EXAM REVIEW: UNIT 1 - BIOCHEMISTRY

Intermolecular Forces

Weak forces that adhere or interact with each other in cell processes, determines the SHAPE of large molecules

Strength of Intermolecular Forces (strongest to weakest)

1. Ion-dipole

2. Ion-Induced dipole

3. Hydrogen bonds

4. Dipole-Dipole interactions

5. Dipole-Induced dipole

6. London dispersion forces

Ion-Dipole

An interaction between an ion (cation or anion) and a polar molecule; the attraction occurs between the ion and the oppositely charged dipole

Ion-Induced Dipole

An interaction that occurs when an ion induces a temporary dipole in a nonpolar molecule, leading to an attraction between them.

Hydrogen Bonds

Strong attractions between a hydrogen atom, covalently bonded to a highly electronegative atom (HFON), and another electronegative atom.

Dipole-Dipole

An interaction between polar molecules where the positive end of one dipole is attracted to the negative end of another dipole.

Dipole-Induced Dipole

An interaction that occurs when a polar molecule induces a temporary dipole in a nonpolar molecule, resulting in an attraction between them.

London Dispersion

forces are weak intermolecular forces arising from temporary dipoles in molecules, significant in nonpolar substances.

Properties of Water

• Water lattice

• High heat capacity

• Adhesion

• Cohesion

• Solid is less dense

• Universal solvent

Water lattice

The H-bonds between water molecules allow for a water lattice; bonds break and reform constantly to give water its fluid properties

Ice

Water lattice becomes a rigid, crystalline structure with more space between molecules, forming hexagons with air inside of them - it is less dense than water

Water heat capacity

H-bond lattice allows for high heat capacity, thermal energy flows through water and is absorbed by BREAKING H-BONDS which helps regulate temperature.

Universal Solvent

Polar nature of water allows it to dissolve other polar things

Adhesion

The attraction between water molecules and other substances, allowing water to stick to surfaces.

Cohesion

The attraction between water molecules due to hydrogen bonding, which helps maintain surface tension and allows for water's unique properties.

Functional Groups - Definition

Small reactive groups that are usually ionic or polar, causes the chemical reactions of organic molecules, determining their properties and reactivity.

Acid Functional Groups (ionic)

• Carboxyl; COOH —> COO^-

• Phosphate; PO₄^2-

Basic functional Groups (ionic)

Amino; NH2 —> NH3+

All functional groups

• Amino

• Carboxyl

• Carbonyl

• Phosphate

• Sulfhydryl

• Hydroxyl

Very EN, forms peptide bonds

Amino

Stronger than phosphate, easy to lose H+, harder to put it back (strong acid; weak conjugate base)

Carboxyl

Carbonyl

Aldehyde vs Ketone

Aldehydes are at the end of a molecule; Ketones are within a molecule

Both are CARBONYLS (C = O)

Acts as a buffer, can give/receive H+ so it constantly transitions, stores and releases energy

Phosphate

Very reactive; forms disulfide bonds that can withstand acids

Sulfhydryl

Hydroxyl

What are functional groups essential for

• Solubility

• Reactivity

• Shaping

What can acid/base functional groups do

regulate pH

Ether bonds

C - O - C

Ester bonds

C - O - C = O

Phosphoester (2 means a phosphodiester)

C - O - P = O

Dehydration Synthesis (condensation reaction)

Removes a water molecule to assemble a larger molecule (makes monomers into polymers)

Hydrolysis

Breaks down compounds with the addition of water

Carbohydrates

• Short and medium-term energy storage

  • Short = monosaccharides

  • Medium = glycogen, starch (polysaccharides)

• Build structures

  • Plant cell walls (cellulose)

  • Insect shells (chitin)

Monosaccharides

3+ carbon sugars, simplest form is glyceraldehyde

Are linear when dry, 5+ carbons will turn into a ring IF IT HAS ALDEHYDE

Alpha vs Beta glycosidic bonds

Only occurs if one of the monosaccharide uses C1 in their bond. The alpha and beta is then dependent on the orientation of the hydroxyl on the other monosaccharide’s C1

Alpha - Hydroxyl is DOWN (opposite of chimney)

Beta - Hydroxyl is UP (same direction as chimney)

Carbohydrate functional groups

• Hydroxyl

• Carbonyl (aldehyde if cyclic, but can also be a ketone)

Carbohydrates - Bonds + linkages

• Ether bonds

• Glycosidic linkages (between carbohydrates)

Disaccharides

2 linked monosaccharides connected with a glycosidic bond

Oligosaccharide

3-10 monosaccharides, acts COMPLEXLY

Has many possible combinations and is VERY VARIABLE

Polysaccharides

Long chains (up to 100s) of monosaccharide repeats - makes complex CARBOHYDRATES, LESS DIVERSE THAN OLIGO (a lot of repetition)

Lipids

Fats, oils, steroids or waxes, typically long chains of non-polar hydrocarbons, (water would rather H-bond with itself)

Ratio of CHO in carbohydrates

1:2:1

Lipids - Function

• Cell membranes

• Long-term energy storage

• Mostly UNREACTIVE

• Steroid hormones

• Insulation

• Organ cushioning

Categories of lipids

• Triglycerides

• Fatty acids

• Phospholipids

• Sterols (cholesterol)

• Waxes

Lipids - Functional Groups

• Carboxyl (fatty acid)

• Hydroxyl (on glycerol)

Lipids - Bonds/Linkages

• Ester bonds (connects fatty acid to glycerol for triglycerides)

• Ether bonds (found within the ether bonds)

Triglycerides

• uses hydroxyls for reactions

• Composed of 3 fatty acids and 1 glycerol molecule

Triglycerides - dehydration synthesis

• H on hydroxyl is easier to give

• OH on carboxyl is easier to give

Fatty acids

Can be:
- Saturated (surrounded by H; straight chain)

- Unsaturated (not fully surrounded by H)

Saturated fatty acids

Tightly packed, straight chain structure that is SOLID AT ROOM TEMPERATURE

Unsaturated fatty acids

Have double bond Cs due to it not being fully surrounded by H, has different types:

• cis-unsaturated fats

• trans-unsaturated fats

Cis-unsaturated fats

Bent/kinked, liquid at room temp because its shape takes up more space (ex. plant oils)

Bent shape is due to the e^- clouds from H ON THE SAME SIDE, repelling each other and bending the molecule

Trans-unsaturated fats

Straight molecules because the e^- clouds are on opposite sides, occurs in HYDROGENATION

Hydrogenation

Created in the presence of a NICKEL CATALYST; Hs are shot at the molecule until cis —> trans (liquid to solid)

Must be done with POLYUNSATURATED FATS, if not then all Hs would flip, and the fat would be over hydrogenated and unusable

Danger of trans fats

Since mostly artificial, enzymes + bacteria cannot recognize the fat since it cannot be broken down

Phospholipids

Similar to triglycerides, but 1 fatty acid is replaced with a phosphate group, the phosphate makes a head that is CHARGED AND POLAR

Phosphoester linkage connects the phosphate

Phospholipid - dehydration synthesis

Phosphate loses OH

Glycerol loses H

Phospholipid - fatty acid tails

Fatty acid tails are nonpolar, they stay together but are on the other side of the phosphate

Type of fatty acid depends on temperature, if stiff is needed: 2 saturated fatty acids, if fluid is needed: 1 saturated 1 cis monounsaturated

Waxes

Long hydrocarbon chains (2-3 fatty acids linked together) formed by an ester link between a long chain alcohol and fatty acid - COMPLETELY NONPOLAR

Steroids (cholesterol)

Only lipids with a multi-ring structure, CHOLESTEROL is a precursor to all steroids

Needed for membrane integrity, to get the ideal fluidity (wedges between or sticks phospholipids together to adjust based on temperature)

Proteins

Long polymers of ~50 amino acids, consists of CHON, and is NEUTRAL, the function is determined by the R-group

Polar proteins (nucleophilic)

Hydroxyl (OH) or suldhydryl (SH)

Nonpolar proteins

Neutral charge across the molecule, may have an S in between the lines

Acidic proteins

Has a second carboxyl APART FROM THE ONE FROM THE PEPTIDE BOND

Basic proteins

Has N outside of the N in the amines

Aromatic proteins

Has a hexagon within its structure

What determines the function of proteins

SHAPE - which is determined by the R-groups, the ones sticking out have the potential to react

Stages of protein folding

• Primary (peptide chain)

• Secondary (a helix or B sheet)

• Tertiary (functional protein)

• Quaternary (complex unit)

Primary folding

Forms a polypeptide chain by linking amino acids together with covalent peptide bonds - dehydration synthesis between AMINE AND CARBOXYL —> amino acids with peptide bonds

Secondary folding

Depending on the properties of R-groups, peptide bonds may interact with H-bonds to make:

• alpha helix - inside is nonpolar, some R-groups are nonpolar and are within the helix

• beta pleated sheet - R groups surround the hydroxyl

Polar and nonpolar R-groups are neither shape, just a chain

Tertiary folding

Final 3D shape formed by R-groups interacting with intermolecular forces + covalent bonds, more disulfide bonds = more heat and acid resistant

Quaternary folding

Multiprotein complex that are formed with the remaining R-groups, only done if the shape and R-groups allow it

Protein - functions

• Structural components of tissues

• Enzymes

• Protein hormones

• Channels for transport

• Antibodies in immune system

Nucleic Acids

Formed from phosphates, CHONP, make different coded instructions for the cell, DNA is long polymers of 4 different types of nucleotide subunits

Components of nucleotides

• 1 sugar molecule (ribose or deoxyribose)

• 1 phosphate group

• Nitrogenous base

Bonds/linkages in nucleotides

• Phosphodiester

• Ester

• Ether

Enzymes

Catalysts that speed up chemical reactions by reducing activation energy

Spontaneous reactions - EXERGONIC

Decrease in free energy; cellular respiration

Nonspontaneous reactions - ENDERGONIC

Increase in free energy; photosynthesis

Active site

Where reactions occur in an enzyme - substrates bind here

Allosteric site

Another site on an enzyme where activation or inhibition may occur

Allosteric Activation

A molecule interacts with the allosteric site, changing the enzyme’s shape and allowing it to fit the shape of the substrate

Cofactor/Coenzyme activation

Organic molecules (coenzymes) or ions (cofactors) that complete the active site

Competitive inhibition

Competitive inhibitors interact, but DO NOT REACT with the enzyme, the rate of reaction decreases

Allosteric inhibition

Enzymes work or don’t work; the interaction with the allosteric site changes the shape of the enzyme, cell chooses when to make something to pull the inhibitor out

Competitive allosteric

Changes the shape of the enzyme TOO MUCH, active site is smaller

Noncompetitive allosteric

Inhibitor interacts with the enzyme and changes its shape, but not enough so the substrate can have a reaction - molecules will INTERACT but will not REACT

Feedback inhibition

A regulatory mechanism where the end product of a pathway inhibits an enzyme that was earlier on in the chain; prevents overproduction of substances and helps maintain homeostasis

Catabolic reactions

Break molecules down into smaller and simpler ones, releasing energy in the process

Anabolic reactions

Construct larger molecules from smaller, simpler units; require energy input

Endothermic reactions

Absorb heat from surroundings, decrease in temperature; energy of products is higher than reactants (endergonic)

Exothermic reactions

Release heat into surroundings, increase of temperature in the environment; energy of products is lower than reactants (exergonic)

Plasma membrane - functions

• Boundary that separates inside of cell from its surroundings

• Selective permeability allows certain substances to pass through and not others

Fluid mosaic model

Membrane is continuously shifting/drifting with a variety of molecules attached to or embedded in it; almost everything moves

Structure of Cell membrane

• Phospholipids

• Cholesterol

• Proteins

• Oligosaccharides (identifiers)

Protein function in cell membranes

• Intercellular joining

• Enzymatic activity

• Transport (active/passive)

• Cell-cell recognition

• Anchorage/attachment

• Signal transduction

Intercellular joinings

Cells are joined together, they still are separate entities, but can collectively create things like tissues

Enzymatic activity

Molecules enter, their shape gets changed, and newly shaped molecules leave

Passive Transport

Things pass through freely - they move down a concentration gradient, types include:

• Osmosis

• Diffusion

• Facilitated diffusion