Biochemistry Review

4 Types of Reactions

-Neutralization

-Redox reactions

-Hydrolysis

-Dehydration synthesis

Neutralization Reaction

A chemical reaction between an acid and a base that results in the formation of a salt and water

pH

A measure of how acidic or basic a solution is

Buffers

Minimize pH changes by taking up or releasing hydrogen ions or hydroxide ions in solution

Redox Reaction

A chemical reaction that involves the transfer of electrons from one reactant to another

Oxidation

Loss of electrons

Reduction

Gain of electrons

Dehydration Synthesis

Create a covalent bond between 2 interacting subunits and remove hydrogen from the functional group of one subunit and a hydroxyl from the other subunit creating water.

Hydrolysis Reactions

Water acts as a reactant to break molecules into smaller subunits. A bond in the reactant molecule is broken and the OH and H form a split water are attached, resulting in two products

Anabolic

Absorb energy and build bigger molecules from smaller ones

Catabolic

These reactions involve the breakdown of large organic molecules into smaller molecules

Functional groups

Reactive clusters where much of the bonding takes place in biological molecules. Each functional group will always form the same number of covalent bonds with adjacent molecules (bonding capacity)

Amino

An “N” bonded to two “H” molecules

Carbonyl

A “C” double bonded to an “O”

Carboxyl

A “C” double bonded to an “O” and bonded to an “OH”

Hydroxyl

Single bonded to an “OH”

Phosphate

“P” double bonded to an “"O” and single bonded to three “O”

Sulfhydryl

An “S” bonded to an “H”

Methyl

“C” bonded to three “H”

Carbohydrates

Contain carbon, hydrogen and oxygen in a 1:2:1 ratio. Used for energy for building materials within the cell and for cell to cell identification. Most are polar and many dissolve in water.

Monosaccharides

Contain 3,5 or 6 carbon atoms (triose, pentose, hexose). Meaning single sugar.

Glucose

Referred to as blood sugar, because it is the sugar that cells in the body use first for energy

Fructose

Called fruit, since it is a principal sugar in fruits

Galactose

Sugar found in milk

Disaccharides

2 monosaccharides joined together, a condensation reaction forms a covalent bond between monomers by the removal of water and they form glycosidic bonds

Polysaccharides

Complex carbs composed of hundred to several thousand monosaccharide subunits joined by glycosidic bonds.

Starch

Form of glucose storage implants. Monomer is glucose. Insoluble due to large size and may be linear or branched.

Glycogen

Stored by humans and other animals in muscle and liver cells. Monomer is glucose. Insoluble and highly branched.

Cellulose

Primary structural unit of plants. Consists of a straight-chain polymer of beta-glucose molecules. Humans cannot digest glycosidic linkages between beta glucose molecules. Hydrogen bonding occurs between two straight chains to produce tight bundles called microfibrils.

Chitin

Makes up exoskeleton of insects and crustaceans. Linear or unbranched.

Fats and Lipids

A non polar molecule made mostly of carbon and hydrogen. Insoluble in water, but are soluble in non polar substances. Used for storing energy, building membranes and cell parts, chemical signaling molecule, insulation

5 Categories of Lipids

-fatty acids

-fats

-phospholipid

-Steroids

-Waxes

Fatty Acids

Consist of a single hydrocarbon atom with a carboxyl group (-COOH) at one end.

Saturated

No double bonds between the carbon atoms in the fatty acid

Unsaturated

If there are double bonds between the carbon atoms in the fatty acid

Fats

A lipid that is made from a fatty acid chain and glycerol. One to three fatty acid chains are joined to a single glycerol molecule through dehydration synthesis.

Phospholipids

Make up cell membranes. Made of glycerol, 2 fatty acids and a phosphate group.

Amphipathic

Polar head is hydrophilic and the 2 non polar tails are hydrophobic

Steroids

A group of lipids that contain 4 fused hydrocarbon rings and several different functional groups

Waxes

Large lipid molecules made of long fatty acid chains linked to alcohols or carbon rings. Hydrophobic.

Proteins

Large molecules that consist of many amino acid subunits that are joined together by peptide bonds folded into a specific 3D shape. The function is related to the shape and the shape is based in the sequence of amino acids.

4 Basic structures of proteins

Primary, Secondary, Tertiary, and Quaternary

Amino Acid Groups

Amino and Carboxyl group

Peptides

These bonds link amino acids into chains of subunits that make proteins. This bond is covalent and formed by dehydration synthesis reaction. A chain of amino acid subunits that are connected by peptide bonds

Polypeptide

Peptide with more than 50 amino acids

Primary Structure

Unique linear sequence of amino acids. A small change in the structure will alter the overall structure to some degree which can affect the function.

Secondary Structure

The peptide chain can take on repeating coil o fold which is due to H-bonding between different parts of the amino acid backbone

2 Common Secondary Structures

-Beta pleated sheet

-Alpha helix

Tertiary Structure

The overall 3D shape of a protein due to H-bonding interactions among R groups. Some R groups are non-polar and will move to the middle of the molecule, some form hydrogen binds and others containing sulphur atoms form disulfide binds between different areas of a protein.

Disulfide bridges

Strong stabilizers of tertiary structure

Denaturation

Loss of structure and function of protein

Quartnerary Structure

Some proteins have more than one polypeptide chain and it is the interactions between 2 or more polypeptide chains in a protein that maintain the quaternary structure.

Nucleic Acids

Polymers made up of many monomer subunits called nucleotides

Nucleotides

Three parts linked by covalent bonds. The three parts are sugar, phosphate group and nitrogenous base

Enzymes

Proteins that act as catalysts. The catalyst itself is not consumed in the process, so it can be used again. Each one has a unique 3D shape which determines which reaction it catalyzes

Substrate

A substance that is recognized by and binds to an enzyme. Interacts with a small part of the enzyme called the active site.

Active site

3D pocket that matches the shape of the substrate in order for binding to occur

Enzyme-substrate complex

When the substrate is bound to the enzyme

2 proposed models of how enzymes work

-Lock and Key

-Induced Fit

Lock and Key

An active site is a perfect fit for the substrate and no modification is necessary for binding.

Induced Fit

Assumes active site is more flexible and conformational change may occur in the enzyme as it binds to the substrate

Cofactor

A non protein group that binds very precisely to an enzyme and this is often a metal

Conenzyme

An organic molecule that acts as a cofactor of an enzyme and this is a non metal

Conditions and Factors that Affect Enzyme Activity

-Enzyme concentration

-Substrate concentration

-pH

-Temperature

Enzyme Inhibitors

Foreign agents that affect the enzyme's ability to work (decrease their activity)

Two locations where substances normally bind on an enzyme

-Active site

-Allosteric site

Allosteric site

This binding can either activate or inactivate an enzymatic pathway

Competitive Inhibition

Resembles a substrate and competes for the active site

Noncompetitive Inhibition

Binds at a site other than the active site, causing the enzyme’s shape to change so that the substrate cannot bind to active site

Allosteric Regulation

Regulatory molecules naturally regulate enzyme activity by bind to the allosteric site and this may either inhibit or stimulate enzyme activity

Feedback Inhibition

Regulation of a pathway by one of the products of this pathway. If a product accumulates in excess, it slows or stops the pathway by acting as an allosteric inhibitor of the enzyme that catalyzes the first step in the pathway

Prokaryotic cells

Lack a true nucleus and its DNA consists of a single chromosome found in a region called the nucleoid

Eukaryotic cells

Have a membrane nucleus that holds DNA within thread-like structures called chromosomes. The rest of the cell is also divide into membrane bound compartments called organelles. Each organelle carries out a specific function which is dependent on its structure

Plasma Membrane

Regulates the passage of molecules into and out of the cell and it is made up of a bilayer of phospholipid. Selectively permeable.

Fluid Mosaic Model

Widely accepted model of the cell surface membrane in which proteins are embedded and float freely within a bed of semi-fluids

Glycolipids and glycoproteins

Involved in cell recognition and cell-cell interactions

Proteins associated with membranes

Integral and peripheral

Integral Proteins

Embedded in the membrane

Peripheral proteins

Loosely and temporarily attached to the outer regions of the membrane

4 Functional categories of membrane poteins

-transport

-enzymatic activity

-triggering signals

-attachment and recognition

Transport

Shape shifting may allow some membrane proteins to shuttle molecules from one side of a membrane to the other

Enzymatic Activity

Proteins associated with respiration and photosynthesis

Triggering Signals

Membrane proteins may bind to specific chemicals such as hormones, binding to these chemical triggers changes on the inner surface of the membrane starting a cascade of events within the cell

Attachment and recognition

Surface points can recognize elements of disease-causing microbes that may try to involve cells triggering an immune response.

Simple Diffusion

The movement of a substance across a membrane without the need to expend chemical energy (unassisted). Spontaneous and requires a concentration gradient

Rate of diffusion

Dependent on the concentration difference

Osmosis

Diffusion of water across a concentration gradient

Concentration gradients

-isotonic

-hypotonic

-hypertonic

Isotonic

Normal

Hypotonic

Dilute

Hypertonic

Concentrated

Facilitated Diffusion

The transport of ions and polar molecules through a membrane via protein complexes. Carrier proteins help biological molecules that are unable to diffuse across the plasma membrane. The molecule is still moving from an area of high concentration to an area of low concentration without using energy

Active transport

Molecules are using carrier proteins to go against the concentration gradient from an area of low concentration to an area of high concentration, requiring energy in the form of ATP

Pumps

Protein carriers that are involved in active transport

Primary Active Transport

Energy is derived directly from the breakdown of ATP

Secondary Active Transport

Uses the concentration gradient of an ion, established by a primary pump as its energy source

Symport

Move in the same direction across the cell membrane.

Antiport

Move in opposite directions across the membrane.

Exocytosis

Secretory vesicles move through the cytosol and contact the plasma membrane, vesicle fuses with plasma membrane and contents of vesicle are released to the cell exterior. Proteins in the vesicle membrane become part of the plasma membrane

Phagocytosis

Cellular process by which specialized cells called phagocytes engulf and ingest large solid particles, such as bacteria, dead cells, and debris.