IB Bio Test #2

Water

Water Structure

Water is made up of two hydrogen atoms covalently bonded to an oxygen atom

  • While there are atoms shared in the covalent bond, they are not shared equally, resulting in polarity

Polarity- the slight difference in charge that occurs at the different poles of the water molecule

  • Oxygen has higher electronegativity and attracts electrons more strongly which results in a slightly negative charge

  • Hydrogen has weaker attractions towards the electrons, resulting in a slightly positive charge

The polarity of water allows it to form weak associations with other polar molecules or charged ions

  • Slightly negative poles will attract slightly positive poles of other molecules and vice versa

Hydrogen Bonds

Hydrogen bonds- intermolecular associations formed as a consequence of the polar covalent bonds within water molecules

  • A slightly positive hydrogen atom is attracted to a slightly negative fluorine, oxygen, or nitrogen atom of another molecule

  • Stronger than standard polar associations due to the high electronegativity of F, O, and N molecules

Hydrogen bonding is responsible for water’s unique thermal, cohesive, and solvent properties

Cohesive Properties

Cohesive- water molecules can stick to other water molecules via hydrogen bonding

  • Allows liquid to resist low levels of external force

  • High surface tension of water allows for small organisms to walk upon it

Adhesive- water molecules stick to other polar or charged molecules via the formation of polar association

  • Allows water to flow oppositional to gravitational forces

  • Strength of capillary action is determined by diameter of the pore it moves through

    • Smaller= more capillary action

Capillary action is necessary to allow water to be transported up plant stems via transpiration stream

  • Evaporation and absorption of water creates a pressure gradient in the stem

  • Water moves along the gradient through the use of capillary action and cohesion

Solvent Properties

Water is referred to as the universal solvent as it can dissolve a large variety of substances

  • Can dissolve any polar molecules or charged ions

  • Polar regions of a water molecule associate with molecular surfaces that have an opposing charge, forming hydrogen shells around the molecule

Since it can dissolve many substances, water plays an important role in metabolic reactions

  • Solutes dissolved in aqueous solutions are more likely to collide with enzymes and undergo necessary chemical reactions

  • Water promotes enzyme activity by absorbing heat from exothermic reactions and maintaining acid-base neutrality

Substances that dissolve in water are hydrophilic, like polar molecules or charged ions

Substances that do not readily dissolve in water are hydrophobic, like large, non-polar molecules

In animals, blood plasma transports dissolved solutes, such as amino acids and simple sugars

In vascular plants, mineral ions are transported via xylem vessels and dissolved nutrients are transported via phloem

Non-soluble substances require assistance when being transported through aqueous solutions

  • Lipids are packaged with proteins to form water-soluble lipoproteins that can be transported through the bloodstream

Physical Properties

Buoyancy- upward force applied to an object in a medium, as determined by the density of the medium

  • Water is much denser than air so it carries a greater upward force, which allows objects to float in it

Viscosity- a measure of a fluid’s tendency to flow (more viscous=more resistant)

  • Water is more viscous than air as it can form more hydrogen bonds which increases the friction of flowing molecules

  • Solutes dissolved by water can increase viscosity of a solution

Thermal conductivity- a measure of a medium’s ability to move heat across a temperature gradient

  • Water absorbs heat more readily than air because its molecules are more tightly packed together

Specific heat capacity- the amount of energy required to raise 1g of a substance by 1 degree celsius

  • Water has a higher specific heat than air as its hydrogen bonds require additional energy to break

    • Makes water an effective coolant in sweat

These properties affect animals in aquatic environments

  • The black-throated loon has less dense bone mass allowing it to float on water (buoyancy). Their legs are located near the rear to help them propel through water (viscosity). Their feathers form interlocking structures that function as barriers to water, preventing heat loss (high thermal conductivity)

  • The ringed seal has denser bones allowing it to stay submerged after diving (buoyancy). They have streamlined bodies to allow them the better propel through the water (viscosity). They have no great cooling mechanisms because water temperatures are usually stable (high specific heat capacity)

Organic Compounds

Organic compound- A compound that contains carbon and is found in living things

  • Exceptions are carbides, carbonates, oxides of carbon, and cyanides

Carbon forms the basis of all organic compounds due to its ability to form large complex molecules via covalent bonding

  • Carbon atoms form four covalent bonds, with bonds between 2 carbon atoms being very stable

  • Allows carbon to form a variety of structures including compounds that are branched or unbranched, chains or single, and multiple rings

Carbohydrates are molecules consisting of carbon, hydrogen, and oxygen

  • The monomeric subunit will commonly adopt a closed ring structure that can form different stereoisomers

  • Commonly used as an energy source, cell recognition, and structure

Lipids are non-polar, hydrophobic molecules that consist of unbranched chains (fatty acids) or ringed structures (steroids)

  • Serve as the main structural component of cell membranes and are utilized in energy storage, and signaling molecules

Nucleic acids consist of a pentose sugar, phosphate group, and nitrogenous base

  • Function as the genetic material of a cell, determining what features are inherited

  • Two types: DNA and RNA

Proteins are composed of one or more chains of amino acid residues and comprise over 50% of the dry weight of the cell

  • Perform a vast array of functions within the cell including structure, catalysts, cell-signaling, and transport

Monomers

Monomers are recurring subunits which are joined together covalently to form polymers

  • Subunit of carbohydrate is a monosaccharide

  • Subunit of nucleic acid is a nucleotide

  • Subunit of protein is amino acid

Lipids do not contain monomers but have distinct subunits called fatty acids

Polymers are can be formed via condensation reactions

  • Hydroxyl group (-OH) of one monomer is combined with a hydrogen (-H) of another monomer, become covalently bonded with a byproduct of a water molecule

Polymers

Carbohydrate: Polysaccharides are formed from monosaccharides via glycosidic linkages

Nucleic Acid: Nucleotides are connected by phosphodiester bonds to form polynucleotide chains

Protein: Amino acids are linked by peptide bonds to form polypeptide chain

Lipids: Not monomers, but fatty acids are connected via ester linkages to form triglycerides/phospholipids

Polymers can be broken down into their monomeric subunits via hydrolysis reactions

  • A water molecule is split into the hydroxyl group and hydrogen required to break the covalent bond between two monomers

Nucleic Acids

Nucleic acids are the genetic material of the cell.

Each nucleic acid is made up of recurring monomeric units called nucleotides.

  • Comprised of a pentose sugar, a phosphate group, and a nitrogenous base

Strand Formation

Many nucleotide monomers are linked together via condensation reactions, where water is produced as a by product.

  • A phosphate group of one monomer is attached to the sugar of another

  • The resulting bond is called a phosphodiester bond

The phosphate and sugar form the backbone of RNA/DNA strands while the nitrogenous bases extend out.

Base Sequences

Nucleic acids are made up of four nitrogenous bases:

  • Guanine and adenine are double-ringed purine bases

  • Cytosine and thymine/uracil are single-ringed pyrimidine bases

These bases always link up (purine:pyrimidine) via hydrogen bonding

  • Guanine pairs up with cytosine (2 bonds)

  • Adenine pairs up with thymine or uracil (3 bonds)

Undergoing base pairing allows for genetic information to be replicated and genetic instructions to be expressed within a cell

DNA vs. RNA

Two types of nucleic acids in a cell: DNA and RNA

  • DNA is more stable and functions as a master template for all genetic instructions

  • RNA is more versatile and functions to transfer genetic information for coding

DNA has a deoxyribose sugar, uses thymine, and is double stranded while RNA has a ribose sugar, uses uracil, and is single stranded.

  • Ribose is a pentose sugar, when an oxygen at the 2’-position is taken away, it becomes deoxyribose

RNA Structure

RNA is used to express genetic instructions within a cell (used in protein synthesis)

  • Produced from a DNA template (gene) via condensation of nucleotide monomers

There are three main types of DNA:

  1. Messenger RNA (mRNA)- a transcript copy of DNA instructions (encodes the protein sequence)

  2. Transfer RNA (tRNA)- carries protein subunits (amino acids) to mRNA transcript

  3. Ribosomal RNA (rRNA)- provides catalytic activity for combining amino acids according to mRNA sequence

mRNA is linear while complementary base pairing can allow tRNA and rRNA to twist and form loops

DNA Structure

DNA is used to pass hereditary information (genes) between generations of cells

Composed of two strands held together by hydrogen bonding between base pairs

  •    Maintains fidelity of base sequence during replication

In order for the bases to pair, the strands must run antiparallel (in opposite directions)

  • Creates a ladder structure, with backbones forming struts and base pairs forming rungs

  • Once the ladder structure gets long enough, it will twist itself into a double-helix shape

    • The most stable energy configuration possible (10-15 bases per twist)

Genetic Information

Nucleic acids are used to store genetic information that acts as a blueprint for the cell

RNA way the first storage to evolve but DNA is the principle data storage molecule now due to its superior chemical stability from a double helix structure.

DNA is the genetic material of all LIVING things

  • Some viruses use RNA, but they cannot undergo independent metabolism and are therefore not considered living

Genetic information in DNA is encoded in the base sequence of the nucleotide chain

  • There are nearly infinite possible base sequences leading to a great deal of genetic diversity

DNA stores the instructions for production of proteins in triplets of bases called codons

  • Codons code for a specific amino acid, the order of codons in a gene sequence determines the order of amino acids in a polypeptide chain

Genetic code: The totality of all codon combinations and the amino acids represented by each

  • Genetic code is universal; all living organisms use same code which is considered evidence for evolution from a universal common ancestor

Carbohydrate

Carbohydrates are made of carbon, hydrogen, and oxygen and composed of recurring monomers called monosaccharides

Monosaccharides

Monosaccharides typically form ring structures due to a chemical reaction between functional groups at opposite ends of a molecule

  • A hydroxyl group (-OH) links to a carbonyl group (=O) to form a cyclical structure connected by an oxygen atom

Most monosaccharides have either 5 carbons (pentose sugars) or 6 carbons (hexose sugars)

  • Ribose is a pentose sugar

  • Glucose is a hexose sugar that can exist as two isomers:

    • a-Glucose: OH in 5’-position is oriented downwards

    • B-Glucose: OH in 5’-position is oriented upwards

Primary function of monosaccharides is be a source of energy for the cell

  • They are oxidized to produce large quantities of ATP via cellular respiration

Glucose has various chemical properties that allow it to be used as an energy source

  1. Solubility- It is polar due to -OH groups and hydrophilic so it will dissolve in water

  2. Stability- Cyclical structure provides more support than linear structure

  3. Transport- Easier to transport in aqueous solutions (blood) due to solubility and stability

  4. Potential Energy- Has many high energy electrons from C-C and C-H bonds that can be released via oxidation

  5. ATP Yield- Can be oxidized to yield a lot of ATP via aerobic respiration

Polysaccharides

Polysaccharides are many monosaccharides linked together via condensation reactions

  • Two monosaccharides joined by a glycosidic linkage from a disaccharide

  • Many monosaccharides joined form a polysaccharide

Three key polysaccharides are produced solely from glucose: cellulose, starch, and glycogen

The polymer formed depends on the isomer of glucose involved and the bonding arrangement between subunits

  • Cellulose is composed of beta-glucose subunits with glycosidic linkages between the 1’- 4’ carbon atoms

  • Starch is composed of alpha-glucose subunits and one of two distinct bonding arrangements

    • Amylose is solely composed of 1’-4’ linkages organized in a helical structural arrangement

    • Amylopectin is comprised of both 1’-4’ linkages and additional 1’-6’ linkages

  • Glycogen is similar to amylopectin but has more frequent 1’-6’ linkages

Sugar Functions

Polymers of alpha-glucose are used in energy storage: glycogen in animals and starch in plants

  • Glucose monomers can be added or removed to build or mobilize the stores

In both glycogen and starch, the alpha-glucose monomers connected via 1’-4’ glycosidic linkages to form helical structures

  • Starch can be linear or branched due to the presence of 1’-6’ linkages

  • Glycogen is more highly branched than amylopectin due to a greater frequency of 1’-6’ linkages

Branching causes the polymers to adopt a more compact structure, but the larger size makes them insoluble in water

  • Thus glycogen and starch are great for storage, but not for transporting through aqueous solutions

  • Carbohydrates can be easily digested to release monomers for transport

Carbohydrates can be attached to proteins via glycocsylation to form glycoproteins

  • When attached to membrane proteins, carbs play a vital role in cell recognition

Human blood cells can be categorized into different blood groups based on structure of a surface glycoprotein

  • Blood group A possess type A glycoproteins, group B type B glycoproteins etc.

Glycoproteins function as identification tags to help the immune system recognize the cells as “self”

Lipids

Lipid Properties

Lipids are a class of organic molecule comprised primarily of hydrocarbon chains (fatty acids) or rings (steroids).

  • Hydrocarbons are non-polar and don’t dissolve in water, making lipids hydrophobic molecules

Hydrophobic properties have many important biological consequences:

  • Wax is used to prevent water loss in leaves and birds coat feathers in oil to waterproof them

  • Phospholipids provide structural framework for cells by forming spontaneous membranes in aqueous solutions

  • Help the body absorb some fat-soluble micronutrients (Vitamin A, D) in food

Hydrophobic properties also make it hard to transport lipids around the body

  • Digested fats are packed within a protein coat to become water soluble lipoproteins

  • Steroid hormones are bound to carrier proteins to facilitate movement through bloodstream

Certain lipids have polar components allowing them to be amphipathic

  • Phospholipids have polar phosphate heads, cholesterol has polar hydroxyl group, glycolipids can have polar carbohydrate chains

  • Have limited ability to interact with water, allowing for maintenance of structural integrity

Types of Lipids

Lipids are not polymers as they do not contain monomers, but most lipids contain at least one fatty acid chain in their structure

  • The exception to this is steroids.

Fatty acids can be linked to the hydroxyl groups of alcohol via condensation reactions to create an ester linkage

  • Triglycerides- three fatty acid chains are linked to a singular glycerol molecule

  • Phospholipids- one fatty acid chain is replaced by a polar phosphate group

There are three commonly recognized groups of lipids:

  1. Simple lipids- Esters of fatty acids and alcohol (Waxes and triglycerides)

  2. Compound lipids- Esters of fatty acids and alcohol linked to an additional group (phospholipids and glycolipids)

  3. Derived lipids- Produced from hydrolysis of simple or compound lipids (Steroids and prostaglandins)

Fatty Acids

Fatty acids are hydrocarbon chains found in most lipids, typically containing 4-24 carbons

There are two main types of fatty acids:

  • Saturated fats- Straight hydrocarbon chains with no double bonds

  • Unsaturated fats- Have 1 double bond (mono-unsaturated) or >1 (poly-unsaturated)

    • Cis isomers- hydrogen atoms attach to carbon double bond on same side, causing a kink

    • Trans isomers- hydrogen atoms attach to carbon double bond on opposite sides, keeping it straight

    • In living organisms, almost all unsaturated fats are cis configurations

Fats are mainly found in animals (endotherms) due to their high melting point and solidity at room temperature

  • Saturated and have straight chains (trans)

Oils are mainly found in plants because of their low melting point and liquidity at room temperature

  • Unsaturated and have kinked chains (cis)

Storage of lipids as either fats or oils depends on the organism’s physiology and environment.

  • Need fatty acids that will remain liquid at their normal body temperature

  • However, organisms will try to produce the most tightly packed fatty acids possible to maximize storage

Endotherms produce more saturated fats, because their higher body temps can keep the fatty acids liquid

Exotherms produce cis-unsaturated oils because they wont solidify at the colder temperatures

Most plants also produce cis-unsaturated fats, but some in more tropical climates produce comparatively larger amounts of saturated fats than temperate plants

Lipid Functions

Triglycerides are used for long-term energy storage in animals

  • Store roughly twice as much energy per gram as carbohydrates, but are more difficult to digest and transport through aqueous solutions

Carbohydrates glycogen are used for short-term energy storage

Triglycerides have low thermal conductivity and are effective thermal insulators

Phospholipids are one of the key structural components of cell membranes as they are responsible for the formation of lipid bilayers

  • Have a hydrophilic head composed of glycerol and a phosphate molecule

  • Have two hydrophobic tails composed of fatty acid chains

  • Because they are comprised of hydrophilic and -phobic pieces, they are considered amphipathic

Phospholipids spontaneously form into a lipid bilayer with the two hydrophobic tails shielded from outside fluids by hydrophilic head

  • Bilayer is only held together by the weak hydrophobic associations between non-polar tails, making the bilayer fluid and flexible

Steroids are lipids composed of four fused carbon rings that are non-polar and lipophilic

  • Do not resemble other lipids as they don’t contain a fatty acid chain but still contain the same properties (they are hydrophobic)

Steroid hormone- a steroid that functions as a signaling molecule within the body

  • Because they are lipophilic, they can freely diffuse across the lipid bilayer and bind to receptors WITHIN the cell

  • However they cannot be easily transported through the bloodstream due to being hydrophobic and must be connected to carrier proteins

Steroid hormones are generally synthesized from cholesterol in the adrenal gland (corticosteroids) or the gonads (s steroids)

Proteins

Amino Acids

Proteins are comprised of long chains of recurring monomers known as amino acids

  • Each amino acid contains a central alpha carbon linked to an amine group, a carboxyl group, a variable group, and a hydrogen atom

There are 20 amino acids that are universal to all living organisms

  • Each amino acid has a different composition in their variable side chain

Amino acids can be essential or nonessential

  • Essential- cannot be produced by body and must be present in diet

  • Non-essential- can be produced by body and don’t have to be present in diet

  • Conditional- can be produced by body but at rates lower than certain conditional requirements

    • Essential at certain times only

A shortage of one or more essential amino acid will hinder the ability to produce certain proteins

Polypeptides

Amino acids can be joined together via condensation reactions to form polypeptides and water

  • Peptide bond- formed between amine and carboxyl groups of adjacent amino acids

Polypeptides can be broken down via hydrolysis reactions

Protein Folding

The side chains of amino acids all have distinct chemical properties and will therefore cause the protein to fold differently according to its distinct position within the polypeptide chain

  • How a protein folds plays a critical role in determining its function and level of biological activity

Since most natural polypeptide chains contain 50 to 2000 amino acid residues, organisms are capable of producing a large range of possible peptides

  • Thus proteins are a very diverse class and serve many functions within a cell

Structure (Collagen)
Hormones (Insulin)
Immunity (Antibodies)
Transport (Protein channels)
Sensations (Rhodopsin)
Movement (Actin)
Enzymes (Amylase)

Denaturation

Denaturation is a permanent change in a protein that results in the loss of its biological properties

  • Because the shape of a protein determines its function, this will alter the protein’s activity

Caused by two conditions: heat and pH

High temperature disrupts the hydrogen bonds that hold the protein together

  • As these bonds are broken, the proteins are unfolded and begin to lose the ability to function as intended

  • Must proteins function optimally at body temperature (37 degrees celsius)

Amino acids are zwitterions, meaning they are neutral molecules possessing both negatively (COO-) and positively (NH3+) charged regions

Changing the pH will alter the charge of a protein, which alters the shape and protein solubility

  • All proteins have an optimal pH at which they function