AP Biology - Unit 1 Biochemistry

How does carbonic acid form?

When CO2 reacts with H2O

Why does CO2 make blood acidic

Because it reacts with water to create carbonic acid (H2CO3).

When blood becomes acidic…

bicarbonate ions neutralize

When blood becomes alkaline

Carbonic acid neutralizes

Primary structure

chain of amino acids connected by peptide bonds. determined by sequences of DNA bases

Secondary structure

• folding or spiraling of amino acid chain due to hydrogen bonding between r-groups.

• “local shape”

• regular, repeated folding peptide chain

Tertiary structure

• 3-dimensional, folded structure due to interactions between R-groups.

• Many proteins are functional at this level.

• Globular proteins

• most enzymes

What are some components of the tertiary protein structure?

Disulfide bridges, hydrogen bonding, hydrophobic interactions, and ionic bonds

Disulfide Bridge

A strong covalent bond (—S—S—) formed between the sulfur-containing R-groups (—SH thiol groups) of two cysteine amino acids. It stabilizes the protein’s tertiary structure.

Quaternary Structure

• Includes 2 or more amino acid chains interacting/bonded to each other.

• Not all proteins reach this structure

• collagen and hemoglobin

What do alpha and beta linkages often in reference to?

Glycosidic bonds

Glycosidic Bonds

Covalent bonds between 2 mono saccharides. Created during dehydration synthesis.

Alpha Ring Structure

OH (hydroxyl) on carbon-1 is below the glucose ring

Beta Ring Structure

OH (hydroxyl) on carbon-1 is above the glucose ring

Starch

A complex carbohydrate polymer made of glucose molecules that plants use to store extra energy.

• polymer of alpha glucose

• alpha 1-4 glycosidic linkages

What kind of linkages do starches have? What do they look like?

1-4 linkage of alpha glucose monomers, all of the OH groups are on the same side. Creates a helical, coiled and often branched shape.

What kind of linkages do celluloses have? What do they look like?

1-4 linkages of beta glucose monomers. OH groups alternate sides. creates a straight, rigic, and unbranched fiber that can stack closely

Isomer

A molecule that has the same chemical formula as another molecule, but a different arrangement of atoms

Why do isomers have different characteristics?

Form follows function: changing how atoms connect or orient in 3D space alters molecular shape, charge distribution, energy states (based on arrangement of electrons), and polarity

Carbonyl Characteristics (5)

• =CO to carbon skeleton

• Polar

• Can have ketones or aldehydes

• Ex: acetone, propanol

• Ketones and aldehydes can be structural isomers with different properties.

Ketones

When carbonyl is within the carbon skeleton

Aldehydes

When carbonyl is at the end of the skeleton (aldehyde, to the side)

Hydroxyl (4)

• -OH bonded to carbon skeleton

• alcohols w/ names usually ending in “-ol”; ex: ethanol (CH3CH2OH)

• Polar, because the electrons spend more time near the electronegative oxygen atom.

• Can form hydrogen bonds with water molecules, helping to dissolve organic compounds such as sugar.

Carboxyl (4)

• COOH

• Acidic properties due to the hydrogen ions because the covalent bond between hydrogen and oxygen is so polar (can release H+ ions more easily).

• Polar

• Ionized with a 1- charge in cellular conditions.

Amino Group (4)

• NH2

• Amines, such as glycine.

• Act as a base; can pick up H+ ions from surrounding solutions (such as water).

• Ionized with a 1+ charge in cellular conditions.

Amine

A nitrogen-containing functional group in amino acids and proteins, affecting charge, folding, and buffering

Why is glycine special?

It has an amine group and a carboxylic group, making it an amino acid.

Phosphate Group (P) (4)

• -OPO3^-2

• Think nucleic acids: DNA, RNA, ATP

• Can release energy when interacting with water

• This functional groups is acidic due to its ability to release H+ ions.

Glycerol phosphate

bonds w/ fatty acids to make phospholipids

Methyl (3)

• -CH3

• Important for allowing biological molecules to function effectively

• Able to form nonpolar covalent bonds

Methylation

Adding a methyl group to a molecule. Can modify the function of a gene in DNA; does not change its integrity, but changes how/when it is expressed.

Sulfhydryl Group (3)

• -SH

• Thiols, such as cysteine (sulfur-containing amino acid, so also an amine group).

• 2 of these can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure.

Thiols

Organic molecules that contain a sulfhydryl group (-SH) bonded to a carbon atom. They are the sulfur analogs of alcohols (which have a hydroxyl group, -OH), which means that they and alcohols have identical structures, except sulfur replaces oxygen.

Saturated Fats (6)

• Only single bonds

• Hold the maximum number of hydrogen atoms

• Straight Structure

• Solid at room temperature

• High Melting Point

• Usually in animal products/tropical oils

Why are saturated fats solid at room temp?

Because of their tight packing that comes from their straight structure.

Unsaturated Fats (6)

• One or more double Bonds

• Liquid at Room Temp

• Kinked Shape

• Double bond means at least one missing hydrogen atom

• Plant and Fish origins

• Improve Blood Cholesterol

Cis and Trans Fats

Geometric isomers of unsaturated fatty acids. They have the same chemical formula, differing only in the spatial arrangement of the hydrogen atoms around their carbon-carbon double bond.

Cis Fats Characteristics

• Hydrogen same side of the double bond

• Bent/kinked

• Loosely packed

• Liquid at room temp

• lower melting point

• increases cell membrane fluidity

Trans Fats Characteristics

• Hydrogen opposite sides of the hydrogen bonds

• Linear shape

• Tightly packed

• solid/semi-solid at room temp

• Higher melting point

• decreases membrane fluidity

Isotopes

Atoms of the same element that have the same number of protons but different numbers of neutrons

What are the strongest bonds in organisms?

Covalent bonds that forma a cell’s molecules

Covalent Bond Characteristics (4)

• Very strong within a molecule (requires significant energy to break).

• Creates partial charges, enabling hydrogen bonding and hydrophilic/hydrophobic interactions.

• Do not dissociate into free-floating mobile ions; do not conduct electricity in aqueous solutions

• Generally lower melting/boiling points than ionic compounds.

Ionic Bond Characteristics

• Form repeating 3D crystal arrays

• Strong electrostatic forces require high thermal energy to break

• Hard and Brittle: Shifting crystal layers aligns like charges, causing repulsive fracture.

• Electrical Conductivity:

  • Solid: Poor conductor (ions locked in lattice).

  • Aqueous / Molten: Good conductor (free-moving charge carriers / electrolytes)

• Polar water molecules surround ions via ion-dipole interactions, significantly weakening the lattice and allowing salts to dissolve

Bond Strength Ranking (not in solution)

• Covalent bonds (Strongest)

• Ionic bonds

• Hydrogen bonds

• Van der Waals interactions (Weakest)

Why are ionic and hydrogen bonds important?

Reinforce shapes of larger molecules and help molecules adhere to each other

Bond Strength Ranking (not in solution)

• Covalent bonds (Strongest)

• Ionic bonds (significantly weakened)

• Hydrogen bonds

• Van der Waals interactions (Weakest)

Four of water’s properties that facilitate an environment for life

1) Cohesive behavior

2) Ability to moderate temperature (high specific heat)

3) Expansion upon freezing (less dense as a solid)

4) Versatility as a solvent (universal!)

Why does ice float in liquid water?

Hydrogen bonds in ice are more “ordered,” making ice less dense

pH Range of most Biological Fluids

6-8

Functional Groups

Specific groups of atoms within molecules that give those molecules unique chemical properties and reactions. The components of organic molecules that are most commonly involved in chemical reactions.

Polymer

a long molecule consisting of many similar building blocks

Monomers and polymers of Carbs

monosaccharide (glucose), polysaccharide (glycogen, cellulose)

Function of Carbs

Short-term energy supply, energy storage, and structural support

How and where to plants store starch?

As granules within chloroplasts and other plastids.

Glycogen

• mainly in liver and muscle cells

• Branched chain

• storage polysaccharide in animals

Cellulose

• Major component of the tough wall of plant cells

• Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ

• Polymer of beta glucose

• Linear and unbranched

Chitin

• found in the exoskeleton of arthropods

• provides structural support for the cell walls of many fungi

• polymer of amino sugar

Starch vs. Cellulose

Starch and cellulose are both polymers of glucose, but they have different glycosidic linkages that determine their structure and function.

• Monomer Configuration: Starch uses alpha linkages where the (-OH) group on carbon-1 points down. Cellulose uses beta linkages where the (-OH) group points up, creating an alternating pattern in the chain.

• Overall Structure: Alpha bonds in starch create a helical, coiled, and often branched shape. Beta bonds in cellulose create a straight, rigid, and unbranched fiber that can stack closely.

• Function: Starch acts as an energy storage molecule in plants. Cellulose provides structural support and rigidity in plant cell walls.

• Digestibility: Animals possess enzymes like amylase to hydrolyze alpha bonds in starch for energy. Most animals lack the specific enzymes needed to break beta bonds in cellulose, making it indigestible (functioning as dietary fiber).

Why can many herbivores digest cellulose?

They have symbiotic relationships with bacteria that can digest it.

Do lipids form polymers?

NO, they are not built from repeating chains of identical or similar single building blocks.

Fat

A lipid molecule made of one glycerol attached to three fatty acid chains via ester linkages. Also called triglycerol.

• energy source

• cushions and insulates

Ester Bond

A covalent bond joining a fatty acid carboxyl group to a glycerol hydroxyl group

Lipid Functions

long-term energy storage, forming cell membranes, and cell signaling.

Phospholipid

Two fatty acids and a phosphate group are attached to glycerol.

• Fatty acid tails = hydrophobic

• Phosphate group = hydrophilic

• major component of cell membranes

Steroids

Lipids characterized by a carbon skeleton consisting of four fused rings (3 6-sided rings, 1 5-sided ring)

Cholesterol

A type of steroid, a component in animal cell membranes

What is the most diverse group?

Proteins

Enzymatic Proteins

Selective acceleration of chemical reactions (digestive enzymes)

Structural Proteins

support (silk fibers, collagin, keratin, etc.)

Storage Proteins

storage of amino acids (Ovalbumin in egg whites, casein, the protein of milk)

Transport Proteins

Transport of other substances (hemoglobin)

Hormonal proteins

Coordination of an organism’s activities (insulin)

Receptor Proteins

Response of cell to chemical stimuli (receptors in nerve cell membranes)

Contractile and motor proteins

Movement (actin and myosin)

Defensive proteins

Protection against disease (antibodies)

Protein polymer/monomer

monomer=amino acids, polymer=polypeptide

What does protein’s function depend on?

structure

Protein structure

twisted, folded, coiled into unique shapes

Polypeptides

A linear polymer chain of amino acids linked together by covalent peptide bonds

Peptide bond

a covalent chemical bond that links amino acids together to form proteins

Nucleic acid monomer and polymer

monomer=nucleotide, polymer=nucleic acid (DNA, RNA)

Nucleic Acids function

store and transmit genetic info

DNA Base Pair Rules

Adenine + Thymine (2 hydrogen bonds), Cytosine + Guanine (3 hydrogen bonds)

RNA base pair rules

Adenine + Uracil (2 hydrogen bonds), Cytosine + Guanine (3 hydrogen bonds)

Why is it important that DNA strands are bonded by H bonds?

Provide a "zipper-like" balance of stability and reversibility, keeping it locked together normally while allowing easy separation for life processes.

What gets rid of H+ in the body?

The kidneys by urinating

R-Groups

side chain of amino acids (20 possibilities)

Factors that can cause protein denaturation

1. Temperature - increases kinetic energy, overcomes weak chemical interactions

2. pH - the H+ ions interact with the charged R-groups, altering ionization state

3. Chemical solutions (salinity, etc) - in aqueous environments, proteins fold so that their hydrophobic R groups are tucked away.

Parts of an Amino Acid

Amino Group (NH2), Carboxyl group (-COOH), R-Group (varies), a hydrogen

Solute

Material being dissolved in

Solvent

Dissolving agent

What is the concentration of H+ at equilibrium?

1×10^-7 M

Lactose

Molecule that consists of a glucose and a galactose covalently bonded (disaccharide)

Maltose

Molecule that consists of 2 glucose molecules covalently bonded (disaccharide)

Sucrose

Molecule that consists of a glucose and a fructose covalently bonded (disaccharide)

Monosachharides

glucose, ribose, fructose, galactose, deoxyribose, glyceraldehyde

Why are lipids insoluble in water?

because they consist mostly of nonpolar carbon-hydrogen and carbon-carbon covalent bonds.Water forces hydrophobic lipid molecules to aggregate together to minimize disruption of hydrogen-bonding networks among water molecules.

3 ways Cholesterol is important or biological structure/function

1. Plasma Membrane Fluidity Buffer

2. Steroid Hormone Precursor

3. Bile Salt and Vitamin D Synthesis

Components of a Fatty Acid

Carboxyl Group, Hydrocarbon chain (r-group0

Waxes

hydrophobic lipids built from long-chain fatty acids joined to long-chain alcohols by ester bonds