Quiz 1

Intersection

Definition of Biochemistry

• The ________ of Biology and Chemistry

  • The molecules and mechanims of living things

  • Describes in molecular terms the structures, mechanism and chemical processes shared by living things.

  • Provides insights and practical applications to medicine, agriculture, nutrition and industry

    • How molecules affect living things!

Fundamental Principles

Foundations in Biochemistry → _______

• Cellular

• Chemical

• Physical

• Genetic

• Evolution

Hierarchy

Cellular Foundations → Cells are the Fundamental Units of Life

• There is a _______ of organization to living things

• At each level of organization, novel properties emerge.

• Life is an emergent property of cells.

• Living organisms have common characteristics

  • Organization

  • The expression and transmission of genetic information

  • The transfer and transformation of energy and matter

  • Interactions

  • Evolution - conservation and diversity

Bacteria

Phylogeny of the Three Domains of Life (associated with different types of cells)

• ___________: inhabit soils, surface waters, and the tissues of other living or decaying organisms → Prokaryotic cells

Archaea

Phylogeny of the Three Domains of Life (associated with different types of cells)

• ___________: inhabit extreme enviornments. More similar to Eukarya

Eukarya

Phylogeny of the Three Domains of Life (associated with different types of cells)

• ___________: All eukaryotic organisms

Organelles

Prokarytoic and Eukaryotic Cells

• All Cells Contain…

  • DNA

  • Ribosomes

  • Cytosol (Cytoplasm)

  • Plasma (cell) membrane

Bacteria/Prokaryotic Cells have no membrane bound _____

nucleus

Prokaryotic and Eukaryotic Cells

• Eukaryotic Cells - DNA in a membrane bound ______ with other membrane bound organelles

Diffusion

Cellular Dimensions are limited by ______

• Cells are microscopic

  • 5 to 100um in diameter (Eukaryotic cells are typically larger)

  • unicellular microorganisms: 1 to 2 um long

• Upper limit cell size is likely set by the rate of diffusion and the need to deliver O2 to all parts of the cell

  • as size increase, surface to volume ration decreases, many animal cells have highly folded or convoluted surfaces

• Actin Filaments

• Microtubules

• Intermediate Filaments

The Cytoskeleton of the Cell (Structure of the Cell)

• Protein filaments form a meshwork → Dynamic

• 3 types:

  • ______ - 6nm width, made from G-actin (interact with each other)

  • _______- 23nm width, made from tubulin (largest)

  • _______- 10nm width, made from alpha-keratin

noncovalently

Cytoskeleton Protein Filaments

• Structure: each filament is composed of protein monomers bound _________ to form a long polymer.

Cell Division

Cytoskeleton Protein Filaments

• Function: provide shape and organization, as well as helping cells and organelles move

  • Important for _____ - cytoskeleton reorganizes cellular componenets to be divided between daughters

• Supramolecular

• Noncovalent Interactions

Cells Build ______ Structures

• Cells use a small set of carbon-based metabolites to create

  • Polymeric machines

  • Supramolecular structures

  • information repositories

• Held together by ________

  • Hydrogen bonds

  • Ionic interactions

  • Van der Waals interactions

  • The hydrophobic effect

Nucleic Acids

Nucleic Acid Macromolecules

• ________ = DNA and RNA = polymers of nucleotides

  • Store and transmit genetic information

  • Some RNA molcules have structural and catalytic roles in supramolecular complexes

  • Phosphate → sugar → base covalently bonded together

Non-covalent

Nucleic Acid Macromolecules

• Nucleic Acid interactions are ______

Intramolecular (of nucleic acid) = covalent

Intermoleculer (between two nucleic acids) = noncovalent H-bond

• Genome

• Genomics

Nucleic Acid Macromolecules

• ______ = entire sequence of a cells DNA or RNA

• _______ = the characterization of the structure, function, evolution and mapping of genomes

Proteins

Protein Macromolecules

• __________ - long polymers of amino acids

  • Can function as enzymes, structural elements, signal receptors, transporters

  • Covalently linked, can fold to secondary structure to form a B-sheet or a- helix

• Proteome

• Proteomics

Protein Macromolecules

• ______- sum of all the proteins functioning in a cell

• _____- the systematic characterization of this protein complement under a specific set of conditions

Simple Sugars

Polysaccharide Macromolecules

• Polysaccharides = polymers of ________

  • energy rich fuel stores

  • rigid structural components of cell walls (in plants and bacteria)

  • extracellular recognition elements that bind to proteins on other cells

• Glycome = entire complement of carbohydrate-containing molecules in a cell

hydrocarbon

Lipid Molecules

• Lipids - water-insoluble _____ derivatives

  • structural components of membranes

  • energy-rich fuel stores

  • pigments

  • intracellular signals

• Lipidome - the lipid containing molecules in a cell

Complex Mixture

Cells are a ______ of Biological Molecules

99%

Chemical Foundations

• Elements are essential for animal life and health

  • less than 30 of the naturally occuring elements are essential to life

  • most at the lowest atomic weight

  • hydrogen, oxygen, nitrogen, and carbon are ____ of an organism

Bulk - essential in large amounts

Trace - essential in small amounts

double bond

Geometry of Carbon Bonding

• Classic 4 bonds = tetrahedral arrangement

• Carbon can form covalent bonds to form linear and branched chains, with free rotation around each single bond

• Carbon can form H,S,P and form form single and double bonds with O and N (limited rotation about the axis of a _____)

Polyfunctional

Many Biomolecules are ______

Configuration

_______: the fixed spatial arrangement of atoms

Stereoisomers

________: molecules with the same chemical bonds and same chemical formula

Stereospecific

_________: requiring specific conformations in the interaction molcules

Geometric Isomers or Cis/trans isomers

________: differ in the arrangement of substituent groups with respect to the double bond

Asymmetric Carbons

Chiral and Achiral Molecules

• Achrial = can be superposed (mirror image is the smae)

• Chiral = cannot be superposed (mirror image is different)

  • R/S

• Chiral centers = _____

A molecule can have 2^n stereoisomers, where n is the number of chiral

carbons

• Each group attached to a chiral carbon is assigned a priority, where:

—OCH3 > —OH > —NH2 > —COOH > —CHO > —CH2OH > —CH3 > —H

• Enantiomers

• Diastereomers

Enantiomers and Diastereomes

• _____: stereoisomers that are mirror images of each other (all chiral centers changed)

• ______: stereoisomers that are not mirror images of each other (not all centers changed)

Dynamic Steady State

Physical Foundations

• Small molecules, macromoleules and supramolecular complexes are CONTINOUSLY synthesized and broken down.

• This constant synthesis and breaking down is known as _________. Living cells maintain themselves in a dynamic steady state distant from equilibrium with its surrounding.

Energy

Maintaining a dynamic steady state requires the constant investment of ______.

• Organisms extract energy from the enviornment in two main ways

  • Photoautotrophs

  • Chemotrophs

Photoautotrophs

Extracting Energy for Dynamic Steady State

This is the process for ______

Chemotrophs

Extracting Energy for Dynamic Steady State

This is the process for ______

First Law of Thermodynamics

The Laws of Thermodynamics

• ________: in any physical or chemical change, the total amount of energy in the universe remains constant, although the frm of the energy may change.

Second Law of Thermodynamics

The Laws of Thermodynamics

• ________: randomness in the universe is constantly increasing

Entropy (S)

_____- represents the randomness or disorder of the components of a chemical system.

• Creating and maintaining order requires work and energy.

• INCREASING entropy makes reactions more spontaneous

Work

Energy is captured in nutrients/sunlight that energy accomplishes ____ → chemical transformations within cells, generates heat, and the synthesis and breakdown of molecules.

• enthalpy

• absolute temperature

• entropy

• Free Energy, G, of a closed system → H - TS

  • H represents ____

  • T represents _______

  • S represents ____

Enthalpy

_____, H - heat content, roughly reflecting the number and kinds of bonds.

Free-Energy Change

When a chemical reaction occurs, ________.

**Know this equation

Spontaneous

Negative DeltaG = _______

Nonspontaneous

Positive DeltaG = _______

Endergonic

_______ Reactions

• Reaction is NOT spontaneous

• Energy is absorbed

• Delta G > 0

Exergonic Reactions

_________ Reactions

• Reaction is spontaneous

• Energy is released

• Delta G < 0

Equilibrium Constant

The _________, Keq

• where [A]eq is the concentration of A, [B]eq is the concentration of B, and so on, when the system has reached equilibrium.

Sponatneous

When Keq > 1

• Products are > Reactants

• Delta Go < 0 (Negative)

• Reaction is _______

Not spontaneous

When Keq < 1

• Products are < Reactnats

• Delta Go > 0 (Positive)

• Reaction is _______

Equilibrium

When Keq = 1

• Products = Reactants

• Delta Go = 0

• Reaction is at ________

Standard free-energy change

__________ of a reaction under standard conditions, 298K pressure, 1 atm; and all solutes at 1M concentration. R is the gas constant. This is a known value.

**Know this formula

ACTUAL

The _____ free-energy change for chemcial reactions under NON-STANDARD conditions is a function of the standard free-enery change. DeltaGo

**Know this formula

Mass-Action Ratio

Q = the __________, the ratio of initial concentration of products over reactants

=

<

>

Exergonic

Living Things require non-spontaneous reactions to proceed, such as this reaction (below that has a postive DeltaGo) → By coupling this reaction to ATP hydrolysis, the reaction proceeds

• Once coupled the reaction becomes _____ and will proceed because it is sponaneous (negative DeltaGo)

deoxyribonucleotides

Genetic Foundations

• Genetic Information is encoded in DNA

• Deoxyribonucleic acid, DNA is a sequence of monomeric subunits, nucleotides, called ____________

  • DNA encode the instrictures for forming all other cellular components

  • provides a template to produce identical DNA molecules

Deoxyribonucleotides

___________- monomeric subunits that make up the DNA polymer, they covalently bond to each other

Native Conformation

• Each deoxyribonucleotide (DNA) in one strand pairs specifically with a complementary deoxyribonucleotide in the opposie strand

• Each DNA molecule deterimes the ________ of a protein or its precise three-dimensional structure

Hydrogen Bonds

DNA strands are held together by ________

Hereditary Instructions

Changes in __________ allow for diversity

Native Conformation

______: precise three-dimensional structure of a protein, crucial to protein function

Nucelotide Sequence

Mutation

• Changes in the ______ of DNA

• changes the instructions for a cellular component

• can be beneficial/detrimental

Unmutated

Wild Type: ______ cells

soluble

Most intermediates of metabolism → nucleic acids and proteins, are _____ in water.

spontaneously

Lipid bilayers, the likely forerunners of biological membranes, form ________ in water, and are stabilized by their interaction with water.

• Lipid + Water = Lipid Bilayers

ionization behavior

The __________ of water, weak acids and bases dissolved in water can be represented by one or more equilibrium constants.

Buffer

An aqueous solution of weak acid and its salt makes a _____ that resists changes in pH in response to added acid or base (narrow pH range)

Neutral Physiological pH

Ezymes which catalyze all the processes inside a cell, function optimally at near _________ (~7).

• Exceptions are enzymes that are in a compartment with a high or low pH.

tetrahedral

Chemical/Physical Properties of Water

• Two sets of electron pairs and hydrogen atoms form a _____ arrangement around oxygen.

Dipole Nature

Chemical/Physical Properties of Water

• Water has _____ due to the localized partial positive charges of hydrogens and the partial negative charge on the oxygen (Oxygen is more electronegative)

Hydrogen Bond

Chemical/Physical Properties of Water

• __________: is the electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another.

Covalent Bonds

Chemical/Physical Properties of Water

• Hydrogen bonds are longer and weaker than _________.

  • hydrogen bond in liquid water = 23 kJ/mol

  • covalent bond in water molecules = 470 kJ/mol

liquid water

Chemical/Physical Properties of Water

• Hydrogen bonds in __________ are fleeting, constantly breaking and reforming and last approximately 1-20ps (10^-12s)

• 4

• 3.4

• 4

____ hyrdogen bonds possible per water molecule, however…

• liquid water averages ____ hydrogen bonds/water molecule.

• Ice occupies all ____ hydrogen bonds/water molecule.

**entropy effect is important for clathrate-like structures (later)

Stable

In ICE hydrogen bonds are _____

break

In liquid water, hydrogen bonds constantly ____ and re-form.

Entropy

Thermodynamic Properties of Water

• During melting or evaporation, heat is taken up by the system, and the ____ of the aqueous system increases.

  • Evaporation/Melting are endothermic.

Spontaneous

At room temperature, melting and evaporation occur ______________:

• Free-energy change (DeltaG) must be negative because Delta H is positive, the increase in Delta S drives these changes.

  • It becomes more random when it becomes a liquid/gas

Amphipathic

Water interacts with Polar, Nonpolar and _________ Biomolecules → molecules that have polar and nonpolar regions.

electronegative atom

Water Forms Hydrogen Bonds with Polar Biolmolecules

• Hydrogen bonds readily form between an ________ (the hydrogen acceptor) and a hydrogen atom covalently bonded to another electronegative atom (the hydrogen donor)

Water

Examples of Hydrogen Bonding Between Molecules

• _____ can act as the hydrogen bond acceptor or donor.

Review

Examples of Hydrogen Bonding Between Biomolecules

• Review

Stronger

Hydrogen Bonds are Directional

• Linear H-bonds are ____ than non-linear H-bonds

• Hydrogen bonding is stronger when the three atoms involved, lie in a line

Number

Noncovalent Interactions are typically very weak and specific but they occur in large ____

charged

Noncovalent Interactions

• Hydrophobic Interactions (displacement of water)

  • 0.4-4 kJ/mol

• Pi stacking (aromatic ring stacking)

  • 0.4-4 kJ/mol

• Van der Waals interactions (weak but many)

  • 0.4-4 kJ/mol

• Hydrogen Bond

  • 4-40 kJ/mol

• Electrostatic (opposite attract, likes repel)

  • 4-40 kJ/mol

• Salt bridge (hydrogen bonding plus electrostatic)

  • e.g. carboxylate amino side-chain (Asp, Glu) to basic amino side-chain (Arg, Lys)

    • 40-400 kJ/mol

**Electrostatic and Salt Bridge are specifically between ___ molecules

soluble

Water interacts with Nonpolar Biomolecules

• Non-polar biomolecules are poorly ____ in water.

• Biologically important gases CO2, O2, N2 are nonpolar

hydrophobic

Water interacts with Nonpolar Biomolecules

• Nonpolar gases are _____, they do not dissolve well in water

Entropy

When nonpolar molecules move into aqueous solutions they decrease ____ by constraining motion

Cage

Nonpolar compounds interfere with hydrogen bonding amounh H2O molecules. The water becomes ordered around the molecule —> creates a water ____ around NP molecule

Unfavorable

The free-energy change for dissolve a nonpolar solute in water is ______

• Delta H is positive

• Delta S is negative (decreased entropy)

• Delta G is positive

Hydrophobic effect

Because NP + water is unfavorable, H2O molecules form a highly ordered, cage-like shell around each nonpolar solute molecule

• Maximizes solvent-solvent hydrogen bonding

• Clustering hydrophobic molecules reduces the amount of ordered water thereby increase entropy

This phenomenon is the ______

Amphipathic Compounds

_______ contain regions that are polar (or charged) and regions that are nonpolar (ex: long chain fatty acids)

• Favorbly

• Avoid Contact

Amphipathic Compounds

• Polar, hydrophilic region interacts ____ with H2O and tends to dissolve

• Nonpolar, hydrophobic region tends to _______ with H2O and cluster together.

Lipid Bilayer

Amphipathic Compounds

• Precursos of _____ formation

• Free energy is unfavorabke, similar to non-polar molecules

Hydrophobic Effect

Amphipathic Molecules in Water

• _______- nonpolar regions cluster together, polar regions arrange regions → cluster to maxiize interactions with each other and not with the solvent.

Micelles

Amphipathic Molecules in Water

• ________: thermodynamically stable structures of amphipathic compounds in water

Hydrophobic Effect

Effect of Water on Enzyme-Substrate Interactions

• Ordred water interacting with substrate and enzyme (to interact the cage must break) → the disordered water is displaced by enzyme-substrate interaction which is stabilized by hydrogen bonding, ionic interactions and ________

Weak Interactions

For macromolecules, the most stable structure usually maximizes _______

• H2O molecules are often found to be bound so tightly to biomolecules that they are part of the crystal structure.

Ionized

Water is partially _____