All life shares descent from a Last Universal Common Ancestor (LUCA)

    • First origin of life

    • Evidence that life has a common origin

B.1.2.1 Generalized structure of an amino acid

  • The amino group is one of the reasons why nitrogen is an important element in living things

  • The carboxylic acid group contains an oxygen double-bonded to the carbon and a hydroxyl group that can be lost to form new bonds

  • In proteins there are 20 amino acids that build up proteins in different ways

B.1.2.2 Condensation reactions forming dipeptides and longer chains of amino acids

Condensation reaction between 2 amino acids

B.1.2.3. Dietary requirements for amino acids

  • Obtained from nutrition

    • Basic things to make amino acids come from food

  • Synthesized by the body

  • Essential amino acids

    • The ones you can’t make

    • Need to get them directly from food

    • Valine

  • Non essential amino acids

    • Once you break down food, your body can make them 

    • Serine

B.1.2.4 Infinite variety of peptide chains

  • Polypeptides are chains of amino acids joined by peptide bonds

  • Proteins are versatile

  • There are 20 different amino acids

    • Can be combined in any order

    • Each amino acid has unique properties

      • Some a polar (hydrophilic)

      • Some are non-polar (Hydrophobic)

      • Some are positively or negatively charged

      • Some contain sulphur

    • Properties determine how a polypeptide folds up into a protein

  • Why are there infinite variety of polypeptides?

    • Because there are 20 amino acids

      • many possibilities in how they are built

      • Many different lengths we can make proteins 

  • If a polypeptide has 7 amino acids there can be 20^7 possible polypeptides generate

  • Proteins have different levels of structure

  • Once a chain is made, it can link with other polypeptide chains

  • Proteins can fold and that gives them versatility

  • Fibrous proteins tend to be structures in nature which means its building material

    • Keratin (hair), collagen

    • Insoluble

      • Doesn’t want to build things that would melt in water

  • Globular proteins are functional in nature

    • Transport, have functions

    • Haemoglobin, insulin

    • Soluble

  • Functions of proteins

    • Digestion

    • Keep us healthy

      • immunoglobulins

    • Muscles

    • Involved in DNA stuff

    • Support to the body

    • Coordination for bodily function

    • Move essential molecules around the body

  • Immunoglobulins

    • Globular protein

    • Keep us healthy    

      • Fight off viruses and bacteria

    • Antibodies

  • Spider silk

    • Structural protein

    • Very strong

B.1.2.5 Effect of pH and temperature on protein structure

  • Denaturation

    • What happens to a protein when subjected to extreme conditions of heat or pH

    • If you burn a protein or drop it in acid it will denature

    • Breaks down

    • Loses shape

    • Loses function

    • Sometimes in high salt or heavy metals can denature proteins

  • Genes are codes for making polypeptides

  • DNA is stored in the nucleus

  • Polypeptide made in the cytoplasm

  • m.