Biochemistry-Review of the BasicsAtoms

Elements

Molecule

Compound

Atomic Structure

Electron Orbits

Smallest unit of matter

Ex. Carbon atoms, Oxygen atoms etc.

Substances made up of ONLY a single type of atom

Ex. A bar of 100% pure gold would ONLY contain gold atoms

Organized based on reactivity on the Periodic Table

Elements important to Biology – C. HOPKINS CaFe

Any combination of atoms of the SAME element

Ex. O2, H2, N2,

Any combination of atoms of 2 or more elements

Ex. CO2, H2O, PO4-

Atoms contain 3 subatomic particles

Protons- + charge- found in nucleus

Neutrons- 0 charge- found in nucleus

Electrons- - charge- orbit nucleus

1st orbit- holds 2 electrons, 2nd and 3rd orbit- hold 8 electrons each

All atoms react so that their electron orbits will become full

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Biochemistry-Ions & Isotopes#'s change

Electrons

Neutrons

Protons

Sometimes atoms may gain or lose protons or neutrons

This makes them behave differently

When an atom gains or loses an electron it is called an ion

Electrons are negatively charged, so gaining an electron makes the atom MORE negative, while losing one makes it MORE positive

Ex. Ca2+ is a calcium atom that has LOST 2 electrons

An important ion in our bodies is HCO3

- which prevents our blood from becoming too acidic

Some atoms may gain neutrons (loss does not usually occur)

Since neutrons have weight, this changes the atomic weight, making them heavier

Ex, 14C is an isotope of carbon with 2 extra neutrons

Isotopes play important roles in radioactive dating and medicine

When an atom gains or loses a proton it becomes a new element

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Biochemistry-BondingChemical

Bonds

Covalent Bonds

Ionic bonds

Chemical reactions

All atoms want complete electron shells and will bond with others to get them

This is because complete shells put atoms at a low energy state

When atoms share electron pairs to complete their shells that is a Covalent Bond

Sharing only 1 pair is known as a single bond

2 pairs can be shared (double bond), as well as 3 (triple bond)

Ex. CO2, N2, O2 all use covalent bonds

Atoms may also take or donate electrons to

complete their shells

This creates ions Ex. NaCl

When 2 or more atoms bond a chemical reaction takes place

Reactants- what you start with

Products- what you end with

Coefficients- how much you have

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Biochemistry-BondingEnergy in

reactions

Exothermic Rx's

Endothermic Rx's

Making or breaking bonds requires energy

Energy is defined as the ability to do work

2 types of energy

Potential- energy that is stored, not being used Ex. a boulder at the top of a hill

Kinetic- energy that is doing work actively Ex. a boulder rolling down a hill

In chemical reactions the energy is usually provided in the form of heat

Exothermic reactions result in products with less potential energy than the reactants

As a result energy (heat) is released from the system

These reactions are able to happen spontaneously

Endothermic reactions result in products with more potential energy than the reactants

As a result, energy (heat) must be added to the system(and thereby removed from the surroundings)

These reactions do not happen spontaneously

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Biochemistry- PolymersOverview

Carbon

Polymers

The 4 major molecules that make up all organisms are carbon-based

Has 4 valence electrons and therefore can form 4 covalent bonds

Multiple bonds allows for ring, chain, & branched chain shapes

Single, double, triple bonds able to be formed

Latin for “Many parts”- long molecules of repeating subunits

Subunits called Monomers- “single part”

A.k.a. Biomolecules/Macromolecules

4 classes of polymers found in living things

Carbohydrates

Polymer- polysaccharide; monomer-monosacharride Contain C,H, &O only Ring structures Function in structure and energy storage

Animals -Plants Structure: Chitin Cellulose

Storage: Glycogen Starch

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Biochemistry-PolymersLipids

Proteins

A.k.a Fats

Polymer- triglycerides; monomers- glycerol and fatty acids

Contains C,H,O only

2 types

Saturated- no double bonds in carbon chain

Unsaturated- double bonds in carbon chain

Monounsaturated- only 1 dbl bond Poly unsaturated- 2 or more dbl bonds

Function in energy storage

Polymer- polypeptides; monomer- amino acid

Contains C,H,O, & N

Diverse functions

Enzymes-speed up chemical reactions

4 levels of structure

Primary “beads on a string”, secondary a helix or b pleated sheet

Tertiary “globular”, and quaternary of 2 or more a.a. chains combined

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Biochemistry-PolymersNucleic

Acids

Polymer- DNA/RNA; monomers- nucleotides

Contains C,H,O,N, & P

Holds heritable instructions for making proteins

Nucleotides made up of 3 parts

5- Carbon Sugar- either deoxyribose or ribose

Phosphate group (PO4)

Nitrogenous base

5 types Adenine Tyrosine Cystiene Guanine Uracil

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Biochemistry- EnzymesDefinition

How enzymes work

Inhibition

Speed of Rx

Proteins that speed up chemical reactions

Do this by lower the energy needed to

break bonds- the activation energy (Ea)

Rx's involve breaking bonds and rearranging

them into products

Takes energy to begin (Ea ), even if

the reaction is exothermic

Provide a place for reactants to meet

This “active site” stresses bonds- lowers Ea

Enzymes are specific for the molecules they

work on (the substrates)- like a lock and key

Competitive-wrong substrate in active site

Non-competitive- molecule binds to an allosteric site which causes an shape change in the enzyme so the substrate can't bind

Enzymes work best at an ideal temp and pH

The speed of the reaction also depends on the amount of enzyme or substrate present

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Biochemistry- Properties of WaterOverview

Polar Covalent Bonds

Water is unique because polar covalent bondingcauses the formation of hydrogen bonds

Oxygen is very electronegative

Electronegativity is the attraction an element has to electrons

As a result pulls electrons from hydrogen, whichcauses partial charges

O becomes slightly more negative H becomes slightly more positive Bond is still covalent but now has “poles”- hence a polar

covalent bond This results in Hydrogen-bonds

bonds between the oxygen of one H2O and the hydrogen of another

Remember opposites attract Indvidually weak but collectively strong

Hydrogen bonds lead to all of the unique properties of water

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Biochemistry- Properties of WaterHigh Specific

Heat

Cohesion/

Adhesion

Less dense as a solid

Good Solvent

Specific Heat = the energy to raise 1g of anything by 1oC

For water this amount of energy = 1 calorie

H-bonds are collectively strong so water can absorb much energy (heat) w/o a big temp change

Leads to high boiling point- keeps earth cool b/c bodies of water absorb a lot of heat without significant temperature change

Cohesion- the ability of molecules to bond with themselves

Water can H-bond with other water molecules

Leads to surface tension across bodies of water

Adhesion- the ability of molecules to bond with other molecules

Water can H-bond with any other slightly charged molecule

Leads to water “climbing” up the tubes in trees against gravity

Density- how much mass something has compared to its size

Ice floats b/c as water freezes H-bonds solidify in a crystalline pattern

Leads to air pockets between molecules and therefore less density

This allows for only the top layer of lakes/streams to freeze, protecting the life below

Bonds to and dissolves any charged thing-helps dissolve medicines & nutrients

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Biochemistry- pHOverview

pH Scale

Definitions & Logic

How acidic or basic a chemical is is measured by the pH scale

A logarithmic scale (multiples of 10) that ranges from 0-14

0 is most acidic 7 is neutral 14 is most basic (alkaline)

Because the scale is logarithmic, a pH of 6 would be 10 times more acidic than a pH of 7. Conversely, a pH of 7 is 10 times more basic than a pH of 6.

5 would be 100 times more acidic than 7, 4 1000x and so on

Acidity is measured in how many H+ ions are formed when a chemical mixes with water

Acids form more H+ ions than Bases

The more H+ ions formed, the stronger then acid.

Ex. pH 12 forms 10x more H+ ions than pH 13 and is therefore 10x more acidic

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The pH Scale

Don’t draw

Biochemistry-Review of the BasicsAtoms

Elements

Molecule

Compound

Atomic Structure

Electron Orbits

When #'s

Smallest unit of matter

ONLY 1 type of atom

C. HOPKINS CaFe

2+ atoms of SAME element

2+ atoms of DIFF elements

3 subatomic particles

Protons- + - nucleus- 1amu

Neutrons- 0 – nucleus- 1amu

Electrons- - - orbits- Ø mass

1st - 2

2Nd - 8

3rd - 8

Atoms want orbits full

Electrons → ions; + lost, - gained ( Ca2+ )

Neutrons → isotopes (14C)

V. useful

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Biochemistry-BondingChemical

Bonds

Covalent Bonds

Ionic bonds

Chemical Rx's

Energy in reactions

Exothermic Rx's

Endothermic Rx's

All want complete electron shells-bond to get them

Complete shells=low energy state

Share electrons

1 pair = single bond, 2=double, 3=triple

Take or donate electrons

Creates ions

Bonds require a chemical reaction

= heat (ability to work)

Potential (in bonds) vs. Kinetic (released)

Energy of products < reactants

Spontaneous- releases heat

Energy of products > reactants

Non-spontaneous- consumes heat

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Biochemistry- PolymersOverview

Carbon

Polymers

All org's C-based (organic)

4 poss. bonds

Rings, chains, branched chains

Single, double, triple bonds

“Many parts”

Monomer subunits

A.k.a. Biomolecules/Macromolecules

4 classes

Carbohydrates (polysaccharides)- monomer (monosachharides)

C.H.O only- fnx in structure/energy Plants- cellulose/starch Animals- chitin/glycogen

Fats/Lipids (triglycerides)- monomer (fatty acids/glycerol)

CHO only- fnx in energy Saturated- Ø dbl bonds Unsaturated- >/= 1 dbl bond

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Biochemistry- PolymersPolymers Proteins: polymer (polypeptides)- monomer (amino acids)

C,H,O, N, P, S

20 a.a's

Most diverse fnx's-made via DNA

Enzymes-speed Rx's 4 levels of structure

1o- “Beads on a string”- Peptide bonds 2o- helix or pleated sheet 3o- “globular” 4o- >/+ 1 polypeptide (Not all)

Nucleic Acids: polymer (DNA/RNA)- monomer (nucleotides)

C,N,O, N, P

Genetic info- makes proteins

Nucleotide parts

Sugar Phosphate N-Base (A,T,G,C,U)

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Biochemistry- EnzymesDefinition

Metabolism

How enzymes work

Inhibition

Regulation

Speed of Rx

Proteins-facilitate Rx's

Lower Ea

Sum of Rx's in org

Rx's break bonds and rearrange

Takes E to begin (Ea ), even if Rx exotherm.

Place for reactants

Stresses bonds- lowers Ea

Specific- lock and key

Competitive-wrong key in active site

Non-competitive-allosteric site → shape

Negative- product blocks active site

Positive- product is coenzyme/cofactor

Depends on:

Temp -Amnt substrate

pH -Amnt enzyme

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Biochemistry- Properties of WaterOverview

Polar Covalent Bonds

Properties

Water unique b/c polar covalent bonding

O v. electronegative

Pulls e-'s unequally → Partial charges

Results in H-bonds → unique properties

High specific heat → High boiling pt

S.H. = E to raise 1g by 1oC = 1 Calorie

High heat of vaporization → evap cooling

HoV = E to vaporize 1g

Cohesion/Adhesion → Surface tension &

Rise against gravity

Less dense as a solid → Insulation of lakes/streams

Good solvent → medicine

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Biochemistry- pHOverview

pH Scale

Definitions & Logic

Acidity/Alkalinity- pH scale measures

Logarithmic scale -0-14

0 most acidic 7 neutral 14 most basic (alkaline)

Acidity measured by H+ ions formed w/water

Acids form more H+

The more H+ ions formed, the stronger then acid.

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The pH Scale

Don’t draw