Biochem Exam 1

Are living systems in equilibrium?

No, they live in a steady, dynamic state

Ribosomes synthesize proteins using

mRNA

What is the function of pili?

Points of adhesion to surfaces of other cells

What is the function of the flagella?

Propels cell

What determines the function of a molecule?

Chemical structure

What carries out programs in a cell?

Proteins and metabolic machines

The energy from a cell’s surroundings is used for what?

Maintaining homeostasis and doing work

All energy obtained by a cell comes from

Flow of electrons

The chemical information in a cell’s genome allows

Self assembly and self replication

Biochemistry definition

Describes in molecular terms the structures, mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie life

Plasma membrane

Made of lipid and protein, defines boundaries of cell, pliable, hydrophobic, free passage of inorganic ions and most charged/polar molecules

Universal features of all living cells

Cytoplasm, plasma membrane, ribosomes, nucleus, nucleoid, nuclear membrane, membrane-bound organelles, ribosomes

Common features of bacterial and archaeal cells

Ribosomes, cell envelope, nucleoid, pili, flagella

Site of most energy-extracting reactions of the cell

Mitochondria

ER and golgi

Synthesis, processing, transportation of lipids/membrane proteins

Peroxisomes

Oxidize long fatty acid chains, detoxify reactive oxygen species

Lysosomes

Digestive enzymes to degrade cellular debris

Vacuoles

*Plant cells store large quantities of organic acids

Chloroplasts

Site of photosynthesis

Cytoskeleton

• Provides structure, organization, and support 

• Actin filaments, microtubules, and intermediate filaments

Site of ribosomal synthesis

Nucleolus

SER synthesizes

Lipids

RER synthesizes

Proteins

Amino acids, nucleic acids, and polysaccharides are held together by 

Covalent bonds

Macromolecules are held together by mostly

Noncovalent interactions (Hydrogen bonds, ionic interactions, Van der Waals, and hydrophobic effect)

2 important factors that influence the reactivity of biomolecules are

Functional group and 3D structure

Conformation vs configuration

• Conformation = arrangement due to rotation

• Configuration = arrangement due to chiral center or double bond (R or S//cis vs trans)

Achiral

Superimposable mirror image

Chiral

Nonsuperimposable mirror images (R/S enantiomers), C attached to 4 diff things

The 3D shape of a molecule is the

Lowest energy conformation

Are most biomolecules chiral or achiral?

Chiral

What are constantly synthesized and broken down?

• Small molecules, macromolecules, and supramolecular complexes

• Requires constant use of energy

Covalent bonds hold together

Amino acids, nucleic acids, and polysaccharides

Macromolecules are held together by

Noncovalent interactions (H bonds, ionic interactions, van der waals, and hydrophobic effect)

Stereoisomers are

Molecules w/ the same chemical bonds and formula in a different conformation

What is used to predict whether a reaction will occur spontaneously or not?

Thermodynamics

A system includes

Reactants, products, solvent, and immediate surroundings

Isolated system

Does not exchange matter or energy with surroundings

Closed system

Exchanges energy (not matter) w/ surroundings

Open system

Exchanges matter and energy w/ surroundings

Enthalpy

Heat contents of system, ∆H is the difference in bond dissociation energies between reactants and products

Exothermic

-∆H, release heat

Endothermic

+∆H, heat input

Exergonic

-∆G, spontaneous

Endergonic

+∆G, nonspontaneous

A reaction coordinate diagram serves to show

How endergonic and exergonic reactions are coupled

Why do most cellular reactions proceed at useful rates?

Enzymes catalyze them

Mass to action ratio

(Q = [B]/[A]) Ratio of product concentrations to reactant concentrations at a specific time

∆G measures

How far away conditions are from equilibrium, how much energy is available in a chemical reaction

Does thermodynamics tell us anything about the rate of a reaction?

No!

Metabolism

Overall network of enzyme-catalyzed pathways

Pathway

Sequence of consecutive reactions where the product of one becomes the reactant of the next

Hydrogen bond

Weak electrostatic attraction between H (which is covalently bonded to an electronegative atom) and another electronegative atom

The strongest H bond occurs when the atoms are lined up

Linearly

Why are nonpolar gasses poorly soluble in water?

Interferes w/ water’s ability to hydrogen bond, decreases entropy by constraining water

Water has more entropy if it can

FLICKER (make/break H bonds)

Water has more entropy if it can do what to hydrophobic molecules?

Contain/cage them together

Water doesn’t like dissolving gasses because

they interfere with water’s ability to hydrogen bond (flicker happily), decreases entropy

Van der Waals

Weak interatomic interactions between 2 uncharged atoms in close proximity due to an induced dipole

Colligative properties of water depend on what?

The number of solute (particles per unit volume of water)

Do colligative properties depend on the chemical properties of the solute?

NO!

Osmosis

Movement of water across a semipermeable membrane driven by a difference in osmotic pressure

Osmotic pressure

Pressure produced as a result of water flowing through a semipermeable membrane from higher water concentration to lower water concentration

Cell in hypertonic solution

Water moves out of cell, it shrinks

Cell in hypotonic solution

Water moves into cell, it may burst

How many molecular interactions does it take to have significant influence?

Lots

Hydrophobic effect

Nonpolar regions of a molecule are clustered together to present the smallest hydrophobic area

How do weak interactions contribute to the most stable macromolecule structure?

Most stable structure = weak interactions maximized

The lower the pKa,

The stronger the tendency to dissociate a proton, therefore the stronger the acid

Keq equation used to find

Where the equilibrium lies

Strong acid vs weak acid dissociation

Strong acid completely dissociates, weak acid dissociates to equilibrium

What helps to stabilize protein structure for nonpolar amino acids?

Hydrophobic effect

Cysteine forms cystine in what kind of environment?

Oxidizing

Zwitterion

molecule with no net charge

Isoelectric point

characteristic pH where net charge on an amino acid is zero

Will electrophoresis work on an amino acid at its pI?

No, there will be no charge so it won’t move

pH above pI, what will the net charge be?

Negative, aa will move toward positive (anode)

Peptide bonds form through what type of reaction?

Condensation

Reasons to purify proteins

Study function, determine sequence

Steps for purifying proteins

1. Source/collect

2. Solubilization

3. Centrifugation

4. Precipitate with lyotropic agent

5. Dialysis

6. Chromatography

Analytical technique

Test component to learn about content

Preparative technique

Use all sample to find what works best

Precipitation w/ lyotropic ions

Ammonium sulfate most common

Add small amounts to precip out proteins until the protein of interest is precipitated out, dialysis to remove ammonium sulfate

Chromatography techniques

polarity = reverse phase chromatography

size = gel filtration chromatography

charge = ion exchange chromatography

specificity = affinity chromatography

Gel filtration chromatography

Sort by size

Stationary phase is column, looks like gel, beads that proteins pass through

*smallest proteins go through all, come out last

*largest proteins can’t fit, skip past and come out first

Ion Exchange Chromatography

Sort by charge

Removal of protein by changing pH or salt conds of buffer

Move through column at rates determined by net charge at the pH being used

Affinity chromatography

Specificity/binding

Commercially bought beads w/ ligand you want to bind to, hella expensive

Electrophoresis in protein purification

Determines purity of protein, possibly quantifies, typically analytical

Native (non-denaturing) and SDS-Page

Native Electrophoresis

Separate based on net charge

SDS-Page

Separates based on size when protein is denatured in presence of anionic detergent (SDS) that strongly binds to protein

3D structure disrupted by heat, proteins of same size have same mass to charge ratio

2 parts of 2D electrophoresis

polyacrylamide gel electrophoresis and isoelectric focusing

Isoelectric focusing

Acrylamide gel is applied to pH gradient where proteins move until they have no net charge

How to make an electropherogram

Separate by isoelectric point, separate by mass

Activity vs specific activity

Activity = total units enzyme in solution

Specific activity = # units enzyme per mg total protein

Edman degredation is used to

sequence aa, now out of date

How does the mass spec work?

Gas phase —> vacuum —> electric field = mass

Electro-spray Ionization Mass Spec

Force (+) things to move through cappilary, force to break apart when they get too big, becomes aerosol spray

Time of flight mass analyzer: E = ½mv²

HPLC

Prep protein for sequencing, add reducing agent to break cysteine bonds, cleave disulfides with BME, proteases *separates peptide fragments

Tandem MS

Some homolytic breakage, 1 e- goes to each side, send to 2nd mass analyzer and use TOF to calc. masses

Bioinformatics

Helps ID functional segments in new/unknown proteins, compares to old proteins

Establishes sequential and structural relationships to known proteins