IB Bio - Biomolecules

Water

  • Made up of two hydrogen atoms covalently bonded to an oxygen atom (H2O).

  • Polarity is the slight difference in charge

    • Oxygen is slightly negative (strong connection) and hydrogen is slightly positive (weak connection).

    • Allows it to form these same weak attractions with other polar molecules of charged ions

  • Hydrogen bonds are formed by the polar covalent bonds within water molecules.

    • Stronger than standard polar bonding due to high electronegativity.

  • Water is cohesive, meaning it can stick to other water molecules through hydrogen bonds.

    • Makes surface tension (resisting low levels of external force)

    • Makes water dense for smaller organisms

      • Water striders move along water utilizing this surface tension (distribute their weight on through their hairs that increase buoyancy)

  • Water is adhesive, meaning it can stick to other polar or charged molecules.

    • allows capillary action (where water moves up through the pores of the stem)

      • smaller diameter = more action

      • necessary to allow water to be transported into the leaves

      • evaporation and osmosis absorption creates a pressure gradient

  • Solvation is when solvent molecules interact with other solvent molecules.

    • a solute is a substance dissolved by a solvent to form a solution

    • insoluble solutes will not form solutions (water and oil)

    • water is the universal solvent due to dissolving range

      • dissolve anything charged or polar

      • the polar regions of water can form hydration shells when bonding with other hydration shells

  • Water is a metabolic medium

    • can promote enzyme activity

    • substances involved can be hydrophilic or hydrophobic

  • Water is a transport medium

    • in animals, blood plasma transports the dissolved solutes, such as amino acids, simple sugars, and wastes

    • in plants, ions are transported via xylem vessels

  • Substances not water-soluble cannot be transported through an aqueous environment.

    • in animals, lipoprotein shells surround the substances and transport via blood.

    • in plants, conjunction to amino acids through the phloem

  • Water is the medium of life (sustains life processes) through the following physical properties:

    • buoyancy: upward forced on an object based on density (water is more dense than air, so objects can float in water)

      • heavier = less buoyant

    • viscosity: the fluidity of water (more viscous = thicker, more resistant to flow)

      • water dissolving solutes can increase the viscosity of solutions

    • thermal conductivity: ability to move heat across a temp. gradient

      • close tightly packed particles = more readily movable

    • specific heat capacity: energy required to raise temp of 1g of substance 1 degree Celsius

      • water has a high heat capacity because of the strong hydrogen bonds

      • makes it effective coolant for sweat

Organic Molecules

  • organic compound means it contains carbons

  • carbon is the basis as it forms large, complex molecules through covalent bonding

    • 4 covalent bonds = stability

    • wide variety of structures

  • four main types of carbon compounds:

    • carbohydrates: CHO (ratio usually CH2O)

      • closed-ring structure

      • fast energy source

      • glycoproteins and cellulose provide cell-cell recognition and structure

      • monomeric subunits are used as components, such as in DNA or ATP

    • lipids: non-polar hydrophobic molecules usually unbranched chains (fatty acids) or ringed structures (steroids)

      • main structural component of cell membranes and sometimes long-term energy storage

    • nucleic acids: made up of nucleotides containing the sugar (ribose or deoxyribose), the phosphate group, and the nitrogenous base

      • genetic material for the features of an organism

      • main nucleic acids are DNA and RNA

    • proteins: one of more amino acid chains

      • perform enzyme activities, provide structure, signal, and transport

  • monomers are recurring subunits that form polymers

    • carbs = monosaccharide

    • nucleic acids = nucleotides

    • protein = amino acids

    • lipids = no monomers

  • polymerisation is the formation of polymers through a condensation reactions

    • hydroxyl group forms with one of the hydrogens on another monomers

    • when they covalently bond, a water molecule is produced as the by-product

  • polymers are macromolecules composed of monomers

    • carbs = polysaccharides via glycosidic linkages

    • nucleic acids = DNA or RNA

    • proteins = peptide chains

    • lipids = ester linkages for triglycerides and phospholipids

  • digestion is polymers being broken down through hydrolysis

    • water molecule split to provide the missing H and OH

Nucleic Acid

  • the genetic material of the cells made of nucleotides

    • nitrogenous base attached to 1’ carbon

    • phosphate group attached to 5’ carbon

      • the ‘ indicates which of the carbons it is

  • nucleotides also link through condensation

    • can form long polynucleotide strands

    • the two strands on the DNA run opposite

      • one runs 5’ to 3’ and the other runs 3’ to 5’

  • nucleic acids combine the nitrogenous bases in sequences

    • AT and CG for DNA

    • AU and CG for RNA

    • the order forms the genetic instructions

    • this capacity to undergo pairing is critical for their function as genetic code

      • allows replication and allows the instructions to expressed in a new cell

  • DNA is more stable (master set of instructions) and RNA is versatile (transfers the info for coding)

    • DNA = deoxyribose, thymine, double strand

    • RNA = ribose, uracil, single strand

    • deoxyribose has one less oxygen at the OH located in the 2’ position

  • RNA has 3 main types:

    • messenger: transcript of the DNA instructions to encode

    • transfer: carries the amino acids to the transcript

    • ribosomal: provides the activity of combining with the instructions

      • messenger is linear, but transfer and ribosomal can be twisting

  • DNA is composed of two hydrogen bonded strands

    • two strands run antiparallel (opposite directions) - provides stablitiy

    • ladder structure

    • double helix shape (10-15 bases per twist)

      • helps maintain fidelity

    • superior chemical stability

  • DNA is the genetic code in all living organisms

    • viruses use RNA for genetic material (no metabolism and non-living)

  • triplets of bases are codons

    • have a specific amino acid

Carbohydrate

  • made of carbon, hydrogen, and oxygen (CHO)

  • ring structures with a hydroxyl group linking to a carbonyl group (double-bonded oxygen)

  • most monosaccharides have 5 (pentose, such as ribose) or 6 carbons (hexose, such as glucose)

    • name describes carbon number

  • alpha-D glucose has downward 1’ OH group and beta-D glucose has upward facing 1’ OH group

  • primary function is to provide energy

    • produce large quantities of ATP

  • glucose is the most commonly used due to:

    • solubility: polarity

    • stability: cyclic structure is more energetically favorable

    • transport: transport through aqueous solutions

    • potential energy: high energy electrons

    • ATP yield

  • monosaccharides link through condensation, making a disaccharide

    • many linkages like this form polysaccharides

  • main types are:

    • cellulose: beta-glucose of 1’ - 4’ carbon linkages

    • starch: alpha-glucose

      • amylose: 1’ - 4’ carbon linkages

      • amylopectin: branched, includes 1’ - 4’ and 1’ - 6’ carbon linkages

    • glycogen: more branched than amylopectin

  • glycogen is used by animals for energy and starch is used by plants

    • branching = more compact structure (prone to insolubility)

  • beta-glucose forms cellular structures

    • cellulose has alternating arrangements of glucose, making it more integral and stable

  • glycoproteins can perform cell-cell recognition

    • red blood cells do this so our body doesn’t mix blood types

    • identity cells as “self”