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Importance of Water in Biochemistry

Chapter 2 discusses the essential properties of water for life, including its stable temperature, ability to dissolve materials, and interactions with biomolecules, which drive processes like the hydrophobic effect and biochemical reactions. Chapter 3 focuses on amino acids as building blocks of proteins, their various functions, and how their structure and sequence influence protein functionality. It highlights the importance of non-covalent interactions in maintaining protein structure and the limitations imposed by evolution and synthesis capabilities.

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6 views13 pages

Importance of Water in Biochemistry

Chapter 2 discusses the essential properties of water for life, including its stable temperature, ability to dissolve materials, and interactions with biomolecules, which drive processes like the hydrophobic effect and biochemical reactions. Chapter 3 focuses on amino acids as building blocks of proteins, their various functions, and how their structure and sequence influence protein functionality. It highlights the importance of non-covalent interactions in maintaining protein structure and the limitations imposed by evolution and synthesis capabilities.

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jenniferyang1029
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We take content rights seriously. If you suspect this is your content, claim it here.
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Chapter 2: Water

Liquid water is essential for life because:


1.​ Has stable temperature
a.​ High heat capacity
b.​ Large heat of fusion
c.​ Large heat of vaporization
2.​ Stability of state (liquid)
a.​ Large liquid range
b.​ Floating ice insulates water below (glaciers), large bodies an stay liquid
3.​ Dissolved materials
a.​ Good solvent
b.​ Protic, amphoteric

Water has only H-bonds


Water has 2 H-bond donors and 2 acceptors

Water interactions with biomolecules:


-​ Water dissolves polar and ionic compounds
-​ Adds richness, hinders access
-​ Water forms electrostatic or H-bonding interactions with polar & ionic groups
-​ Stabilizes structure, link interactors
-​ Water pushes nonpolar compounds together
-​ Creates ‘order’

Hydrophobic effect driven by changes in entropy


-​ Water entropy is major contributor to hydrophobic effect
Water participates in biochemical reactions
-​ ATP hydrolysis drives muscle contraction
-​ Proteins and polysaccharides are hydrolyzed into component amino acids or sugars
-​ Water adds to alkenes to form alcohols
-​ Ex. fumarase reaction of citric acid cycle

Buffer region: slow rise in pH when titrating weak acid with strong base
Some weak acids (like amino acids) are polyprotic acid can buffer over multiple pH ranges
Isoelectric point (pI): pH of highest ocurrence of zero charge state and pH at which average
charge on molecules is zero
-​ pI = (pKa1 + pka2)/2
Chapter 3: Amino acids
Functions:
1.​ Subunits (building blocks) of peptides and proteins
2.​ Neurotranmitters
3.​ Metabolic intermediates

Proteins are made from 20 alpha-amino acids


Amino acids pKa vary because of attached functional groups (microenvironment influences
acidity)
Nonpolar/neutral: Grandma Always Visits London In May For Winston Churchill’s Party

Polar/Neutral: Santa’s Team Darns New Quilts Every Year

Polar/+ Charged: Really Happy Kittens

Polar/- Charged: Don’t Eat


Protein-folded, functional polypeptide (not just any polymer of amino acids)
Proteins vary in size and number of chains, as well as compositions (what amino acids it’s made
of)

Many possibilities in variability because of:


-​ Variation in chain length
-​ Variation in number of chains
-​ Protein modifications
-​ Binding of prosthetic groups

Realistic limitations:
-​ Length limited by ability and fidelity of synthesis
-​ Parameters limited by usefulness, does it fold? Useful?
-​ Parameters of natural proteins limited by evolution, did nature find useful?

Protein’s function derives from its structure, and its structure is determined by its
sequence, structure determiend by sequence
-​ Properties of amino acids determine which can interact and how
-​ Connectivity (sequence) limits possible interactions and dictates positions of polypeptide
chain

Non-covalent interactions and reversible bonds are important in structure of proteins


1.​ Electrostatic interactions
a.​ Ionic interactions (aka ion pairs or salt bridges)
b.​ H bonds
c.​ Van der Waals forces
2.​ Other interactions
a.​ Hydrophobic effect
b.​ Disulfide bonds

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