IB Bio Test 1 Study Guide

Water As Medium Of Life

Water As Medium Of Life

Charles Darwin made first statement saying that life came from water

Water Bonds

Covalent bonds between O & H atom, electronegativity means O has a slight negative charge and H is positive

Water molecules form hydrogen bonds (H can hydrogen bond to O, N or F)

Hydrogen bonds by themselves are weak, so there are multiple per unit volume of water

Cohesion with Xylem

Water molecules sticking together

Xylem: Cohesion allows water to be transported through tension in plants (attractions between soil and water occur as water is lost by evaporation and interactions between water molecules and cell walls

Cohesion with Water Surfaces

Surface tension: surface of pond or body of water acts like an elastic membrane that shrinks to the smallest possible area. Because of this, it’s possible to float objects on the surface because cohesion of water molecules is greater than the attractions between water and the floating object. Water striders are a good example.

Adhesion

Water sticks to the surface of a solid when hydrogen bonds between water and solids composed of polar molecules

This can be seen in capillary action, when water is drawn through narrow tubes. It occurs in plants when water adheres to the cellulose molecules, helping to keep cell walls moist.

Adhesion in Porous Solids

Porous solids such as paper have large surface areas attractive to water, allowing for extra suction forces

If soil is porous, water gets drawn by capillary action

Hydrophilic

Polar molecules (glucose), particles with + or - (Na or Cl ions). This describes substances that are chemically attracted to water, and also adheresHy

Hydrophobic

Non-polar, no + or - charges, all lipids. Describes substances that are not chemically attracted to water, but can dissolve in other solvents

Cytoplasm

Complex mixture of dissolved substances. Because it’s aqueous it allows itself to interact with other molecules.

Dissolved enzymes catalyze specific chemical reactions (known as metabolism)Cyt

Cytoplasm in Plants

Mineral ions transported in xylem sap

Sucrose & other particles of photosynthesis transported in phloem sap

Cytoplasm in Humans

In our cytoplasm we have:

Blood: NaCl dissolves and carries in blood plasma

Amino Acids: They get dissolved in blood plasma

Glucose: Gets carried in plasma

Oxygen: Dissolves sparingly & water gets saturated at low concentrations

Red blood cells have haemoglobin that include bonding sites for oxygen

Fat molecules are insoluble, but phospholipids coat the fat molecules to prevent large droplets

Air Vs Water

Air is less dense than water, so organisms need to generate lift

Pure water has a low viscosity, but sea water is higher than air

Water has a relatively high thermal conductivity. Air is about 5% of water

Heat capacity of water is high

Carbohydrates vs Lipids

Carbohydrates are in starch or glycogen form and are for short-term energy storage

Lipids are fats and oils and are for long-term energy storage

Both use oxidation in cell respiration to release energy

Importance of Carbon Atoms

Carbon atoms can form covalent bonds with other atoms (up to 4 with C, H, O, N, or P)

They can bond with 4 atoms of one element (CH4)

They can bond to more than one element (C-O-H)

They can make extremely long chains, such as fatty acids, which are branched by an oxygen. These chains can spread as far as a tetrahedral shape, but can only be as straight as a zig-zag

Carbons can form rings based on their bond angles

Macromolecules

Molecules with large number of atoms and a relative mass of 10,000 amu

Main classes are: polysaccharides, polypeptides and nucleic acids. They are linked by subunits (monomers)

Energy is required to make these macromolecules (usually ATP)

Condensation Reaction

Happens when a monomer links to a polymer

2 molecules link together and release a smaller molecule simultaneously (H2O). The hydroxyl (-OH) removes itself and links to another hydrogen

Polysaccharides

Made up of a chain of monosaccharides. Glucose is the mono used to make glycogen, starch and cellulose

Glucose molecules link up to glycosidic bonds (C-O-C), which are formed during condensation reactions

Monosaccharide Types

Glucose, Fructose, Galactose

Disaccharide Types

Sucrose, Maltose, Lactose

Deconstructing Polymers

Polymers are deconstructed so the monomers can be reused to make new polymers or as energy

This reaction is called hydrolysis. Polysaccharides deconstruct to monosaccharides, polypeptides deconstruct into amino acids, and nucleic acids deconstruct into nucleotides

Monosaccharide Properties

Between 3-7 carbon atoms, with each ring usually having one oxygen in them

Glucose properties

Glucose is soluble and small, allowing it to be easily transported. It circulates in blood and is dissolved in plasma

Glucose is chemically stable, which is helpful for food storage. Glucose can convert to starch or glycogen, but by itself it can release energy when oxidized

Starch

Found in plants, composed of large amounts of alpha-glucose molecules.

Amylose is a type of starch that’s unbranched linked by 1→4 glycosidic bonds. Usually chain is helical'

Amylopectin has a similar structure but there are some 1→6 bonds making it branched. They can contain up to a 100,000 glucose subunits

In both, hydrolysis releases a glucose molecule by breaking the 1→4 bond

Glycogen

Found in animals, also composed of large amounts of alpha-glucose molecules. They usually have tens of thousands of glucose subunits

Similar to amylopectin’s structure, with glycosidic bonds between 1→4 and branched by 1→6

Cellulose

Composed of beta-glucose. All links are 1→4 so the entire molecule is unbranched

C₁’s OH is angled up while C₄’s OH is angled down, meaning the subunits must be inverted to join

Chains allow the cellulose to be in parallel formation. These bundles are called microfibrils and are the basis of plant cell walls. They have high tensile strength

Glycoproteins

Composed of polypeptides with carbohydrate attached (usually an oligosaccharide, which is a short chain of monosaccharides linked by glycosidic bonds)

Component of plasma membranes in animal cells and position with the carbohydrate facing outwards. This allows cells to recognize each other via receptors, allowing them to organize tissues or identify and kill foreign or infected cells

Red Blood Cells

Red blood cells have glycoproteins, with the oligosaccharides either O, A, or B. One or two can be present, but not all three

If blood glycoprotein A is injected into someone who doesn’t produce it, it will be rejected (same as B). However, O doesn’t have rejection problems because it has the same structure minus one monosaccharide

Lipids

In living organisms that dissolve in non-polar solvents, but they are sparingly soluble in aqueous solvents.

Oils (melt under 20C), Fats (melt between 20-37C), Waxes (melt above 37C), Steroids

Triglyceride

3 fatty acids linked to one glycerol via condensation reaction (3 H2O molecules are formed)

The bond between the acid and glycerol is called an ester bond, and forms between the acid and the hydroxyl group.

Triglyceride Properties

Chemically very stable, allows to keep energy

Immiscible in water, meaning it naturally forms harmless droplets in the cytoplasm

Release 2x the energy per gram in cell respiration compared to carbohydrates, but they take longer to build up

Can be used as a thermal insulator (located in adipose tissue)

Liquid at room temperature, allowing it to act as a shock absorber

Phospholipids

2 fatty acids plus a phosphate group linked to a glycerol

Phosphate group is hydrophilic, hydrocarbons are hydrophobic, giving it a unique property: amphipathic

When phospholipids mix with H2O, phosphate heads attract to water but hydrocarbon tails attract to each other. These form phospholipid bilayers, which are the basis of cell membranes

Fatty Acids

Unbranched chain of C atoms, with H atoms covalently bonded

Acid part is carboxyl (-COOH), Methyl is on other end (CH3)

Fatty acids with all single bonds are saturated (usually fats from animal sources)

Fatty acids with one double bond is monounsaturated, & multiple double is polyunsaturated. Unsaturated fats are oils, and are mainly from (but not always) plants)

Types of Unsaturated Fatty Acids

H atoms on double bonds all on same side mean that the fatty acid is cis-unsaturated (these are found in nature)

Alternating sides means it’s trans-unsaturated (these are only made through food processing)

Steroids

Group of lipids similar to sterol (4 fused rings of carbon)

3 cyclohexane rings, 1 cyclopentane ring (17 total carbon atoms)

Hundreds of different types of steroids, but all are made from hydrocarbon and are hydrophobic, allowing it to pass through phospholipid bilayers and enter or leave cells

Cholesterol is the precursor to all other steroids. It’s found in animal cell membranes, keeping them fluid and flexible.

Waxes

Hydrophobic and are used to create waterproof structures and coatings

Amino Acids

Building blocks of proteins, amphiprotic

Central carbon is called alpha-carbon, and has covalent bonds to 4 other subunits

Covalently bonded to N atom of amine group (H2N) (acid)

Covalently bonded to C atom of carboxyl group (COOH) (base)

Covalently bonded to H atom

Covalently bonded to R-Group (20 different kinds)

Multiple Amino Acids

2 amino acids join via condensation reaction to form a dipeptide. Oligopeptides are less than 20 amino acids together, while polypeptides are 20 or more

Once the condensation reaction finishes, the amino acids join via peptide bonds (C-N). This is catalyzed in cells by ribosomes

Free amino acid uses amine group to link to carboxyl of growing chain. All bonds are the same

Multiple Amino Acids (cont.)

20 different amino acids are used by ribosomes to make polypeptides

Plants make all of these via photosynthesis, but animals need to obtain some of these through food

Essential vs Non-essential Amino Acids

Non-essential amino acids means that they can be synthesized by an animal through metabolic pathways

Essential amino acids means that they cannot be synthesized, therefore they must be ingested into diet

Animal-based foods (milk, fish, meat, eggs) provide a balance of amino acids

Plant-based foods may lack a balance, but traditional plant-based diets provide sufficient amounts

Linking Amino Acids

Ribosomes link amino acids one at a time until a polypeptide is formed.

Even though they can link as many as they want, genetic code gives information to the ribosomes as to what they need to create

For a polypeptide of n amino acids, there are 20^n possible sequences

The polypeptide sequences are called your proteome

Bonds & Interactions

When bonds and interactions break, there is a change in the structure, called denaturation

Denaturation is permanent, and sometimes soluble proteins become insoluble & form precipitates because hydrophobic R-groups are exposed to H2O

Heat can cause denaturation because vibrations can break intermolecular bonds. Each protein has a different heat tolerance

Extreme pH can cause denaturation because the positive or negative charges can change the R-groups

Genetic Material

Store of information. If copied it can pass cell to cell or parent to offspring

Usually called hereditary info because it’s inherited

DNA Properties

All living organisms use DNA to store hereditary info

2 polynucleotide strands, Nucleotides (pentose, phosphate, base), Antiparallel orientation, Hydrogen bond between bases, Covalent bond between other subunits (called phosphodiester bonds)

All nucleotides link phosphate to pentose, forming a strong sugar-phosphate backbone in DNA & RNA molecules that conserve the sequence of bases

If the strands were not antiparallel, no hydrogen bonds would form

DNA & RNA Bases

Adenine, Thymine, Guanine & Cytosine

Adenine, Uracil, Guanine, & Cytosine

These are called complementary base pairings (Chargaff’s Rule)RNA

RNA Properties

Single unbranched polymer of nucleotides. All nucleotides are linked via condensation reaction (hydroxyl group of phosphate and on pentose sugar)

DNA Replication

Two strands of the double helix separate, with the original strands serving as a template to build the new strand. The new strands form by adding nucleotides one by one and linking them together

Gene

Genetic info consisting of sections of DNA to code for proteins

Gene Expression

When info on a gene has an effect on the cellT

Transcription

Copies base sequence out of DNA. One of 2 strands used as a template. The adenine pairs with the uracil

RNA made by transcription is either used for regulatory or structural role in a cell, or it could be used for protein synthesis

Decoding DNA

Info in DNA & RNA is decoded during protein synthesis

Groups of 3 bases are called codons are have meaning

Most codons specify a particular amino acid, but one codon signals to start protein synthesis while 3 signals to stop

Purines & Pyrimidines

Purines are double-ringed nitrogenous bases (Adenine & Guanine)

Pyrimidines are single-ringed nitrogenous bases (Thymine, Cytosine, Uracil)