Biochemistry

Functional Group - Specific group of atoms that can be added to a hydrocarbon to modify its chemical behavior

Hydrocarbon - organic compound consisting entirely of hydrogen and carbon atoms

Chemical Behavior Changes

Polarity

Influences Solubility

Can become more prone to certain types of bonds

Types of Functional Groups

Carbonyl

oxygen double bonded to a carbon

Polar

Found in Lipids

2 Categories of Carbonyls

Aldehyde

Double Bonded oxygen is on the terminal carbon (End of the chain)

If one R-group is a hydrogen, the compound is an aldehyde

Ketone

Carbonyl category sits on carbon that isn’t a terminal carbon

If both R-group represent carbons, the compound is a ketone

Carboxyl

Carbon double-bonded to an oxygen AND single-bonded to an oxygen-hydrogen (OH) group

Polar

Can lose H (acidic)

Can become charged

Found in Proteins

Hydroxyl

OH group bound to a carbon

Polar

Found in alcohols and carbohydrates

Amino

Nitrogen and two hydrogen form a (primary) amino group

Polar

Can Gain H (alkaline)

can become charged (positive)

Found in Porteins

Phosphate

can be represented with the two hydrogens missing, in which case their respective oxygen atoms would be negatively charged

Polar

Can lose H (acidic)

Can become charged

Found in DNA, RNA

Sulfhydryl/Thiol

Sulfur-hydrogen group attached to a carbon chain

Polar

Rotten egg smell

Found in certain amino acids - Co-A

Methyl

Additional carbon (and its 3 hydrogens) added to a hydrocarbon

Non-Polar

Doesn’t change much about the initial molecule

Needs to be branching off the longest hydrocarbon chain

Electronegativity Difference (of Elements)

Greater than 1.7 - Ionic Bonding

Example : HF - Hydrogen : 2.1, Fluorine : 4.0, Difference : 1.9

Less than 1.7 - Covalent Bonding

Example : HCL - Hydrogen : 2.1, Chlorine : 3.0, Difference : 0.9

Polarity

Between 0.5 and 1.7 - Polar Covalent Bond

Asymmetry Needed

Unequal Sharing of Electrons

Less than 0.5 - Non-Polar Covalent Bond

Symmetry Needed

Equal Sharing of Electrons

1.2 - Solubility and Intermolecular Bonding

Polarity (Rule of Solubility)

Polar Solutes Dissolve in Polar Solvents

Non-Polar Solutes Dissolve in Non-Polar Solvents

Solubility

Soluble - Able to Dissolve (especially in water)

Insoluble - Incapable to Dissolve

Hydrophilic Compounds (Water-Loving)

Polar Substance that Dissolves in Water (Soluble)

Hydrophobic Compounds (Water-Fearing)

Non-Polar Substance that will not Dissolve in Water

Intermolecular Bond - Forces of attraction between molecules

3 Types of Intermolecular Bonds

London Dispersion Force

Weakest of the 3

Temporary forces attraction due to unequal distribution of electrons in a molecule at any given moment

Dipole-Dipole Interactions

Stronger than London Dispersion Force

Refers to forces of attraction between polar molecules

Strongest of the 3

Interactions between 3 specific elements

Nitrogen

Oxygen

Fluorine

Cohesion

Ability of water molecules to form hydrogen bonds with other water molecules

Adhesion

Ability of water to form hydrogen bonds with other substances

6.1 - Phospholipid Bilayer

Function

Divides and protects the interior of the cell from the exterior

Regulates what can enter and exit the cell

Selective Permeability

Based on the size and solubility of the molecule and the availability of specific protein channels

Fluid Mosaic Model

Fluidity

The phospholipids and proteins move laterally. The components are not static

Mosaic-like

The membrane is composed of many types of macromolecules

Funtions of Membrane Proteins

Transport of large molecules such as glucose across the membrane

Enzymatic activity

Signal Triggering (eg. hormones)

Attachment and Recognition

Components

Phospholipids

Serve as the main component of the membrane, and create a barrier

Resulting membrane is impermeable to water-soluble molecules

Cholesterol

Regulates the fluidity of the membrane - serves as a kind of membrane lubricant

At high temperatures, it reduces fluidity

At low temperatures, it increases fluidity

Integral Membrane Proteins

Are permanent and usually transmembrane

Ex : Insulin receptors, ion channels

Peripheral Membrane Proteins

These proteins are capable of moving around the cell membrane

Ex : Cytochrome C

Glycoproteins

A carbohydrate bound to a membrane protein

The carbohydrate stick out of the cell

Provides structural support, is involved in cell recognition, and plays a role in cell to cell interactions

Ex : Mucins, antibodies

Glycolipids

A lipid molecule bound to a carbohydrate

These play a role in maintaining stability of the membrane and in cellular recognition

Ex : ABO Blood markers

6.2 - Transport Across Membranes

Types of Movements

Passive Transport (Does not Require Energy)

Osmosis

The movement of water, across a semipermeable membrane, down the concentration gradient

The semi-permeable membrane doesn’t allow the solute through, so the solvent - water - moves to balance out the concentrations instead

Facilitated Diffusion

Since they cannot get through the phospholipid bilayer, they must pass through a protein channel instead.

Different Types of Channels

Ion channels (Na+ channels, K+ channels)

Voltage-gated channels (open in response to electrical potential)

Ligand-gated channels (open in response to certain chemical interactions)

There is also facilitated diffusion with carrier proteins for larger molecules like amino acids, sugars, and small proteins

Simple Diffusion

Movement of solute down a concentration gradient (from high to low)

In the context of molecules moving across the cell membrane, this works for small, lipid soluble molecules, O2, and CO2

Active Transport (Requires Energy)

Protein Carriers

Coupled Transport

Solution Terminology

Solute

the substance being dissolved

Solvent

the substance doing the dissolving

Concentration Gradient

a gradual change in the concentration of solute from one area of the solvent to another

Types of Solutions

Hypotonic

Lower relative solute concentration

Hypertonic

Higher relative solute concentration

Isotonic

Same solute concentrations

Aquaporins

Proteins the allow for facilitated diffusion of water across the membrane

Ex : Water reabsorption in the kidney

Active Transport

Requires Energy

In form of ATP

Molecules are moving UP the concentration gradient

From low concentration to high concentration

Usually requires a specific carrier protein

Antiporters

Move two different solutes in opposite directions

Example : a sodium-potassium pump

Coupled Transporter

Two proteins working together

Bulk Transport

Used for molecules that simply can’t get through the membrane by any other means

Phagocytosis

“Cell Eating”

Particles are engulfed by a section of the membrane which pinches in to become a vesicle

Pinocytosis

“Cell Drinking”

Basically the same thing, except it’s used for the intake of fluid droplets

Receptor-Mediated Endocytosis

Very similar to phagocytosis, except it is prompted by molecules binding to specific receptors

Exocytosis

“Cell spitting”

Just the reverse of the three forms of endocytosis

When the cell needs to release molecules that can’t pass through the membrane

3.1 - Building and Breaking Macromolecules

2 Types of Biochemical Reactions

Anabolic Reactions

Builds larger molecules out of smaller molecules - Polymers out of Monomers

They do so through dehydration synthesis

Requires Energy

Catabolic Reactions

Break down larger molecules into smaller molecules - Polymers into Monomers

Done through a hydrolysis reaction

Releases Energy

Macromolecule - a molecule containing a very large number of atoms, such as a protein, nucleic acid, or synthetic polymer

Building Macromolecules

Monomer

A small molecule

Examples - glucose, amino acids, nucleotides

Polymer

Long-chain molecule made up of repeated patterns of monomers

Examples - starch, proteins, DNA

3.2 - Carbohydrates

Structure and Function

Monosaccharides

One Subunit

Energy Source

Ex: Glucose, Fructose

Disaccharides / Oligosaccharides

2-7 monosaccharides

Energy Source

Ex: Maltose, Lactose

Formation of Disaccharides

Bonds between monosaccharides are called glycosidic linkages. Usually identify which carbon on each monosaccharide is involved

Polysaccharides

Many monosaccharides

Energy source, Structural support, cell to cell communication

Ex: Starch, Glycogen, Cellulose, Chitin

Cellulose : Structural molecule in plants. Straight chains of 𝛽-glucose (Result in great structural molecule for plants). We can’t digest cellulose because we don't have the ability to break 𝛽-linkages.

Starch : Energy storage molecule in plants. Straight and branched chains of 𝛼-glucose (Zigzaggy structure resulting in weak structural support)

Glycogen : Energy storage in animals (and fungi and bacteria). Highly branched chains of 𝛼-glucose

Chitin : Structural molecule in organisms like insects and crustaceans (exoskeleton strength)

𝝰-linkages and 𝞫-linkages

𝝰-linkages occur when -OH groups involved in reaction are oriented the same way - both up or both down

𝞫-linkages occur when the -OH groups are oriented in opposite directions

Molecular Structure

Possess 1:2:1 ratio of C:H:O

Isomers

Molecules with same chemical formula but different structures

3.3 - Lipids

Structure and Function

Non-Polar

Chains or Rings

Composed of C, H , and O

4 Categories

Triglycerides

Energy Storage

Insulation

Composed of a glycerol molecule and 3 fatty acid chains

Phospholipids

Cell Membrane

Selective Permeability

Steroids

Hormonal Signaling

Cell response to the environment

Growth

Characterized by 4 carbon rings and varying functional groups

Waxes

Water Resistance

Protection

Combination of a fatty acid bound to an alcohol

Saturated vs Unsaturated Fatty Acids

Saturated Fatty Acids

Found in animal fats

Usually solid at room temperature

Saturated by hydrogen bonds

Every carbon is bonded to the maximum number of hydrogen atoms

Unsaturated Fatty Acids

Found in plant-based fats

Liquid at room temperature

NOT saturated by hydrogen atoms, because there is at least one double-bond between carbons

Trans Fatty Acids

Modified Unsaturated Fatty Acids

Happens when one of the hydrogen atoms connected to the double-bonded carbons is not on the same sides as each other

Resulting in no repulsion between hydrogen atoms on top of the unsaturated fatty acid creating the bend

Acts like a solid saturated fat

Phospholipid

Composition

Two fatty acids

The fatty acid “tail” is nonpolar and hydrophobic.

Resulting molecule is amphipathic - it is both partly hydrophilic and hydrophobic

One phosphate group

Makes the “head” polar and therefore hydrophilic.

3.4 - Proteins

Functions

Structural Support - Connective Tissues

Transport of Substances - Ion Channels

Cell Signaling - Insulin, Antibodies

Movement Between Cells - Protein Channels

Coordination and Regulation of Activities - Shape Changes

Acceleration of Chemical Reactions - Enzymes

Amino Acids Structure

Protein is a polymer - its monomers are amino acids

20 amino acids - 8 are “essential” (our body cannot synthesize them) - we need to include them in our diet

Categories

R- ground can make an amino acid

Polar and Non-Polar

Subtacidic/negatively charged, alkaline/positively charged, or neutralopic

Linkage between NH bond and double bonded oxygen divides the amino acid groups

Polymer of Amino Acids - Polypeptide Chain

Created in a watery environment

Protein Structure

Primary Structure - specific sequence of amino acids

Secondary Structure - hydrogen bonding of the peptide backbone (α-helix or β-pleated sheet)

Tertiary Structure - Folding of the polypeptide due to interactions between side chains - some proteins will stop here for their specific functionality

Some R-groups give the amino acids the properties of being nonpolar therefore hydrophobic or to others polar properties therefore hydrophilic

Nonpolar amino acids will cluster together inwards whereas the polar ones will move outwards - to be close to the water (protects nonpolar from water)

R-groups will become positively charged or negatively charged - attraction or repulsion between each other

Will fold up in an extremely precise way every time

Quaternary Structure - Multiple folded polypeptides joining together (not all proteins reach this stage)

Will fold up in precisely the same way every time - specific interactions between side chains

Protein Denaturation

Alternation of structure of a protein since function of a protein is dependent on its structure, denaturation ALSO disrupts its function.

Can be caused by heat, pH, salt, and mechanical agitation

Permanent - cooking an egg

Temporary - Heating up milk

3.8 - Nucleic Acids

Functions

General Structure of Nucleotide (Nucleotide - Monomer which make up a Nucleic Acid)

3 Main Components

Nitrogenous Base

Adenine (A)

Guanine (G)

Cytosine (C)

Thymine (T)

Uracil (U)

Pentose Sugar (5 carbons)

Deoxyribose in DNA

Ribose in RNA

Phosphate Group

Formation of a Polymer

When two nucleotides join, the nitrogenous base is not involved. The phosphate group from one nucleotide binds to a hydroxyl group on the sugar of the second nucleotide

The bond created is called a phosphodiester bond

Shape of DNA

Bases are joined together with hydrogen bonds

4.1 - Enzymes

Is a Biological Catalyst

Role :is to speed up biological reactions by lowering activation energy (EA)

Activation energy : energy needed to be added before a reaction can proceed

Energy profile

Exergonic Reaction

Free energy - a measure of the energy available to do something

Results in an overall release of energy

More energy in the reactants than the products

Typically Catabolic

Endergonic Reaction

Results in an “absorption” of energy

More energy in the products than in the reactants

Typically Anabolic

Strategies to Decrease Activation Energy

M - Microenvironment

Enzyme creates a more suitable mini-environment for the reaction to occur

O - Orientation

Enzyme orients the substrate in such a way that it makes it more likely bonding sites come into contact with one another

D - Direct Participation

Enzyme, well, participates directly in the reaction in some way

S - Straining Bonds

Enzyme pulls on intramolecular bonds causing strain, and making it more likely for them to break with lower input of energy

Why rely on enzymes?

Heat - for instance, will generally speed up reactions by getting particles to move around faster, increasing the chance that reactants will bump into each other

Enzymes are not consumed during the reaction, and are therefore reusable

Enzymes exhibit substrate specificity - so they only encourage reactions the cell wants

4.2 - Enzyme Function

Enzyme Catalyzed Reaction

1 : Substrates binds to the active site

2 : Enzyme changes shape accordingly

3 : Substrates are held in the active site through weak intermolecular forces like H-bonds

4 : Enzyme lowers EA

5 : Substrates are converted into new product, new bonds are formed

6 : Product is released

7 : The active site becomes available for another set of substrates

Factors Affecting Enzyme Activity

Substrate concentration

The more substrate the there is, the higher the rate of reaction - up to a point

Temperature

Higher temperature can increase rate of reaction up until the point that it denatures the enzyme

pH

Certain enzymes are designed to function within a very narrow range of pH conditions

Enzyme Co-Factor

Substances other than the enzyme and substrate. Their job is to help activate the enzyme itself

Metal ions, such as Ca2+, Zn2+ and Cu2+

Coenzymes, which are organic molecules. Their job is to transfer energy in the form of electrons

They include vitamins, and an important molecule we’ll see much more of later called NAD+

Allosteric Regulation

More complex method of controlling enzyme activity

If a cell wants the ability to turn on and off a particular enzyme. Allosteric regulation is one mechanism it can use.

An allosteric site on an enzyme is any site that is NOT the active site. It can be used as an on-off switch

Competitive Inhibition

The inhibitor molecule is similar in shape to the substrate, and can bind directly to the active site - substrate is now blocked from binding

Feedback Inhibition

Can take place when there is a series of enzyme catalyzed reactions, where a product from each reaction becomes part of the next reaction

Occurs when a product from one of the reaction inhibits a previous step

Can be competitive or non-competitive inhibition

Cell Theory

All living things are composed of cells or cell products

The cell is the smallest unit of life

Cells only come from pre-existing cells

Common Cell Structures

Genetic Material

Cell Membrane

Cytoplasm

Types of Cells

Prokaryote

Bacteria

Cyanobacteria

Eukaryote

Animal

Plant

Cell Structure and Functions

Nucleus

Nuclear Envelopment

Single bilayer surrounding the nucleus

Protect the genetic material inside the nucleus

Both in Animal & Plant Cells - not present in prokaryotic cells

Nucleolus

Cluster of protein - RNA in the center of the nucleus

Production of ribosomes

Both in Animal & Plant Cells - not present in prokaryotic cells

Genetic Material

DNA/RNA

Contains all instructions to govern cell function

Present in all cells in some form

Ribosomes

Freely floating in the cytoplasm or attached to the endoplasmic reticulum

Made of rRNA and protein

Constructs proteins

In all cells

Packaging and Transport Organelles

Endoplastic Reticulum

Network of tubes/membranes extending outwards from the nucleus to the membrane

Smooth - no ribosomes attached

Rough - embedded with ribosomes

Transport of molecules within the cell

In all eukaryotes

Golgi Body

Stacks of flattened membrane sacs

Processes and packages proteins to be sent out of the cell

Modifies proteins

In all eukaryotes

Single Membrane-Bound Organelles

Vesicle/Vacuole

Literally just membrane balls

Vesicles transport materials out of the cell and store materials inside the cell

Vacuoles tend to be larger, especially in plants, and are typically used for storage

All cells have vesicles

Plant cells tend to have one large vacuole, while animal cells will have a few smaller ones, if any

Lysosome

Membrane balls containing digestive enzymes

The digestive enzymes they possess are used to break down a variety of things, including the cell itself!

In both Animal and Plant Cells

Double Membrane-Bound Organelles

Mitochondrion

Double-membrane bound

Smooth outer membrane

Folded inner membrane (cristae)

Has its own DNA

Site of aerobic respiration

Releases energy from glucose

In all eukaryotes

Plant-Only Organelles

Cell Wall

Rigid outer layer, composed of cellulose

Structural support and protection

Found in Plant cells (also fungi and bacteria)

Chloroplast

Green oval

Contains pigments - especially chlorophyll

Inner and outer membrane

Contains stacks (called grana) of pancake-like structures (called thylakoids)

Site of photosynthesis - the production of glucose using the sun’s energy

Found in Plants and Algae