Biochemistry Chapter 3. Biochemistry Water Review 3-1 Carbon Compounds3-2 Molecules of Life.
Biochemistry-Review of the Basics
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Transcript of Biochemistry-Review of the Basics
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