Unit 1: Biological Molecules

Water

Chemical

Formula - H2O

Only substance that naturally occurs in all 3 states

Covalent bond

Bond is polar. Meaning it will create hydrogen bonds, where multiple 'H2O's bond with one another

Highest cohesion of any non-metal liquid

This is why you see water droplets when you pour some water on wax paper. This is because the cohesion forces are stronger than the adhesion forces

Great solvent

This is ALSO why you see water 'defy' gravity. When you suck on a straw, water will climb up due to it's cohesion to itself, and the adhesion to the straw

Hydrophillic - Can dissolve in water

Hydrophobic - CANNOT dissolve in water

Denser when in liquid state, as opposed to solid state

Very high heat capacity

Info

Polarity and Intermolecular Forces of Attraction

Intermolecular Forces of Attraction (Ranked from strongest to weakest)

Polarity

Some elements, like carbon and hydrogen share electrons almost equally. We describe this as Non-Polar.

Some elements, like carbon and hydrogen share electrons almost equally. We describe this as Polar

An interaction between two molecules that can be attractive or repulsive

Ionic - The electrons are unequally shared so the functional group is negatively charged or positively charged. Oppositely charged functional groups attract.

Hydrogen Bonding - A special case of dipole involving functional groups containing H bonded to N or O because electrons are more unequally shared. The partial negative and positive charges are stronger. Oppositely charged ends of functional groups on two different molecules attract.

Dipole - The electrons in a covalent bond in a functional group are not shared equally. This causes a partial negative charge to exist on one end of the functional group, and a partial positive charge on the other. Oppositely charged ends of functional groups on two different molecules attract.

Dispersion - The electrons around an atom in a molecule are, on average, evenly distributed around the nuclei, but at any time they could all be found on one side of a molecule. At this instant, a mini-negative charge would result which can repel electrons in a nearby molecule. The two molecules attract.

Functional groups

Biological molecules are characterized by common groups of atoms. These groups of atoms are called Functional Groups , as they are the locations are interact and react with other molecules.

Ketone

Carboxyl

Aldehyde

Amine

Phosphate

Sulfhydryl

Hydroxyl

Found in aldo- type sugars

Found in keto- type sugard

Found in organic acids such as amino acids and fatty acids

Found in amino acids, proteins, and other N-containing compounds

Found in the amino acid: cysteine. Also found in most proteins

Found in nucleic acids (DNA, RNA). ADP, ATP, phospholipids

OH is polar because O attracts electrons strongly compared to H

CO is polar because O attracts electrons strongly compared to C

COOH is polar, because O attracts electrons more strongly than C or H

PO4 can’t be defined as polar or non-polar because the functional group is an ion so electrons were donated from another functional group

SH is polar, because S attracts electron strongly compared to H

NH3 is polar, because N attracts electrons strongly compared to H

Found in carbohydrates and many other cellular compounds

NH2

PO4

COH

They determine how they interact with each other. Do they attract, or do they repel? Is this a strong attraction or weak attraction? This will determine if a substance is a liquid because it melts easily, or a solid because the molecules are attracted tightly together. Or if it’s hard or soft. Soluble or insoluble.

Carbohydrates

Nutrition and Macromolecules

Essential nutrients - Nutrients that an organism can only get from their environment

We must ingest as much as we can, and include as much as we can into a balanced diet.

One of these nutrients are carbohydrates

A type of neutral compound made of carbon, hydrogen, and oxygen. Mostly formed by green plants and is a major class of animal foods.

We convert these nutrients into biological molecules

Without carbohydrates, we would run out of energy fast

Various foods have distinct flavors and textures because they contain different types of carbohydrates.

How all biological molecules are used by cells and the body depends on the structure of those molecules.

The functional groups that make up different biological molecules are related to the types of intermolecular force of attraction

Shape and size of the molecule is also important

Four main types of nutrients we need in large amounts. These are called macronutrients/biomolecules.

Macronutrients are unique because they are made of smaller molecules called monomers

These monomers put together to create polymers

Monomers

Polymers

Small chemical molecules that can be connected together to make larger molecules

A chemical molecule made from many smaller monomer molcules

4 Macronutrients/Biomolecules

Lipids ("Fats")

Proteins

Carbohydrate

Nucleic acids

Fast source of energy

Ex. Pasta and bread are heavy in carbohydrates

Monosaccharides are the monomers of Carbohydrates

Glycerol and Fatty acids are the monomers of Lipids

Ex. Butter, oil, cholesterol

Great source of long term energy. We use them after we burn up all of our carbohydrates

Lipids make up cell membranes

Ex. Meats and beans

Amino acids are the monomers of Proteins

They contribute to muscle building, working in immune system, acting as enzymes (enzymes are made of proteins)

Nucleotides are the monomers of Nucleic acids

Makes up the DNA in the nucleus of all cells

Major elements

Carbon

Hydrogen

Oxygen

Major elements

Carbon

Oxygen

Hydrogen

Major elements

Carbon

Hydrogen

Oxygen

Nitrogen

Major elements

Carbon

Hydrogen

Oxygen

Nitrogen

Phosphorus

4 types

Disaccharides

Oligosaccharides

Monosaccharides

Polysaccharides

Saccharides come from the Greek word for sugar

Simple sugars

3 main monosaccharides

Makes up all carbohydrates

Galactose

Glucose

Main source of energy for humans

Contains 6 carbon atoms

Types of Glucose

Alpha Glucose - The OH of C1 (Carbon 1) is pointing in the opposite direction to the CH2OH (C6)

Beta Glucose - The OH of C1 and the CH2OH of C6 are pointing in the same direction

Types of saccharides/carbohydrates

Alpha - The OH of C1 and the CH2OH of C6 are pointing in the same direction

Beta - The OH of C1 (Carbon 1) is pointing in the opposite direction to the CH2OH (C6)

Made up of 2 Monosaccharides

Ex. 2 Alpha Glucose molecules form a bond together to create Maltose through condensation/removal of water. You can reverse this by adding water (hydrolysis)

Alpha Glucose + Alpha Glucose ->(Condensation) Maltose (C1 of Galactose and C4 of Glucose bond together)

Beta Galactose + Beta Glucose ->(Condensation) Lactose (C1 of Galactose and C4 of Glucose bond together)

Alpha Glucose + Beta Fructose ->(Condensation) Sucrose (C1 of Glucose and C2 of Fructose bond together)

Sucrose is formed by plants, not animals

Short chain of Monosaccharides, less than 20 monosaccharides

Maltose + Alpha Glucose ->(Condensation) Maltotriose [3 Alpha Glucose, can keep growing with more glucose molecules] (C1 and C4 being bonded)

Homopolysaccharide

Heterosaccharides

aka. Glycans

1 type of Monosaccharides

Two or more Monosaccharides

Branched

Unbranched

Branched

Unbranched

Serves as storage forms of monosaccharides

Starch

Found in bread, cereal and rice

Only made of Glucose

Only bonded through 1-4 glycosidic bonds (C1 and C4 bonds together)

Uses 1-4 and 1-6 glycosidic bonds

Glycogen

Storage form of glucose in animals

Amylopectin

Amylose

Contains Amylose AND Amylopectin

Only made of Glucose

Branch points occurs every 8-12 glucose residues (More branch points than Starch)

Branch points occurse every 24-30 glucose residues

Dextrans

Structural component in bacteria and yeast

Made of 1-3 and 1-6 glycosidic bonds (may contain 1-2 and 1-4)

Cellulose

Made of Beta Glucose

Made of Glucose

1-4 glycosidic bonds

Isomers - Molecules that have the same amount of elements, but different configurations and placements of

Lipids

Fructose

Most energy dense nutrient

20 different fatty acids in food. 2 are essential to Humans.

These 2 fatty acids are used for biological processes like cell membrane structure and hormone production. Not energy production.

Predominantly non-polar molecules

Hydrophobic interactions

The molecule of oleic acid, for example, is made of a long chain of 18 carbon atoms. Carbon and hydrogen share electrons relatively equally so it’s true to describe this section of oleic acid as non-polar or hydrophobic. Yet oleic acid also has a polar, hydrophilic, carboxyl group to the left. Clearly our current definitions aren’t adequate to describe the whole molecule.

Instead, we can use the term amphiphatic to describe a molecule with both polar and non-polar functional groups.

We’ve already seen amphipathic molecules when we looked at the folding of polypeptide chains. Hydrophobic amino acids come together because of Hydrophobic interactions and dispersion forces between non-polar side chains.

Hydrophilic amino acids tend to attract to each other, or watery environments. Hydrophobic amino acids, tend to be excluded from this attraction and stay together because of weaker dispersion forces

Hydrophilic amino acids come together because of stronger dipole-dipole, hydrogen bonding, and ionic-dipole interactions between polar and charged side chains. The hydrophilic amino acids also make strong intermolecular forces of attraction with water so they are located around a core of hydrophobic amino acids.

Uses

Energy

Insulation

Lubrication

Protection

Precursors of some hormones

Key components of cell membranes

Types of Lipids

Phospholipids

Steroids

Triglycerides

Waxes

Insoluble in water

Oils

Fats

Solid at room temperature

Liquid at room temperature

Used by animals as long term energy, protection, and insulation

Used by plants as long term energy storage

Molecular

Glycerol

3 Fatty Acids

Hydrophobic chain (Chain of Hydrogen and Carbon)

Methyl group

Acid group

Saturated

Unsaturated

Only single carbon to carbon bonds. This makes the Carbon saturated with Hydrogen bonds.

1 or more double bonds

Unsaturated

Saturated

Trans fats

Unsaturated fatty acid, but the Hydrogen atoms are opposite of one another at the double bonds

They come together (Glycerol and the 3 Fatty acids) by Dehydration synthesis (So take H2O out of the 3 Fatty acids)

Molecular

Glycerol and 2 Fatty acids + a Phosphate group that attaches to the 3rd Carbon

Hydro-stuff

Glycerol + Phosphate = Hydrophillic

Fatty acids = Hydrophobic

So they arrange themselves like this

Hydrophilic head on outside

Major component of plasma membranes of the cell

4 fused rings of carbon to which different functional groups attach

Ex. Cholesterol

Testosterone

Estrogen

Vitamin D

Cortisone

Present in plasma membranes

Non-polar. Repels water

Found on leaves and animals

Cis Fatty Acids

Trans Fatty Acids

Carbon chain is arranged on the same side of the double bond. As a result, the molecules make a concave shape at the double bond. This kink in the shape is important in the increased fluidity between these fatty acid molecules.

There is, however, a chemical method of arranging the double bond such that the molecule makes a zigzag shape. This type of fatty acid is called a trans fatty acid.

Memorize trick

S - Storage and Source of energy

H - Hormonal roles

I - Insulation

P - Protection

S - Structural components

Proteins

Micelles

A spherical arrangement of amphipathic molecules, hydrophobic side on the inside, hydrophilic side on the outside

Phospholipid bilayer

Phospholipid bilayers are found in the membranes in the cell. Membranes define the compartments of the cell. These include the cell membrane and cell organelles: the nucleus, endoplasmic reticulum, vacuoles, lysosomes, golgi apparatus, mitochondria and chloroplasts

These membranes create fluid mosaics, having proteins and components within the cell membrane that aid in the filtration of molecules and structures coming in and out of the cell membrane

Structures

Progression

Amino acids are made up of an amine, carboxyl, and a side-chain/R group

Secondary structures

Tertiary structures

Primary structures

Quaternary structures

Peptide bonds

The amino acids then bond together to create dipeptides using peptide bonds

Dipeptides

2 amino acids bonded together

Polypeptides

The dipeptides bond together to create polypeptides/primary structures

Later structures

This primary structure then folds in different ways to make secondary structures and finally a whole 3D tertiary structure.

Polypeptide/Multiple amino acids bonded together

Primary structures fold into beta-sheets and alpha-helices to create secondary structures due to intermolecular forces

Multiple secondary structures fold together and make structures depending on intermolecular forces

Multiple tertiary structures bonded together

Functions

Hormones

Antibodies

Receptors - Helps in cell membranes

Enzymes

Transports

Nucleic Acids

Essential amino acids - In humans, we can make 11 of the 20 amino acids in our cells. The other 9 amino acids must come from our diet and are called essential amino acids

ATP

In autotrophs , like plants, sunlight energy is captured first as ATP. Most of this energy is used by the autotroph in its daily biological processes, such as growing new tissue like cellulose or storing energy in the form of amylose or fatty acids.

As matter is passed to heterotrophs in the next trophic level in the food chain only about 5-20 % of the original energy the autotroph received is passed on. In the consumers, enzymes convert the energy consumed into ATP.

Monomers

Nucleotides

one or more phosphate functional groups, a 5-carbon sugar, and a nitrogenous base.

There are five common nitrogenous bases: guanine, adenine, cytosine, thymine and uracil.

Purines (Double ring) - Adenine and Guanine

Pyrimidines (single ring) - Cytosine, Thymine, Uracil

Structuring

Like proteins, polymer forms of nucleic acids can make 3D structures as a result of intermolecular forces of attraction. Unlike proteins, though, nucleic acids have more predictable rules for which nitrogenous bases are attracted to each other.

DNA

RNA

Deoxyribose is used to make polymers of deoxyribonucleotides, also called DNA

Ribose, on the other hand is used to make polymers of ribonucleotides, also called RNA

Nucleotides are connected between their phosphate group and a hydroxyl group on the 5-carbon sugar to make a phosphodiester bond

In other nucleic acids, like dinucleotides, cyclic AMP (cAMP), and ATP, the phosphate is connected differently to the ribose sugar.

NADP+

NAD+

FAD

CoA

DNA and RNA can exist as either single strands of one polymer or double strands made of two polymers.

When two strands come together, though, they always line up and connect with one strand inverted compared to the other. This orientation is called antiparallel

Cellular structures

Imaging

Eye: The eye is the easiest tool for viewing biological samples. The ability to be able to tell two separate objects apart is called resolution. For the trained naked eye, our resolution is about 75 μm;

Light Microscopy: Improvements to optical microscopy over the past 300 years have increased magnification up to 1,500x and allowed optical microscopes to resolve objects as small as 200 nm. This resolution is a physical limit dictated by the wavelength of light

Electron Microscope: Electron microscopes (EM) use accelerated electrons and magnetic coils to make an image instead of light and glass lenses. Electrons have a wavelength (size) that is 104 to 105 times smaller than the wavelength of light. EMs can resolve objects that are 103 times smaller than the smallest resolvable object in a light microscope. The high-resolution transmission EM can magnify a sample up to 50,000x and provide a resolution of 0.1 nm. In cryo-EM, specimens are frozen rapidly to eliminate ice crystals from forming that can distort the specimen’s structure. Samples are then viewed at temperatures as low as –185ºC. Two- and three-dimensional models of the sample can be reconstructed using a computer program that averages many electron micrographs taken from different angles. Electron microscopy requires a sample thin enough to allow electrons to pass through. Samples smaller than 1/500th the diameter of a human hair are used

X-ray Crystallography: X-rays, with wavelengths approximately the same size as the spacing between atoms, are directed through a crystal of the substance under study. The X-rays are bent by the electrons surrounding the atoms in the crystal. The scattered X-rays produce a pattern as they exit the crystal. Sophisticated computer programs use measurements of the angles of the scattered X-rays and their intensities to calculate the three-dimensional positions of the atoms in the crystal. By rotating the crystal and making many two-dimensional images, it is possible to combine results to produce a three-dimensional picture of the molecule

Cell Tagging: In many cases, it can be difficult to pick out a cellular structure in a light microscope or electron microscope image. Cell tagging takes advantage of being able to follow individual molecules that make up a part of the cell. There are different methods of tagging biomolecules. For example, radioactive isotopes of atoms can be introduced to cells. Isotopes are used the exact same way as regular atoms except that their radioactive emissions can be detected with X-ray film. As cells consume the isotopes, they incorporate them into their cell structures. Another method involves adding a coloured or fluorescent chemical that binds to specific functional groups. In all cases, the final result is that the cell structure is highlighted compared to the rest of the cell.

Experimenting

Variables

Independant

Dependant

Controlled

Everything you want to remain constant and unchanging

The change that happens because of the Independent variable

The one thing you change