BMSC 200 Midterm 1

Definition of Biochem

Study of life at a molecular level and the application of the principles of chemistry to explain biology

What are the 4 Major classes of biomolecules?

1. Proteins

2. Nucleic Acids

3. Lipids

4. Carbohydrates

Does the considerable difference in all living life mean they are different molecularly?

All organisms are remarkably uniform at a molecular level

What do all organisms use?

Common building blocks to create common biomolecules (nucleic acids, proteins, polysaccharides, and lipids)

4 Different Foundations of Life

1. Chemical

2. Energy

3. Genetic

4. Evolutionary

What are the four main elements that compose around 98% of most organisms?

Carbon

Oxygen

Hydrogen

Nitrogen

What are all known life forms based from?

Carbon

How many people could naturally occuring nitrogen in the world feed?

4 Billion

Who was able to get "bread from air" using nitrogen from the air as fertilizer

Fritz Haber

How much is a human worth?

-Chemically only less than a dollar

-Looking at the chemical components like tissues, organs, and biomolecules have an estimated value of $45 000 000

What is the next best candidate as the chemical foundation of life?

Silicon

Why does Carbon work better than Silicon?

-C-C bonds are stronger than S-S bonds

-C-C bonds release more energy on combustion than S-S bonds

-Combustion of C-C bonds are soluble and remain active in biosphere

What do functional groups determine?

The collective properties of functional groups determine the structure, function, and propeties of the biomolecule

What does understanding the structure-function relationship of biomolecules help predict?

Molecular function, complex biology, and rational development of treatments

Conformation

Flexible spatial arrangment of atoms within a molecule (changeable without breaking bonds)

Configuration

Fixed spatial arrangement of atoms with a molecule (Not changeable unless covalent bond is broken)

-Conferredby either double bonds or chiral centers

Geometric Isomers

(Cis-trans) Same chemical formula but different configuration of groups attached to a non-rotating double bond

Cis

Same side of double bond

Trans

Opposite side of double bond

Chiral Carbon

4 different substituents attach to a single carbon that can be arranged differently in space creating 2 stereoisomers

Construction

Biomolecules are often constructed from one stereoisomer

Interactions

Interactions between biomolecules, as well as between biomolecules and small molecules, are stereospecific

Simplicity

Simple, conserved reactions for synthesis and degradation

What do chemical synthesis of molecules with asymmettric carbons create?

A mixture of all chiral forms

-Each form can have different effects

4 Major Classes of Biomolecules

1. Protein

2. Carbohydrates

3. Nucleic Acids

4. Lipids

The Case of Thalidomide

Ex. chemical synthesis of molecules created a different mix of chiral forms

-One helped with nausea and the other caused birth defects

-Dr. Francis Kelsey a reviewer from the FDA denied the drug

3 Biological Polymers

1. Simplicity- Simple, conserved reactions for synthesis and degration

2. Recycling-Biomolecules can be digested back to component building blocks which are reusable

3. Diversity- Molecules of incredible complexity can be generated

Proteins

-Linear polymers of aminoacids

-20 different amino acids

-Amino acids link into chains that create complex patterns with distinctly different purposes (proteins)

Polysaccharides

-Carbohydrate

-Monosaccharides that are linked together to form a polymer

-Serve biological roles like structure, energy storage, and cellular recognition

Nucleic Acids

-Linear polymers of nucleotide building blocks

-5 "building blocks"

Lipids

Lipids are aggregates of "building blocks"

-Serve in energy storage, formation of membranes, and signalling

Prokaryotes

-Small single cell organism

-Growth is rapid allowing quick adaptation

-Single compartment , the nucleoid

Eukaryotes

Large complex cells

-Make up multi-cellular organisms

-Contain organelles

Around how many prokaryotic and eukaryotic cells are in your body?

30 trillion eukaryotic cells and 100 trillion prokaryotic cells

What does bacteria in the gut do?

Bacteria in the gut helps digest foo and maintain a functional immune system

What does Microflora in the gut do?

Impacts health

-Depression, anxiety, obesity, and intelligence

"some people are calling the gut the second brain" - Scott Napper

Are bacteria friends?

Yes, bacteria are my friends

Vitro

Studies the behaviour of molecules outside the context of the cell and or organism (in glass)

Vivo

Studies that occur within the cell or organism (in the living)

First Law of Thermodynamics

Energy can be transferred and transformed, but it cannot be created or destroyed.

Second Law of Thermodynamics

Nature has a tendency toward greater total entropy of the universe as it continually increases

Gibbs Free Energy Theory

Energy changes during chemical reactions

-Free energy can be defind in terms of:

Enthalpy- # and kinds of bonds Entropy- Degree of randomness Temperature-In Kelvin

G = H - TS

G > 0 = endergonic

G < 0 = exergonic (spontaneous)

G = 0 = equilibrium

Enthalpy (H)

Reflects the number and kinds of bonds

Entropy (S)

The degree of randomness

Temperature

Degrees Kelvin

Energy Coupling

Cells thermodynamically drive unfavourable ractions by couply endergonic(energy requiring) and exergonic reactions (energy releasing)

ATP in Metabolism

-Serves as an energy currency

-ATP serves as the link between catabolic reactions and anabolic reactions

Steps of Replication

1. DNA undergoes transcription

2. RNA undergoes translation

3. Results in a protein

Nucleotide Sequence

Dictates the sequence of amino acids added into a protein

What does amino acid sequence do?

Dictates proteins structure

Water

-Abundant molecule in living organisms

-Both passive and active roles

Passive Role of Water

Structure of biomolecules forms in response to interactions with water

Active Role of Water

Water is a participant in many biochemical reactions

What gives water a permanent dipole?

Oxygen is more electronegative than hydrogen

-Forms electrostatic interactions

-Forms hydrogen bonds

What can random changes in genotypes do?

Can change the phenotype that can lead to an advantage or disadvantage for the organism

(Evolution)

What is the basic unit of DNA?

Two complimentary strands

-Each strand is a linear polymer of 4 types of building blocks

What is the most abundant molecule in living organisms?

Water

Passive Water Molecule

Structure of biomolecules forms in response to interaction with water

Active Water Molecule

Water is a participant in biochemical reactions

Alternate liquids that could support life

Ammonia and Formamide

What does the dipole of a water molecule influence?

-Forms electrostatic interactions with charged molecules

-Forms hydrogen bonds

What can both Oxygens and nitrogens serve as?

Hydrogen bond donors and acceptors

How strong is a hydrogen bond relative to a covalent bond?

5% the strength of a covalent bond

What does the strength of a hydrogen bond depend on?

its geometry

-anti-parallel beta sheets more stable than parallel

How many hydrogen bonds can a water molecule form?

4- 2 as a donor and 2 as an acceptor

In water water is the average hydrogen bond per molecule?

3.4 "flickering cluster"

What can influence the properties of water?

Great internal cohesion between water molecules and hydrogen bonds

Heat Vaporization

The amount of heat required to vaporize a liquid at its boiling point

Specific Heat Capacity

The amount of heat required to raise the temp of a substance by one degree

Unusual Properties of Water

When in solid form the arrangement of ice has a lower density than liquid water making ice float

-Water has a higher melting, and boiling point

Polywater

Form of water with higher boiling point, lower freezing point, and higher viscosity

-Fear it could be weaponized

Electrostatic Interactions

Molecules interact with charged solutes through formation of payers of hydration

-Small size and permanent dipole makes water great in interacting both positively and negatively charged ions

-Water shields charged groups and diminishes strength

Molecule Solubility in water

Hydrophilic = molecules polar

Hydrophobic = molecules non-polar

Amphipathic = both hydrophobic and hydrophilic portions (most molecules)

What do non-covalent interactions enable?

-Transient, dynamic interactions

-Flexibility, formation of structure and function

-Binding of reactants to enzymes

-Recognition between molecules

Non-covalent Interactions Include

1. Hydrogen bonds

2. Ionic interactions

3. Hydrophobic interactions

4. Van Der Waals interactions

What are Hydrogen bonds critical for?

Specificity of biomolecular interactions not for the formation of biomulecular structures

Van Der Waals Forces

Interaction between permanent and induced dipoles (short range, low magnitude interactions

-When two surfaces come together a large # of atoms are brought into VDW contact

-Abundant in the core of folded proteins

Hydrophobic Effect

Drive to have polar groups interactin with water and non-polar regions shielded away from it

-Proteins fold to make this happen

What does the folding of a polypeptide do?

Decreases entropy of polypeptide but increases the entropy of the associated water

What is the ion product of water?

Kw

ph = ?

the difference of 1 pH unit equals a 10-fold difference in H+

Which acids and bases dissociate completely in water?

Strong acids and bases

Amphipathic Molecules

Hydrophilic regions interact with water but hydrophobic regions cluster together presenting the smallest surface to water

Which acids and bases do not dissociate completely in water?

Weak acids and bases

-Dissociation can be quantified

pKa =?

-log Ka

What happens when pH = pKa

Solution is best able to resist changes in pH

Stronge acid = ____pKa

Low

Peptide bonds

Covalent linkages between carboxyl group of one AA and amino group of another

How do peptide bonds form?

Condensationg reaction involving generation of a water molecule

Repeating pattern of Polypeptide main chain

NCCNCC

Primary Structure

Linear sequence of Amino Acids

-Info for specifying correct folding contained here

Secondary Structure

Localized interactions within a polypeptide

-Maintained by hydrogen bonds between main chain amide and carbonyl groups

-Peptide bond has both hydrogen bond acceptors and donors

-Is favoured

Tertiary Structure

Final folding pattern of a single polypeptide

-Amino Acid sequence determines tertiary structure

Quaternary Structure

Folding pattern when multiple polypeptides are involved

-Help facilitate unique dynamic combinations of structure/function

Amino Acids

The building blocks of proteins

Phi and Psi

Can range from -180 to 180

Simplicity of Chemistry

One reaction for polymerization the other for degradation

Recycling

Biomolecules can be digested into reusable building blocks

Henserson-Hasselbalch Equation

1. Relationship of the pH of the solution

2. The pKa of the weak acid

3. Relative concentrations of the weak acid and conjugate base

Diversity

Potential for vast # of molecules of different lengths and sequences