Biolchem Exam 1 Lecs 1-5

What is Biochemistry

Understand a system @ molecular level

• Into component parts

• Study isolated components, & reconstruct from isolated components

In the structures of life, there are ___ major biomolecules, what are they?

4

Proteins

Carbohydrates

Lipids

Nucleic Acids

Energetics of Life: ______

Thermodynamics (Free Energy, G)

What makes a rxn/pathway favorable?

What is required to drive unfavorable rxn/pathway?

What are the 4 most abundant elements of life? Their % of total atoms?

CHON (99.4% total atoms)

What are the most abundant atoms of life?

What atoms appear in structure of nucleic acids and proteins?

What ions play an important role in metabolism?

CHON (99.4% of total atoms)

P & S

Metal ions (Na+, Cl-, K+, Ca2+, Mg2+, & trace elements for metabolism)

Identify Abdundant, Moderate, & Trace elements in life

CHON abundant, 3 below moderate (PSCl & left sided ions), rest are trace

» Carbon forms ___ bonds

» ___ & ___ bonds most common

» Free rotation around ___ bonds

» Double bonds (sp² trigonal planar) are limited in ___, w/ atoms in a ___ plane

» 4 covalent bonds

» Single & double bonds

» Free rotation around single bonds (sp³ tetrahedral)

» Double bonds limited in rotation, w/ atoms in a single plane

Stereoisomers:

Can it interconvert w/o breaking bonds

Same chemical formula & connectivity, differ in 3-D orientation of atoms

Can have diff physical, chemical, & biological properties

No, must break bond to switch

Enantiomer:

Chiral center/stereocenter:

Cis-trans isomers:

Nonsuperimposable mirror image bc stereocenter

C w/ 4 diff substituents

In double bond

Biomolecule chemical properties are decided by ___________

Oxidized species:

Reduced species:

functional groups

Oxidized species: More bonds to O, fewer to H, less e-

Reduced species: Fewer bonds to O, more bonds to H, more e-

• Oil Rig & assign -1 to more eN atom in bond, +1 to other

Review functional groups

Note guanidium is arginine

Gibbs Free Energy

Equation & variables, – & + ΔG

What does coupling do

Direction & spontaneity of rxn

H: Heat

S: Entropy, disorder

T: Temp (in kelvins, usually +)

- Downhill process→ – ΔG (Gf - Gi), spontaneous & favorable, released energy

- Uphill process→ + ΔG (Gf - Gi), non-spontaneous & non-favorable, increased input energy

- Unfavorable rxns can couple to favorable rxns

How do the following impact ΔG spontaneity

-ΔG

-ΔH

+ΔS

◦ Protein:

◦ Nucleic Acid:

◦ Carbohydrates:

◦ Lipid:

Is Lipid a polymer?

◦ Protein: Linear polymer of Amino Acid

• For signal transduction, catalysis, energy production, structure, adhesion, motility, immunity

◦ Nucleic Acid: Nucleotide monomers (RNA & DNA)

• Genetic info, energy, catalysis

◦ Carbohydrates: Sugar mono, di, poly saccharide monomer

• Fuel source, energy store, adhesion, immunity

◦ Lipid: Hydrophobic, water insoluble

• Membranes, fuel & energy source, signaling

Polymers provide ____ from ____

# possible oligomers: ?

Polymers→Combinatorial diversity from limited building blocks

# possible oligomers: (Monomers)^length

In terms of linkages,

Protein:

Carbohydrate:

Nucleic acid:

Protein (dipeptide): Peptide bond (amide)

Carbohydrate (disaccharide): Glycosidic (joins a Carbohydrate sugar to something else) bond (acetal/ketal)

Nucleic acid (dinucleotide): Phosphodiester bond

Polymers built by ___ rxns (_____ H20), broken down by _____ rxns (____ H20)

Polymers built by condensation rxns (release H20), broken down by hydrolysis rxns (require H20)

Nucleotide consists of…

Phosphate + 5 C sugar saccharide (RNA or DNA at C2) + Nitrogenous base

• Bases: 2 purines (AG) & 3 pyrimidines (CTU)

Nucleotides can have one (mono-M), two (di-D), or three (tri-T) ____, attached @ C___?

• “d” in dATP indicates what?

(Mono-M), two (di-D), or three (tri-T) phosphates, attached @ C5

• “d” indicates deoxyribose

DNA is the ____ for most organisms

Some viruses have ___ genomes

DNA is the inherited genetic material for most organisms (the genome)

Some viruses have RNA genomes

The genome contains all info needed for organism function

What is the central dogma

DNA → RNA → Protein

Transcription Translation

(Francis Crick)

Replication:

Transcription:

Translation:

Replication: DNA is copied each time a cell divides into two new cells

• Transcription: DNA sequence is copied into an mRNA (messenger RNA)

• Translation: RNA sequence is decoded into a protein (amino acids)

Interactions between biomolecules are ___

Chemical structure of macromolecules determines ____ (& list examples)

Amphipathic & how that leads to bilayer?

Stereospecific (w/ specific chirality)

Structure determines function

• Proteins have binding sites to catalyze rxns

• Nucleic acids fold into complementary double stranded structures

Amphipathic: Have both hydrophobic & hydrophilic parts, hydrophilic head & hydrophobic tail

• Form hydrophobic barrier between two hydrophilic sides

• Head points to aqueous environment, no water in barrier

• Allows for compartmentalization inside cells

The plasma membrane is what?

Plasma membrane is ____ to polar molecules

Transporters/channels in membrane allow for _________

Lipid bilayer

Plasma membrane is mostly impermeable to polar molecules

Transporters/channels→selective permeability

All living cells have:

• Nucleus in ____, nucleoid in ____ hold ____.

• Cytoplasm vs cytosol

• Cytoplasm organized by what?

Nucleus in eukaryotes (membrane bound)

Nucleoid in prokaryotes, open/unmembraned

Hold DNA

• Cytoplasm is everything inside the cell membrane excluding the nucleus (in both prokaryotes & eukaryotes)

• Cytosol is the jelly water

• Cytoplasm organized by cytoskeleton

Eukaryotic cells have what?

Membrane bound organelles (mitochondria, chloroplasts)

Nuclear envelope surrounding nucleus

Mitochondria: Energy extraction

ER & Golgi: Synthesis, processing, & sorting lipids/proteins (UPS Truck)

Endosome: Endocytosis, bits of bilayer taken inside

Lysosome: Waste and recycling macromolecules

Vacoule: Storage (large in plant cells)

Chloroplast: Photosynthesis

Cytoplasm is everything inside membrane but nucleus, cytosol is only the liquid. Both prokaryotes & eukaryotes have both cytoplasm & cytosol

Cell Wall: In plants, turgor

From last common ancestor, what emerged?

Bacteria, archea, & eukarya

Prokaryotic cells are not structured: True or false & why?

False, highly structured

Genes defined positions in nucleoid

Protein positions specific in cell

• Bacteria have primitive cytoskeleton

Scale of things

Lec 2 Begin

Noncovalent Interactions

What are these interactions dependent on?

4 kJ/mol = ? Kcal/mol

(Decrease in strength 10x)

Electrostatic interactions (ionic bonds, salt bridges)

• Ionic Interactions: Between 2 charged atoms (strongest)

Dipole-Dipole: Between polar molecules

LDFs (Induced dipole-induced dipole & Van der Waals): Weak, temporary attractive forces

4 kJ/mol = 1 Kcal/mol

Interactions→Distance-Dependent

What are electrostatic interactions

What are they called in proteins?

What are they dependent on? Equation for it? Variables?

Ionic interactions between 2 full charges

Called salt bridges in proteins

Distance-dependent

Dipoles, in ________ bonds have a difference in ______ and ______ between atoms.

Must be ______.

Dipoles, in polar covalent bonds have a difference in electronegativity and electron distribution between atoms

• One end is δ⁺ (less e- dense) and other is δ- (more e- dense)

Must be asymmetric (not cancel out)

Are these polar or not, and why?

CO2 nonpolar, no net dipole

H20 is polar, has net dipole toward Oxygen

Dipole-Dipole Interaction

Attraction between permanent dipoles

Ion Dipole Interaction

Polar molecules orient around charged ion

Cation-π Interaction

π system in double bond (like aromatic ring) has δ- below & above plane of atoms

• Cations near face attracted

Induced Dipoles

Where can the charge come from (…-induced dipole interaction)?

Eqn for London Dispersion Forces?

Nonpolar molecule’s e- cloud shifts when charge near, temporary partial charge “induces dipole“

• Charge can come from ion (ion-induced dipole interaction), permanent dipole (dipole-induced dipole interaction), or another induced dipole (induced-dipole-induced dipole interaction) known as LDF

• LDFs equation E=α1α2/r^6

Van der Waals Interaction?

Van der Waals Contact Distance?

Is one weak or strong?

What is stabilized by Van der Waals Interactions?

Attractive force when two non-bonded atoms close (LDFs), but too close→repel

Van der Waals Contact Distance: Min energy (max attraction & stability), “bottom of energy well“

• Depends on radius/size of atoms

One is weak, many are strong

Van der Waals stabilizes interiors of tight macromolecule

Hydrogen Bonds? Covalent character percentage?

What is typical bond strength

Does direction matter?

Dipole-dipole w/ covalent-bond character (≈10%)

• Small & close

• e- orbital overlap

• H-FON

Bond strength 8-20 kJ/mol, 2x avg dipole & 2-5% of covalent bond

H-bonds are directional

Is H20 SP2?

How many H-bond donating & accepting sites?

Water has _____ mp/bp, why?

Solid water is _____ dense than liquid water, why?

No, H20 is SP3 & polar

2 H-bond donor sites & 2 H-bond acceptor sites

Water has high mp/bp bc of H bonding

Solid water is less dense than liquid water, bc ice has more H-bonding (all 4), more space.

Liquid water has ___% more/less H-bonds than ice

15%, less

Give 3 examples of H bonding in biological systems.

Base pairing in DNA & RNA

Protein structure stability in amide backbones

H-bonding activating nuc in protease active site

Water is a ____ solvent, meaning _____ compounds dissolve in it.

What dissolves in water, and what does not?

Water is a polar solvent, meaning hydrophilic compounds dissolve in it

Polar AA, carbs, nucleic acids, & OHs dissolve in water

Aliphatic chains, aromatics, & lipids don’t dissolve (hydrophobic)

Dissolved ions & polar solutes surrounded by __________ of ________

To interact, solutes must ____ to interact in polar solvent

Hydration shell of water molecules

Desolvate

Hydration shell favorable w/ polar solute (interaction, increased enthalpy), nonfavorable with nonpolar solute (bc entropy)

Nonpolar solute in water→what forms?

Why is it thermodynamically unfavorable?

Hydration shell forms

Unfavorable bc water trapped surrounding non-polar solute, lower entropy (no H bonding or dipole-dipole interactions between solute & water)

Thermodynamically unfavorable bc water entropy ↓, water cannot dance freely, so ↑ΔG (non-spontaneous & non-favorable)

What happens when oil + water

What drives this?

Nonpolar oil comes together, oil layer and water layer.

Minimizes oil molecules having hydration shells (unfavorable), want smallest SA.

Hydrophobic effect, not interaction bc no attractive force, entropy-driven (to free up water so it can freely dance ↑S, not bound in hydration shell (↓S). Avoid hydration shell

Hydrophobic effect drives what?

Protein folding: Hydrophobic AA don’t interact w/ water

Lipid Bilayer: Hydrophobic tails don’t interact w/ water

Ka Eqn

Henderson-Hasselbalch Eqn

When pH=PKA, what does that mean?

pH=PKA, [A-] = [HA], amount protonated species = deproted species

pH larger than PKA, deprotonate

pH less than PKA, protonated

Slide 22 & 23 for the pH/PKA charts review

What is a buffer

What range is a good buffer

Buffer maintains & resists change in pH.

Mix of weak acid [HA] & conjugate base [A-]

Good buffer range is pH=PKA±1

What are the 3 biological buffers must know?

Phosphate (H2PO4-) → PKA = 7

Bicarbonate (HCO3-) → PKA = 6 (for blood)

Histidine → PKA = 6.6

In an amino acid, the amino group (R-NH2) is ____ and the carboxylic acid is ____

What is C1?

What is the alpha carbon?

In an amino acid, the amino group (R-NH2) is basic and the carboxylic acid is acidic.

Carboxyl carbon is C1

Alpha carbon is in the middle (C2)

Explain the CORN rule

Using D or L amino acids for translation?

Place the H in the back then trace out the carboxyl → R group → Amino group (CO-R-N):

• Counterclockwise is L (think negative, left-hand)

• Clockwise is D

• Diff bc does not recognize priority groups like R/S does

Only L Amino Acids for translation

Practice CORN Rule

Explain Fischer Projection (orientation & direction)?

Which side is L or D?

Carboxyl on top, R on bottom, heteroatom (non C/H) & H on horizontal

Horizontal hugs you (coming forward), top/bottom backwards

• Heteroatom on left → L

• Heteroatom on right → D

Assign L or D based on Fischer projection

Enantiomers ____ plane polarized ____ in ____ opposite direction.

Do L & D indicate direction of rotation? What does?

What does not rotate light?

Chiral molecules have ____ interactions (give example)

Enantiomers rotate plane polarized light in opposite direction.

L & D do not indicate direction of rotation? +/- do

Racemic mix does not rotate light

Chiral molecules have stereospecific interactions (diff functions)

• Only 1 enantiomer of ibuprofen gives anti-inflammatory effect, other is filler

Isoelectric point

Zwitterion

All AAs have at least ___ ionizable groups

pH @ which net charge is 0

• Molecule least soluble in water here,

Zwitterion: + & - charge on same molecule, net neutral

All AAs have at least 2 ionizable groups (amino & carboxyl)

Pick up on part 2 of Lec 3, grind & finish lecs 4 & 5 today. Finish practice 1, and do 2 & 3. Then discussion 1 redo!

Soc reading

EEB reading

Out of the aromatic PTT, which one is polar?

What is the only achiral AA

Tyrosine, bc has OH

Glycine (bc R group is H)

Why is Glycine helpful

What are the 2 simplest AA?

Bc R group is H (small), helpful for tight turns in polypeptides.

• Glycine & Alanine simplest AA

What 2 AA are structural isomers

Which AAs has two stereocenters?

What AA causes a bend/kink in polypeptide chain?

What AAs can be phosphorylated?

Leucine & Isoleucine structural isomers (same formula, different connectivity)

Iso meaning same as Leucine, just CH3 moved up to the side

• Isoleucine & threonine has 2 stereocenters

Proline causes bend/kink bc limited rotation between C alpha — N, cyclic

Hydroxyls in Serine, Threonine, & Tyrosine can be phosphorylated.

Aromatic AAs can engage in ___-___ interactions, and they _____ UV light at _____ nm for most proteins

Aromatic AAs can engage in π-cation interactions, and they absorb UV light at 280 nm for most proteins.

Aside from PTT, what is one aromatic AA (has another property thus not in PTT)

Histidine (HALGA) is + charged (but basicity & + charge considered more significant)

Cysteine sulfhydryl is ____ & ____. Has PKA =

Ionized forms ___

Oxidized forms ___

Cysteine sulfhydryl is ionizable & redox-sensitive.

PKA 8.3

Ionized forms thiolate (S-), deproted

Oxidized forms disulfide bridge

Asp & Glu, because of their negative charge, can form what?

Salt bridges with basic amino acids (being opposite charge w/ H bonding)

PKA impacted by _____

• Give an example using Lysine

List the gist of PKAs to know in relation to each other

PKA impacted by local environment

• Lysine in a hydrophobic environment does not want to be + charged (polar & hydrophilic), so it will be deproted (↓ PKA)

Arginine, Lysine, & Tyrosine have highest PKA

C alpha Carboxyl has lowest PKA (most acidic) followed by R group’s carboxyl.

List post-translational Amino Acid modifications, what they do?

What are the 2 non-standard AAs (encoded)

Phosphorylation: Adding phosphate group on OHs

N-acetylation: Acetyl group (usually to Lys)

N-methylation: Methyl group (usually to Lys)

Glycosylation: Adding carbohydrate

Lipidation: Adding lipid

Selenocysteine & Pyrrolysine

___ amino acids are essential, what are they?

____ amino acids are non-essential, what are they?

• How many can bacteria make?

9 essential (from diet), 11 nonessential (synthesized in humans)

• Bacteria make all 20

Don’t need to know them yet, needed for Exam 3

Amino (NH3+) & Carboxyl → Forms ____ in a ___ rxn

Peptide bond is between ____ & ____

Peptide vs. polypeptide?

Amino (NH3+) & Carboxyl → Forms Amide in a condensation rxn

Peptide bond is between carbonyl & NH

Peptide is short chain of AA

Polypeptide: Chain long enough to fold into functional protein

What is a protein sequence? How is it read?

What is a residue?

Peptide backbone vs side chains?

Protein sequence: Order of amino acids

• Read from N-terminus to C-terminus, (matching addition in translation)

Residue: Individual amino acid

Backbone is N-Cα-C (carbonyl) → N-Cα-C-N-Cα-C

Side chains: R groups attached to backbone

Primary Structure

Order of amino acids

Secondary structure

Backbone of a polypeptide, alpha helices & beta sheets (backbone H bonding), excludes R group

Tertiary Structure

• What types of interactions (4)?

• Specific to what?

3D shape/folding based on side chains

How secondary structures are oriented/folded.

Depends on R group residue side chain interactions:

• H-bonding (polar)

• Hydrophobic packing (nonpolar)

• Disulfide bonds, covalent linked between 2 Cys

• Salt bridges, (ionic interaction in proteins)

Specific to water-soluble globular proteins

Quaternary structure

• What is a subunit

• Multi-subunit Proteins described by ____ (give examples)

• What is trimer of dimers?

Multiple polypeptide chains

• Subunit: Single polypeptide chain

• Multi-subunit Proteins described by their numbers dimer (2), trimer (3), tetramer (4)

• Combos → Trimer of dimers (3 groups of 2 subunits)

Polypeptides ____ into unique shape to form protein, undergo ____ changes by rotating around covalent bonds. Stabilized by ____ interactions.

Polypeptides fold into unique shape to form protein, undergo conformational changes by rotating around covalent bonds. Stabilized by noncovalent interactions.

Conformational Change

By rotating around bond (unrelated to stereochem)

Rotating around covalent bond is _____ or _____.

What are the 3 repeating dihedrals in backbone?

Dihedral angle or torsion angle.

• Phi (Φ): N-C_α

• Psi (Ψ): C_α-C

• Omega (ω): C-N (peptide bond, top right

In angles for Ramachandran, which is CW & CCW from + & -

Clockwise (+)

Counterclockwise (-)

Is there rotation around amide bonds? Why or why not?

Amides→double bond character, shorter bond, SP2 trig planar), can’t rotate around double bond

So Phi & Psi rotate, what does not?

6 atoms lie in peptide bond plane, no rotation (only rotation from C_α to C_α)

Peptide bond, C-N cannot rotate (partial double bond strcture)

Peptide bond (ω) can only be what angles?

ω only 0 or 180 bc is planar & no rotation

____ conformation in peptide bond is favored, by how much?

Trans (180^o) favored, w/ C_α & C_α opposite of peptide (C-N) bond, less steric hindrance

• Favored 1000x

Cis (0^o) C_α & C_α same side unfavored, steric clash

What can form cis peptide bond? Why?

Proline can form cis bc C_α-N is ring (10%)

• Isomerization catalyzed by cis-trans prolyl isomerase

But cis-proline makes larger kink in peptide chain than fixed ring (Φ = -60^o)

Ramachandran Plot

Shows favorable, possible combo of phi/psi angles w/o steric clash (clusters/dots best)

• 25% of combos allowed

• 2 major regions α (Φ: -60, Ψ: -50) & β (Φ: -120, Ψ: 120)

Does side chain identity impact allowed combos of Φ and Ψ? What are the two exceptions

No, R group has little impact except for:

• Proline (fewer conformations, more restricted), no rotation at Φ bc of ring

• Glycine (more conformations, more flexible)

Spacefill Model:

Backbone Trace Model:

Ribbon (Cartoon) Model:

• Where do arrows on ribbons point?

Spacefill Model: Shows Van der Waals radii (packing)

Backbone Trace Model: Follows polypeptide backbone

Ribbon (Cartoon) Model: Shows secondary structure

• Arrows on ribbons point from N to C -terminus (as read)

Secondary structures defined by _______ between ________ and ________.

• Two main types are _____ & _____

Secondary structures defined by H-bonding between backbone carbonyl and amide.

• Two main types are ɑ-helix (cylindrical spiral ribbons) & β-strand (arrows w/ thickness)

What is a random coil

Random bc no defined secondary structure, but we do know where it is

True or False: Regular 2^o structures have similar psi & phi values?

True, specific ɑ-helix appears in ɑ-helical region, & specific β strand will appear in the β-sheet region.

• Peptide backbone has a repeating structure & consistent phi and psi values clustered on Ramachandran plot for ɑ helices & β sheets

ɑ helix is usually _____ handed

_____ amino acids per 360^o turn, ____ Å (10^-10 m) rise per turn

How do the side chains project?

How is the interior?

Right handed (left possible but rare)

3.6 amino acids per 360^o turn, 5.4 Å rise per turn

Side chains out % down toward N terminus, C=O toward C terminus

Tightly packed interior

In ɑ helix, H-bonds between what two groups?

_____ of residue i h-bonds to _____ of residue i+4

Backbone amide & Carbonyl

Carbonyl in residue i H-bonds to amide in residue i+4

In ɑ helix, H bond describes one _____ (____ residues)

Carbonyls point _____, such that _____ terminus is δ- and _____ terminus is δ⁺

H bond describes one turn (3.6 residues)

Carbonyls point downward, such that C terminus is δ- and N terminus is δ⁺

Does the ɑ-helix dipole have a strong dipole moment, why or why not?

Yes, the carbonyls all point down toward C terminus (parallel to helix axis)

In amphipathic ɑ helix, have _____ hydrophobic face and ____ hydrophilic face.

With 3.6 residues per turn, every _____ residues have similar properties (polar or nonpolar)

Nonpolar residues face _____ of protein, polar face ____

Are all ɑ helices amphipathic?

One hydrophobic face, one hydrophilic face.

With 3.6 residues per turn, every 3-4 residues have similar properties (polar or nonpolar)

Nonpolar residues face interior of protein, polar face exterior.

Not all ɑ helices amphipathic, can be all polar or not

β strands → β sheet

How do β strands form β sheets?

β strands are ____, β sheets are ____

β strands form β sheets through backbone H-bonds

β strands are pleated, β sheets are slightly twisted

Side chains project on _____ sides of β strand

Side chain on same face _____ Å apart

Side chains project on opposite, alternating sides of β strand

Side chain on same face are 7Å apart

In ɑ helices, neighbor residues are ____ Å apart

In β strands, they are ____ Å apart

In ɑ-helices, neighbor residues are 1.5Å apart

In β-strands, they are 3.5Å apart

Antiparallel β-sheets run in _____ direction, H-bonds are _____ stable. Are connected by __ amino acid reverse turns (using __ & __ AAs).

Parallel β-sheets run in ____ direction, H-bonds are ____ stable, connected by _____

Antiparallel β-sheets run in opposite direction, H-bonds are more stable. Are connected by 4 amino acid reverse turns (using Proline & Glycine AAs).

Parallel β-sheets run in same direction, H-bonds are less stable (bent geometry), connected by ɑ-helix or large loop.

Mixed β sheets

Both parallel & anti-parallel oriented strands.