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BIOCHEMISTRY REVIEW
Water, carbon and more….
About 25 elements are essential for life
Four elements make up 96% of living
matter: • carbon (C)
• hydrogen (H)
• oxygen (O)
•nitrogen (N)
Four elements make up most of
remaining 4%:
• phosphorus (P)
• calcium (Ca)
• sulfur (S)
• potassium (K)
Weak bonds
hydrogen bonds
attraction between + and –
hydrophobic & hydrophilic interactions
interaction with H2O
van derWaals forces
(ionic)
Strong bonds
covalent bonds
–
–
H2 (hydrogen gas)
Why are covalent bonds
strong bonds?
two atoms share a pair
of electrons
both atoms holding
onto the electrons
very stable
Forms molecules
H
Oxygen
H
H2O molecules form H-bonds
with each other
+H attracted to –O
creates a
sticky molecule
Special properties of water
1. cohesion & adhesion
surface tension, capillary action
2. good solvent
many molecules dissolve in H2O
hydrophilic vs. hydrophobic
3. lower density as a solid
ice floats!
4. high specific heat
water stores heat
5. high heat of vaporization
heats & cools slowly
Cohesion
H bonding between H2O
molecules
water is “sticky”
surface tension
drinking straw
Adhesion
H bonding between H2O &
other substances
capillary action
meniscus
water climbs up
paper towel or cloth
Polarity makes H2O a good solvent
polar H2O molecules surround +
& – ions
solvents dissolve solutes
creating solutions
Most (all?) substances are more dense
when they are solid, but
not water…
Ice floats!
H bonds form a crystal
H2O resists changes in temperature
high specific heat
takes a lot to heat it up
takes a lot to cool it down
H2O moderates temperatures on Earth
H+ Ion
Concentration
pH
Examples of Solutions
100
0
10–1
1
10–2
2
Stomach acid, Lemon juice
10–3
3
Vinegar, cola, beer
10–4
4
Tomatoes
10–5
5
Black coffee, Rainwater
10–6
6
Urine, Saliva
10–7
7
Pure water, Blood
10–8
8
Seawater
10–9
9
Baking soda
10–10
10
Great Salt Lake
10–11
11
Household ammonia
10–12
12
Household bleach
10–13
13
Oven cleaner
10–14
14
Sodium hydroxide
Hydrochloric acid
pH
pH of cells must be kept ~7
pH affects shape of molecules
shape of molecules affect function
pH affects cellular function
Control pH by buffers
reservoir of H+
donate H+ when
9
[H+] falls
8
absorb H+ when
7
[H+] rises
6
5
Buffering
range
4
3
2
1
0
0
1
2
3
4
Amount of base added
5
All of life is built on carbon
Cells
~72% H2O
~25% carbon compounds
carbohydrates
lipids
proteins
nucleic acids
~3% salts
Na, Cl, K…
HYDROCARBONS
Combinations of C & H
non-polar
not soluble in H2O
hydrophobic
stable
very little attraction
between molecules
a gas at room temperature
METHANE
Simplest
hydrocarbon
FUNCTIONAL GROUPS
Parts of organic molecules that are involved
in chemical reactions
give organic molecules distinctive
properties
hydroxyl
amino
carbonyl
sulfhydryl
carboxyl
phosphate
Affect reactivity
makes hydrocarbons hydrophilic
increase solubility in water
Basic structure of male & female
hormones is identical
identical carbon skeleton
attachment of different functional
groups
interact with different targets in the
body
different effects
January 17, 2014
Guided Reading due Monday
Get ready for QQ
POLYMERS
• Long molecules built by linking repeating
building blocks in a chain
– monomers
• building blocks
• repeated small units
– covalent bonds
H 2O
HO
HO
H HO
H
H
Dehydration Synthesis-
HOW TO BUILD A POLYMER
• Synthesis
– joins monomers by “taking” H2O out
• one monomer donates OH–
• other monomer donates H+
• together these form H2O
– requires energy & enzymes
H 2O
DEHYDRATION
SYNTHESIS
HO
HO
H HO
H
H
HOW TO BREAK DOWN A
POLYMER
• Digestion
– use H2O to breakdown polymers
• reverse of dehydration synthesis
• cleave off one monomer at a time
• H2O is split into H+ and OH–
– H+ & OH– attach to ends
– requires enzymes
– releases energy
H2O
HO
HO
HYDROLYSIS
H
H HO
H
CARBOHYDRATES
• Structure / monomer
– monosaccharide
• Function
– energy
– raw materials
– energy storage
– structural compounds
• Examples
– glucose, starch, cellulose, glycogen
CH2OH
H
O
H
OH
H
HO
H
OH
CH2OH
O
H
H
OH
Glucose
HO
H
O
C
H
HO
OH
H
H
C
OH
Ribose
H
C
OH
H
H
Glyceraldehyde
GLUCOSE + GLUCOSE  MALTOSE
GLUCOSE + FRUCTOSE  SUCROSE
POLYSACCHARIDES
• Polymers of sugars
– costs little energy to build
– easily reversible = release energy
Glycogen-glucagon-glycogenolysis;
How are these terms related to each other?
LIPIDS
• Structure / building block
– glycerol, fatty acid, cholesterol, H-C chains
• Function
– energy storage
– membranes
– hormones
• Examples
– fat, phospholipids, steroids
STEROIDS
PROTEINS
• Structure / monomer
– amino acids
– levels of structure
• Function
– enzymes
– transport
– signals
-defense
-structure
-receptors
• Examples
– digestive enzymes, membrane channels, insulin, actin
Structure
central carbon
amino group
carboxyl group (acid)
R group (side chain)
variable group
different for each amino acid
confers unique chemical properties to each
amino acid
like 20 different letters of an alphabet
can make many words (proteins)
PROTEIN STRUCTURE
• Function depends on structure
– 3-D structure
• twisted, folded, coiled into unique shape
PRIMARY STRUCTURE
– slight change in amino acid sequence can
affect protein’s structure & its function
• even just one amino acid change can make all the
difference!
– amino acid sequence determined by gene
(DNA)
IS PRIMARY STRUCTURE
IMPORTANT?
SECONDARY STRUCTURE
TERTIARY STRUCTURE
QUATERNARY STRUCTURE
NUCLEIC ACIDS
• Function:
– genetic material
• stores information
– genes
– blueprint for building proteins
» DNA  RNA  proteins
• transfers information
– blueprint for new cells
– blueprint for next generation
G
C
T
A
A
C
G
T
A
C
G
T
A
Examples:
RNA (ribonucleic acid)
single helix
DNA (deoxyribonucleic acid)
double helix
Structure:
monomers = nucleotides
• 3 parts
NUCLEOTIDES
– nitrogen base (CN ring)
– pentose sugar
(5C)
• ribose in RNA
• deoxyribose in
DNA
– phosphate (PO4)
group
2 types of nucleotides
different nitrogen bases
purines
double ring N base
adenine (A)
guanine (G)
pyrimidines
single ring N base
cytosine (C)
thymine (T)
uracil (U)
NUCLEIC POLYMER
• Backbone
– sugar to PO4 bond
– phosphodiester bond
• new base added to sugar of previous base
• polymer grows in one direction
– N bases hang off the
sugar-phosphate backbone
Nucleotides bond between
DNA strands
H bonds
purine :: pyrimidine
A :: T
2 H bonds
G :: C
3 H bonds
DNA DOUBLE HELIX
• Double helix
– H bonds between bases join the 2 strands
• A :: T
• C :: G
DNA REPLICATION
“It has not escaped our notice that the specific pairing
we have postulated immediately suggests a possible
copying mechanism for the genetic material.”
James Watson
Francis Crick
1953