Unit 1 - Biochemistry

Dehydration Rxn

Covalent bond formed by the removal of H+ and OH- (which forms water)

Anabolic

Smaller to bigger molecules

Hydrolysis Rxn

Opposite of Dehydration Rxn, where water is split into OH- and H+ which bind to the two molecules

Catabolic

Bigger to smaller molecule

Neutralization Rxn

When an acid and base react to form water and a salt

4

The number of H-bonds that can be formed with other H20 molecules at a time

High specific heat and heat vaporization, Freezing, cohesion, adhesion

4 Unique properties of Water

High Specific Heat

Lots of energy is required to heat water, since H-bonds need to be broken

Evaporative Cooling

When water does evaporate, the kinetic energy goes with it, leaving less E mlcls behind. Some benefits are: sweating, lake and ocean temperatures don't change rapidly

Freezing

Water has a greater density as a liquid than a solid, so ice floats on to of water (water will form 4 H-bonds to make a lattice that takes up more space). Some benefits are: floating ice creates arctic habitats and protects ecosystems in lakes and other bodies of water from ice in the winter

Cohesion

H-Bonds between water molecules will create a surface that will sometimes not allow things to slip between the bonds (surface tension), a benefit of this is some animals and insects can run on water

Adhesion

H-bonds form between water and polar molecules, a benefit of this is it helps transport water through plants

Polarity of Water

Makes it the universal solvent as it can dissolve both ionic and covalent molecules

Hydrophobic

Avoids water

Hydrophilic

Dissolves in/is attracted to water

Autoionization of Water

The spontaneous breaking of water's covalent bonds to form a hydroxide ion and a proton

Acid

pH less than 7, sour taste, conducts electricity, proton donor

Base

Proton acceptor (or can release OH), pH greater than 7, bitter taste, slippery feel, conducts electricity

Weak Acids and Bases

Acids and bases that only partially ionize in water

pH

Measure of the concentration of H3O ions

Ocean pH

Should be at 8 but is dropping because of excessive CO2 in the air. Effects calcifying species of oysters, clams, corals, ect. that need calcium carbonate to make shells

7\.4

Human Blood pH

Buffers

The creation of carbonic acid and bicarbonate ions in order to balance blood pH

Carbon

Can make up to 4 covalent bonds, can bond to itself and form chains/rings, can form single, double, and triple bonds

Monomer

A molecule that can be bonded to other identical molecules to form a polymer

Polymer

A group of monomers

Amino Acid

Compound containing an amino group and a carboxylic acid group

N-C-C

Backbone of A.A.

Peptide Bond

Bonds between amino acids. Formed by a dehydration rxn between the carboxyl and amino groups

Primary Structure

A single Polypeptide

Secondary Structure

Folds or coils of a polypeptide (α-helix and β-pleated sheets) created by H-bonding between adjacent amino acids

Tertiary Structures

Side chains interact to fold the polypeptide in a unique way

Quaternary Structure

A cluster of more than one polypeptide (a protein)

Polypeptide

A long strand of aa, one or several fold together to form a functional protein (non-functional)

Denaturation

Extreme conditions (such as changes in heat, pH, salt, etc) that causes bonds to break and the protein loses shape and function

Nucleotides

Monomer of DNA, composed of a pentose sugar, a phosphate group, and a nitrogenous base

Ribonucleotide

Has the same structure as a DNA Nucleotide, but the 2nd C has a OH attached to it rather than an H

DNA Shape

2 strands of polynucleotides that have aligned in an antiparallel orientation to form a helix

RNA Shape

Exists as a single strand or with folded portions

Nitrogenous Bases

Adenine (A), Cytosine (C), Guanine (G), and Thymine (T) or Uracil (U) (uracil instead of thymine in RNA)

Purines

Two ring nitrogenous bases

Pyrimidines

Single ring nitrogenous bases

Cytosine, Thymine, and Uracil

The Pyrimidines

Adenine and Guanine

The Purines

Phosphodiester Bond

Bond between the phosphate of one nucleotide and the sugar of another (creates the sugar-phosphate backbone of DNA)

H-Bonds

Nitrogenous bases are bonded by...

Polynucleotide

Strand of nucleotides linked together by phosphodiester bonds

Carbohydrates

Polymers of simple sugars that are molecules of C, H, and O in a ratio of 1:2:1; used as energy storage and/or structure, depending on the polymer

Isomer

Molecules with the same chemical formula but different chemical structures

Monosaccharides

Simple sugars

Glucose, fructose, and galactose

The Three Kinds of Monosaccharides

Honey

Ex. of where glucose can be found

Fruit

Ex. of where fructose can be found

Milk

Ex. of where galactose can be found

Disaccharides

Two monosaccharides joined by a glycosidic bond through a dehydration rxn

Maltose

Glucose + Glucose

Linkage of Maltose

⍺1-4 Glycosidic linkage

Sucrose

Glucose + Fructose

Linkage of Sucrose

⍺1-2 glycosidic linkage

Lactose

Glucose + Galactose

Linkage of Lactose

β1-4 glycosidic linkage (usually)

Polysaccharides

Chains of hundreds or thousands of monosaccharides linked together by dehydration reactions

Starch, Glycogen, Cellulose, and Chitin

Name Four Polysaccharides

Monomer

A simple compound whose molecules can join together to form polymers

Polymer

Formed by repeating units of monomers

Starch

Form of energy storage in plants. Composed of amylose and some amylopectin, which allows it to break off into new chains.

Cellulose

Structural component formed by plants that cannot be digested by animals because of the β1-4 glycosidic linkages

Glycogen

Polysaccharide formed by amylose and amylopectin (more amylopectin than starch). Used as a form of energy storage in animals

Chitin

Forms exoskeletons

Amylose

Chains of ⍺1-4 glycosidic linkages

Amylopectin

Amylose with branches due to ⍺1-6 glycosidic linkages

Lipids

Non-polar molecules mostly composed of hydrocarbons and some oxygen

Triglycerides

Composed of 3 fatty acids and 1 glycerol. Used in energy storage (can store 2x as much energy as polysaccharides)

Fatty Acid

A long hydrocarbon chain with a carboxyl group (the acid)

Saturated Fatty Acid

Fatty acid with the maximum number of H attached to the carbons, usually solid at room temperature and found in most animal fat and butter

Unsaturated Fatty Acid

Fatty acid without the maximum number of H attached, a double bond is instead formed between two carbons, giving the molecule a bent shape. Found in plants and fish and is usually considered healthy to eat

Glycerol

A chain of three C with hydroxyl groups that joins with fatty acids through dehydration reactions

Ester Bond

Bonds between hydroxyl and carboxyl groups

Phospholipid

Composed of a glycerol, 2 fatty acids, and a phosphate group attached to a choline

Hydrophilic head, hydrophobic tail

Structure of Phospholipids

Phospholipid Bilayer

The double layer membrane created by the tails of the phospholipids aligning inward and the heads aligning outwards, protecting the hydrophobic tails from the outside water

Steroids

Group of lipids that are structured with 4 carbon rings and side groups that distinguish the type of steroid

Sterols

Steroids with dual-solubility properties (due to a polar -OH group at the end)

Sex Hormones

Control the development of sexual traits and cells

Anabolic Steroids

Mimic testosterone and help athletes boost muscle mass. Not healthy, banned in most competitions, and have serious side effects

Waxes

Large lipid molecules made of long fatty acid chains linked to alcohols or carbon rings, they are hydrophobic and extremely non-polar

Hydrophobic Coatings

Use of waxes

Enzymes

Protein catalysts that speed up reactions without being consumed

Activation Energy

The energy required for a reaction to occur

Substrate

The reactant in a reaction using an enzyme

Active Site

Location on the enzyme where the substrate attaches

Enzyme-Substrate Complex

An enzyme with a substrate attached

Induced Fit Model

The enzyme slightly changes shape to better fit the substrate and hold it in place

Cofactors

Non organic molecules that may be necessary for enzyme activity. Ex. Zn or Mn

Coenzyme

Organic molecule required for enzyme activity. Ex derivatives of some vitamins

Enzyme Concentration

More enzymes speed up the reaction because a substrate is more likely to hit an enzyme and bind to it

Substrate Concentration

Will increase the rate of reaction until saturation is reached (all enzymes have a substrate attached)

Competitive Inhibitors

Inhibitors that block the active site and prevent substrates from binding

Non Competitive Inhibitors

Bind to a location other than the active site to change the shape of the active site, thus preventing substrates from binding

Allosteric Regulation

Non competitive and reversible activators or inhibitors of enzyme activity