Unit 1

Cell Theory

• Living organisms are made of cells

• Cells are the basic unit of structure and function

• All cells are made of other cells

History of Cells

• ~3900-2500 mya

  • Prokaryotes appear, chemoautotrophs, use CO2 as carbon source and inorganic materials for energy

• 1850 mya

  • Unicellular eukaryotes appear

Evolutionary Tree

• Bacteria and archaea are prokaryotes

• Archaea and eukaryotes are more similar, meaning they have a more recent common ancestor

Characteristics of Life

• Genetic information is stored as DNA

• DNA used as a template for copying the genome

• Plasma membrane surrounds cell, creates barrier

• RNA used as an intermediary *vulnerable

• Proteins are used as catalysts for almost all reactions *enzymes, vulnerable

• Free energy must be consumed

Eukaryotes vs. Prokaryotes

• Prokaryotes

  • Small

  • No nucleus

  • No membrane-bound organelles

• Eukaryotes

  • Large

  • Nucleus, DNA storage

  • Membrane-bound organelles

Endosymbiotic Theory

• Archaea ate bacteria

  • Formed symbiotic relationship

  • Formed mitochondria

• Again with photosynthetic cell

  • Formed chloroplast

Covalent Bonds

• Non polar covalent

  • Equal sharing of e- due to similar electronegativities

  • Greater potential energy

  • Ex. CH4

• Polar covalent bonds

  • Unequal sharing of e- due to differing electronegativities

  • Not as reactive, creates dipole moments

  • Ex. H2O

Non Covalent Bonds

• Weaker than covalent bonds

• Individually weak, collectively strong

• Ionic

  • Taken, not shared e-

  • Little importance in cells

  • Ex. NaCl

• Hydrogen

  • Requires hydrogen in a polar bond with + charge

  • Another polar atom with - charge

  • Hydration shells surround most biological materials

  • Ex. H2O and H2O

• Van der Waals interactions

  • Weak non polar bonds

  • Ex. C2 and C2

Hydrophobic Effect

• Forming hydration shells is unfavorable, low entropy

• Non polar molecules in water associate with each other

• Entropy=disorder, higher disorder is energetically favorable

• Hydration shells=water spread out into shell over non polar molecules

  • Form separately or together around molecules

  • Together is more favorable, takes less water

Molecular Complementarity

• Generally protein-protein, protein-DNA, etc. are not covalent

• Why use weaker non covalent bonds? They’re reversible

• Why do non covalent interactions matter?

• Reversible, motor protein “foot”, moves to area of more complementarity

• Complementary shape and portions of molecules

• Polar: Not always on outside, can interact with each other

• Non polar: Can be outside, interact with each other

Redox Reactions

• OIL RIG

  • Oxidation is lost, reduction is gained

• Gain or loss of time with electrons

• Ex. Methane to methanol , C-OH bond losing time with C-H bonds

Building Blocks

• Sugars → Polysaccharides

• Nucleotides → Nucleic acids

• Amino acids → Proteins

• Fatty acids → Fats

• Sugars, amino acids, and nucleotides form long chain polymers

Monosaccharides

• General form (CH2O)n

• Aldose, top of sugar, top of alphabet

• Ketose, middle of sugar, middle of alphabet

• Carbon number (3=triose, 5=pentose, etc.)

Disaccharides and Polysaccharides

• Defined by a and B links

• B hydroxyl, OH group sticks up the same as the outside carbon

• a hydroxyl, OH group sticks down opposite as outside carbon

• Oligosaccharides- short chains

• Polysaccharides- Long chains

• Branched sugar, whether sugar has a or B hydroxyls

pH

• Measuring how basic or acid a substance is using amount of hydrogen ions

• Amino acid zwitterions

  • Low pH, protonated

  • Neutral, not charged but charges within

  • High pH, deprotonated

Polymerization

• Condensation reaction

  • Anabolic, builds polymer and H2O is a byproduct

• Hydrolysis

  • Catabolic, use H2O to break apart polymer

• Composition of a cell

  • 70% water, 30% chemicals (proteins, small others)

Reaction Rate

• Reactants are converted to products

• Catalysts lower activation energy and speed up reaction

• Intracellular reactions are more complex and usually include many reactants

Energetics

• Δ G = Δ H - TΔ S

• Δ G, endergonic or exergonic reactions

  • Endergonic- spontaneous, losing energy

  • Exergonic, non spontaneous, needs catalyst

• Δ H, exothermic or endothermic

  • Exothermic, releases heat

  • Endothermic, takes in heat

• Δ S, disorder

  • More disorder is energetically favorable

  • Energy is needed to lower disorder

Enzyme and Reaction Rates

• Some RNA act as catalysts

• Catalysts lower activation energy

• Enzymes as catalysts

  • Sucrose binds to sucrase

  • Converts products, releases products

  • Separate enzyme needed for reverse reaction due to complementarity

Protein Structure and Function

• Primary

  • Sequence of AA, properties of side chains n → c terminus

• Secondary (local folding)

  • Folding of localized areas, AAs near

• Tertiary (overall conformation)

  • Folding of secondary structures

• Quaternary (multimeric structure)

  • Two or more proteins

• Supramolecular (large-scale assembly)

• Function (regulation, structure, movement, catalysis, signalling, transport)

Condensation Reaction

• Amino acid (carboxyl reacts with amino group, forms peptide bond)

• Peptide (N-terminus, amino end and C-terminus, carboxyl end)

• Protein

• Zwitterion (+ and - charge, charge is neutral, backbone of protein

Anatomy of a Protein

• N-terminus: amino (+)

• C-terminus: carboxyl (-)

• Side chains

• Peptide bonds

Amino Acid Rotation

• Rotation is constrained around the peptide bond

• Phi and psi angles

Acidic AA (-)

• Aspartic acid: Asp, D

• Glutamic acid: Glu, E

Basic AA (+)

• Arginine: Arg, R

• Lysine: Lys, K

• Histidine: His, H

Uncharged Polar AA

• Asparagine: Asn, N

• Glutamine: Gln, Q

• Serine: Ser, S

• Threonine: Thr, T

• Tyrosine: Tyr, Y

• S, T, Y are most commonly phosphorylated

Non Polar Amino Acids

• Alanine: Ala, A

• Glycine: Gly, G (smallest)

• Valine: Val, V

• Leucine: Leu, L

• Isoleucine: Ile, I

• Proline: Pro, P (cyclic, sharp kinks)

• Phenylalanine: Phe, F

• Methionine: Met, M

• Tryptophan: Trp, W

• Cysteine: Cys, C (can form disulphide bonds only when oxidized, usually extracellular)

Secondary Structures

• α-helices

  • Backbone twist

  • Hydrogen bonds between

• β-strands

  • Can be antiparallel (easy) or parallel (long route, extra AA)

  • Hydrogen bonds between strands

  • Zig-zag pattern

• β-turns

  • Sharp turns

  • Usually by proline

• Random coils

  • Unstructured

Intrinsically Disordered Proteins

• Binding

  • Flexible region wraps around partner molecule to bind

• Signalling

  • Flexible structures allow phosphate groups to easily be added or removed, molecular switch

• Tethering

  • Flexible leash to hold 2 domains together while allowing movement

• Diffusion barrier

  • Protein network forms filters that regulate what passes through

• Elastin

  • Forms network that stretches under force, giving tissues elasticity, held together by disulfide bonds

Secondary to Tertiary Structures

• Decreasing entropy as moves to tertiary structure

• Intermediate tertiary structures form but are not stable or functional

• Native state is the lowest energy but is the most stable

• Driving force is side chain interactions: Hydrophobic effect, ionic bonds, disulfide bridges, hydrogen bonding, van der Waals forces

Representations of Protein Structures

• Backbone trace (no side chains)

• Ribbon diagram (no side chains)

• Ball and stick (side chains)

• Space filling model (shows specific shape)

Protein Domains and Quaternary Structure

• Structurally, usually functionally distinct subunits

• Assembly of quaternary structure

  • Dozens of the same protein lined up

  • Homo (same protein) or hetero (different protein)

  • Monomer, dimer, trimer…=# of proteins in a complex

Chaperones and Chaperonins

Chaperones

• Helps protein fold correctly

• Unfolded protein binds to nonpolar binding site (short segment)

• ATP hydrolyses to ADP, “mouth” closes

• Protein folds correctly, binding domain gets a new ATP

• Protein releases

Chaperonins

• Double barrel shape

• Incorrect or incompletely folded protein enters cage

• GroES cap and add ATP

• Shake up protein, hydrolyse ATP to ADP

• Barrel lengthenes

• Add new ATP and release protein

Post-Translational Modifications

• Phosphorylation: Kinase adds phosphate to protein, phosphatase pulls it off

  • Phosphate is from ATP

  • Can turn protein “on” or “off”

• G-proteins

  • GAPs: Accelerate GTP hydrolysis

  • GEFs: Facilitate GDP to GTP exchange, inactive

Co-Factor Binding

• Vitamins derivatives as coenzymes

  • Vitamins need to be converted to coenzymes for enzyme catalytic activity

• Hem around protein: Hemoglobin

  • Cofactor binds to enable visual signalling

Proteolytic Activation

• Rapidly activate proteins through cleavage

• Single polypeptide chain, folding by disulfide bonds

• Central peptide is removed

• Active insulin released

Polyubuqitylation

• Ubiquitin attaches to target protein to regulate its function

• Monoubiquitylation- Histone regulation

• Multiubiquitylation- Endocytosis

• Polyubiquitylation- Lys48 (proteasomal degradation) or Lys63 (DNA repair)

Protein Interactions

• Surface-string

• Helix-helix

• Surface-surface

• Proteins need to find their binding partner and form a strong bond

Protein-Ligand Interactions

• Forms non covalent bonds

• Binding site formation via folding

  • Unfolded: AA side chains are far apart

  • Protein folds to native state

  • Binding site is for a specific ligand

  • Ligand=non enzyme, substrate=enzyme

Rates of Binding

• Kon=rate constant for formation of complex

• Koff=rate constant for dissociation of complex

• R (receptor) + L (ligand) →← RL (ligand receptor complex)

• Equil, Kon=Koff

• Koff=[R][L]/[RL]=Kd

• The more stable and tight RL complex, smaller Kd

• 10-100nM is very tight

• Kd is binding affinity

Binding Curves

To find Kd, y-axis is highest point on line. Then divide in half and see the Kd reflected on the x-axis