Biochemistry

Covalent Bonds

Covalent Bonds

• Sharing of valance electrons by 2 atoms

• Strongest bond

• form molecules in cell

  • Single Cov → sharing 1 pair of electrons

  • Double Cov → sharing 2 pairs of electrons

• Polar & Non-polar Cov Bonds

Polar Covalent Bonds

Unequal sharing of electrons in the cov. bond

Electronegative Atom

Has a strong pull on electrons

Non-Polar Covalent Bond

Equal sharing of electrons in cov. bond

Ionic Bond

Transfer of electrons from 1 atom to another → causes both atoms to have a charge

Cation

Pos Atom in ionic bond

Anion

Neg Atom in Ionic bond

Ion

Just a charged atom

Weaker Bonds

1. reenforce shape of large molecules

2. help molecules adhere to each other

3. allow for temporary interactions

Hydrogen Bonds

• form when H is cov. bonded to one atom and then is also attracted to another electroneg. atom

• ex: H on H20 is attracted to O on another H2o molecule

Water

• all living orgs. need water

• cell = 70-95% water

• water is a polar molecule

  • able to h-bond with other polar molecules

4 emergent properties of water:

1. Cohesion & Adhesion

2. Temp Moderation

3. Expansion Upon Freezing

4. Versatility as a solvent

Cohesion & Adhesion

Cohesion: H2O molecules stick to each other thru h-bonding

Adhesion: H2O molecules sticking to other polar molecules thru h-bonding

Both contribute to surface tension

Surface Tension

• how hard it is to break the surface of a liquid

• Connect to cohesion and adhesion

Temp. Moderation

• water has a ^ specific heat

  • measure of how well a substance resists a change in temp (when it absorbs/ releases heat)

• water resists a change in it’s temp

• ex: biological relevance: bodies of water have stable temps

  • allows for the health of species that live there

  • milder climate

Expansion upon Freezing

• ice is ~10% less dense than water

• ice floats on top of water

• as liquid, water’s h-bonds are irregular/unstable

• as solid, water’s h-bonds are stable/organized so h2o expands as it freezes

Versatile Solvent

• like dissolves like

• H20 is polar

• water can dissolve other polar substances

Hydrophillic

• water-loving

• affinity for H2O

• polar/charged particles/molecules, sodium chloride

Hydrophobic

• water fearing

• repels water

• ex: non-polar, non-ionic

• Oil

pH scale

• relative concentration of H ions

• Acids < 7, excess of H

• Bases > 7, excess of OH

• Neutral = 7

Physiological pH

7.4

Carbon Chem/ Orgo

• Carbon can form macromolecules

• Tetravalent

• Major partners = (C, H, O, N)

Macromolecules

• diverse, large, and complex molecules

• C forms

• Carbs

• Nucleic Acids

• Protein

• lipids

Tetravalent

• 4 valance electrons

• can form 4 cov. bonds

• ex: C

Hydrocarbons

• non-polar, hydrophobic

• molecules made up of H & C

• in living things, in lipids

Functional Groups

• 6 groups

• components of macromolecule involved in chemical rxns

• ex: phosphate

Polymer

• large molecules composed of building blocks called monomers

• 3 macromolecules are polymers

Monomer

• cov. linked to form polymers

Synthesis

• to make something

Dehydration Synthesis

• allows the formation of polymers

• h20 is taken away & a new cov. bond is left in its place

• how monomers are added to make polymers

Hydrolysis Rxns

• reverse of dehydration synthesis

• breaking w/ water

• breaking apart polymers into monomers

• h20 is added, breaks cov. bond b/w monomer & polymer chain

Carbs

• monomers = monosaccharides

• molecular formula is usually multiple of CH2O

• Sugars -ose

• 2 monosaccharides → disaccharides

  • covalent bond = glycosidic linkage

  • b/w two monosaccs.

• 3 or more monosaccs. → produces polysaccharides

Monosaccharides

Monomers of Carbs

Disaccharides

2 or more monosaccharides

Polysaccharides

• 3 or more monosaccharides

• Glycogen

• Chitin

• Starch

• Cellulose

Glycosidic Linkage

Covalent bond between monosaccharides

Glycogen

• Animal: Energy Storage

• helical shape

• stored in liver & muscles

Chitin

• Animal: Structural

• linear shape

• exoskeleton of arthropods

• ex: surgical thread

Starch

• Plant: enegry storage

• helical shape

• store starch in chloroplasts

*plants access energy by breaking down starch

Cellulose

• Plant Structure

• linear

• straight form string building material

• major compound of plant cells

Proteins

• macromolecules

• have diverse fxns

• do all jobs in the cell

• Made of amino acids and polypeptides

Amino Acids

monomer of proteins

20 types

Polypeptide

polymer of protein

Peptide Bond

cov. bond b/w monomers

R group

• part of the a.a that is different from 1 a.a to another

• connected to main carbon

Primary Structure

• sequence of a.a monomers

• held together by peptide bonds (strong bonds)

Secondary Structure

• coils and folds in the polypeptide

• result from h-bonding

Tertiary Structure

• caused by interactions b/w R groups of the a.a’s

• Every protein has tertiary, secondary, and primary structure

Quaternary Structure

• only found in proteins made of multiple polypeptides

• 2 or more polypeptides

Denaturation

• loss of protein shape ( 2nd, 3rd, & 4th structure)

• denatured protein = biologically inactive ( loses function)

• 1st structure is not effected b/c it is held together by cov. bonds

• Causes:

  • extreme pH

  • high temps

  • high salinity

Renaturation

• protein gaining shape & function again

Nucleic Acids

• DNA & RNA

RNA

• ribonucleic acid

• Monomers: A, G, C, U

• Sugar: Ribose

DNA

• Deoxyribonucleic acid

• genetic code

• directs the synthesis of proteins

• Letters: A, G, C, T

• Pentose: deoxyribose

Nucleotide

Monomer of nucleic acids

Polynucleotide

Polymer of nucleic acids

Phosphodiester Linkage

Cov. bond b/w monomers

Lipids

• do not form polymers

• mainly hydrocarbons

• most important:

  • fats

  • phospholipids

  • steroids

Fats (Triglycerides/triglycerals)

• 3-carbon molecule w/ hydroxyl group attached to each carbon

• 3 fatty acids = carboxyl group + hydrocarbon (16-18 carbons)

• fatty acids attached to glycerol thru dehydration syn.

• major function = energy storage

• Sat & UnSat

Phospholipids

• Phosphate -

• made up pf glycerol + 2 F.A + 1 P

• F.A = hydrophobic

• P = hydrophilic

Steroids

• carbon stack w/ 4 fused rings and functional groups attached

Ester Linkage

Cov. bond b/w lipids

Saturated Fats

• saturated w/ H

• no double bonds b/w carbon

• solid at room temp

• animal fats

Unsaturated Fat

• “unsaturated with H”

• 1 or more double bonds w/ carbon

• oils

• liquid at room temp

• * double bond prevents tight packing of molecules

Metabolism

Metabolic Pathway

Catalyze

Catabolic

Anabolic

Non-Spontaneous

• requires input of energy

• cannot

Spontaneous

• occur w/o input of energy

• can be fast or slow

Free Energy (G)

• potential energy that can do work in a cell

• Change in G for a rxn = G final - G initial

• Rxns w/ a - Change in G are spontaneous

• rxns w/ a + change in G are non-spontaneous/anabolic/endergonic

Exergonic

• - Change in free eneergy (G)

• release G (used to do work in the cell)

• Exergonic / Catabolic / Spontaneous

Endergonic

• consume/ Use G

• Store G in molecules

• Endergonic / Non-Spontaneous / Anabolic

Mechanical Work

Physical change

Transport Work

Moving substances across membrane

Chemical Work

Ex: Synthesis of polymers

ATP

• Energy molecules

• Hydrolysis rxn breaks a p-p cov bod

  • G is released

  • products are ADP + P

• Renewable resource

• Energy Intermediate

  • stores potential energy

  • provides G for cellular work

Energy Coupling

exergonic process drives endergonic process