Chapter 1: Life

Nucleic Acid Research Database

por MUHAMMAD HAFIZUDDIN BIN YUSOF

Carbs

por Grace Hill

Symbol: C Atomic number: 6 Nonmetallic Atomic mass : 12.0107 amu. Ground state electron configuration is 1s22s22p2 Oxidation state ranges from 4 to -4 Electronegativity value of 2.55 The geometry in organic molecules are linear, trigonal planar, tetrahedral.

por Shelby Williams

Mind Map Assignment - PF4014-2024

por Jordan Warren

Chapter 4: Proteins

Fibrous Proteins

Structure of Collagen

Significant Gly, Pro content

Skin, Tendons, Cartilage, Bones

Structure of Silk

Fibroin consists of layers of antiparallel B-sheets rich in Ala and Gly residues

The fibers in silk cloth and in a spider web are made up of the protein fibroin

Chemical Reduction of the Cystine

Reduce --> Curl --> Oxidize

Crosslinking Keratin Fibrils: to curl or not to curl

Structure of Hair

Keratin

Significant Cys content

Hair, Claws, Outer Epidermal Layer

Not Globular

Hydrophilic, but not soluble

Very tough- occur in skin, nails, cocoons

Long rope or sheet-like structures

Levels of Protein Structure

Quartenary Structure

Assembled subunits

Interactions between polypeptide chains

Tertiary Structure

Polypeptide chain

Independently Folding Regions (domains)

Distinct Interactions

Secondary Structure

B-turn

Type I occur 2x more frequently than Type II

Hydrogen bond between the peptide bonds of 1st and 4th residues

Type II have Gly in 3rd position

Glycine: small side chain allows for tight corners

Proline are preferred in 2nd position

Proline: conformationally restricted with fixed phi angle keeps turn rigid

B- sheet

Extended chains

Peptide chains align side-by-side

Parallel and Antiparallel

Amide groups Hydrogen bond

Extended peptide anions- pleated geometry

Planar peptide bonds are in the pleat

R-groups alternate (up, down, up, down..)

At Carbons are the apices

a- helix

Geometry

This allows for helix faces

Charged: helix with a string of similarly charged residues

Amphipathic: hydrophobic face and hydrophilic face

There are 3.6 residues per turn- roughly every 3rd to 4th residue will be on same face

All side chains point outward from core

Very compact structure

Stabilized by intramolecular Hydrogen bonds between peptide bonds

Peptide "backbone" is the core of the coil

R-groups protrude outwards

Right-handed twist

Chain is coiled like a spring

Local Interactions

Primary Structure

Ramachandran plot

Primary Structure dictates fold...but it's complicated

Proteins may fold in one environment, then move to another environment

Other proteins can help fold the protein

Proteins start to fold before they are completely made

Amino Acid Residue

Protein folding

Assume the native state is folded and is the most stable state

Why is the Native state more stable?

Denatured state is less stable

Noncovalent forces stabilize the native state relative to the unfolded state

Hydrophobic Interactions: Drive burial of hydrophobics in the protein interior

London Dispersion Forces: Between hydrophobic residues in the protein interior

Ionic Interactions: Acidic and Basic groups (e.g. Asp-Lys)

Hydrogen bonding: Inter- and Intramolecular Hydrogen bonds

Revised

Changing primary structure can change the energetics of folded state or the folding energy landscape

Some proteins require chaperones to fold

They help overcome energy barriers or alter salvation to change the folding landscape

Protein dynamics may play a crucial role in functions e.g. Histones!

Folded proteins may have many conformations. Proteins move!

"Native" structure is not always folded. Intrinsically Disordered Proteins!

Not random

Molten globule by a spontaneous hydrophobic collapse first, followed by formation of secondary structures

Hierarchic process in which local secondary structures form first, followed by hydrophobic collapse

Fast process

Protein Stability

Hydrophobic collapse drives the energetics of most protein folding

Denaturants

Chemicals

Guanidine

Urea

Heat

Denaturation

Monitor a signal

Enthalpy

Spectral

Fluorescense

Circular Dichroism

Unfolding is cooperative

Protein Structure Determination

Circular Dichroism Spectroscopy

Chiral Centers

Secondary structures are unique arrangements of chiral centers leading to unique spectra

Unique absorption of circularly polarized light

Monitors protein structure by recognizing secondary structures

Differential absorption of circularly polarized light

NMR Spectroscopy

No direct image of protein is obtained, just a series of spatical constraints

Complicated

Only small proteins can be studied

Dynamics of protein-ligand interactions

Motional dynamics of whole molecule

Protein is in solution

Rate of recovery is related to the environment of the nucleus

After pulse- recover to original angle

Pulse of radio frequency resonant to precession frequency of nucleus: nucleus will flip to precess at different angle

In high strength magnetic field- unpaired nuclei process

Track nuclear spin on unpaired nuclei (1H, 13C (6 protons and 7 neuts), 19F (9 prots and 10 neuts))

X-Ray Crystallography

Disadvantages

Solution conditions are not "native"

Crystal contacts can distort important regions of proteins

Structure is static

Proteins must crystallize; not aqueous structure

Advantages

Large proteins and protein complexes

Very High resolution - 1.5 A

Diffraction pattern is used to construct a 3D arrangement of atoms

X-rays diffract off of electron clouds of C,N,S,O- but usually not H

Crystals are blasted with X-rays

Proteins are crystallized into 3-D lattices

Chapter 3: Amino Acids

Methods of Separation

Isoelectric Focusing

Proteins migrate to pH=pI

Ampholytes establish stable pH gradient

Isoelectric Point

Estimating the Molecular Weight of a Protein by Electrophoresis

Migration depends on Charge and Size

Migration of ions in electric field

Chromatography

Affinity Chromatography

PolyT

Elution: Free Thymine

Immobilized PolyT

Purpose: mRNA purification

His Tag

Elution: High imidazole in elution buffer

Imidazole chelates Ni 2+ on column, so His-tagged protein sticks on column

Proteins are engineered to have a His6 sequence

Ni 2+ is immobilized on column

Engineered into gene sequence

Ion Exchange Chromatography

Cation Exchange

Wash off impurities (-) and neutral impurities

Choose buffer so analyte is (+) charged

Cations stick to (-) charged column

Anion Exchange

Elute analyte with High salt or basic conditions (deprotonates analyte)

Wash off impurities (+) and neutral impurities

Equilibrate column then adsorb analyte to column

Choose buffer so analyte is (-) charged

Anion stick to (+) charged column

Size Exclusion Chromatography

Separates based on size

Exchanges buffer components between sample matrix and column buffer

No adhesion to the stationary phase

Large molecules are more often in flow path, so they elute first

Small molecules explore internal space and are out of flow path

Porous particles

Centrifugation

Separate Soluble from Insoluble

Membrane Components

Soluble Proteins

Separate Mitochondria

Isopycnic Centrifugation

Takes a sample and the more dense component settles to the botton while the least dense component floats in the center

Separate Organelles

Differential Centrifugation

Left with pellets containing ribosomes and large macromolecules

Keeps breaking up the materials so that they become soluble proteins

Spins very fast and separates organelles

Disulfide Bonds

Covalent link between side chains

Polar, Charged Amino Acids

Acidic

Glutamate

Aspartate

Basic

Histidine

Arginine

Lysine

Polar, Uncharged Amino Acids

Glutamine

Asparagine

Cysteine

Threonine

Serine

Aromatic Amino Acids

Tryptophan

Tyrosine

Phenylalanine

Hydrophobic Amino Acids (Aliphatic)

Methionine

Isoleucine

Leucine

Valine

Proline

Alanine

Glycine

Ionizable Groups on Amino Acids (pKa)

Arginine : 12

Lysine : 10

Histidine : 6

Glutamate : 4

Aspartate : 4

a-amino : 10

a-carboxylate : 2

Biological View of Chemical Bonding

Hydrophobic Interactions

Water forms cages around hydrophobics (antiparallel orientation of water dipoles); Very LOW Entropy of solvent

Decrease in entropy of water drives the burial of hydrophobic surface area

Hydrophobic groups condense. Preleases trapped water to bulk

Micelle forms. Water released to bulk solvent

Micelle formation: High Entropy of solvent

Van der Waals Interactions

Dipole-Dipole Interactions

London Dispersion Factors

Biomolecule

Fatty Acid

Micelle

Globular Protein

Hydrophobic amino acids interact in center of proteins

Hydrophobic tails in center of the micelle interact with London Dispersion Forces

Always attractive interactions

Weak, local interactions between the fluffy, deformable electron clouds of hydrophobic groups

Occur in the absence of water

Favorable Interactions between hydrophobic molecules

Ionic Interactions

Biomolecules

Critical for folding and function of biological molecules

Like charges attract and opposite charges repel

Charged side chains and Nitrogen and Carbon termini

Solubility of NaCl

Water is dipole

Orients Hydrogen toward anions and Oxygen toward cations

Bent is weaker Hydrogen Bond

Linear is stronger Hydrogen Bond

Covalent Bonds

Bond dissociation energy

Difinition

Life: A diverse collection of proteins, nucleic acids, lipids, and carbohydrates that undergo chemical reactions allowing for:

Use Energy from environment to do chemical work

Metabolism

Makes ATP and reduced conenzymes

Degradative

Oxidative

More bonds to Oxygen

Anabolism requires energy input

Reductive

More bonds to Hydrogen

Uses ATP and reduced coenzymes

Eat

Synthetic

Kinetics

Thermodynamics

Free Energy (delta G)

Excess Energy that can be used as work or heat

Equilibrium

Dynamic interconversion of products and reactants

"How far?"

Heat, work, and energy of chemical reactions

Catalysts: lower activation energy barrier

Enzymes Stabilize Transition State conformation

Activation Energy (delta G+)

Energy required to overcome the Activation Barrier

Activation Barrier

Determined by energy of Transition State

Transition State:

Intermediate between substrate and product

Unstable

Distinct conformation

Slow rate results from high activation energy barrier

"How fast?"

Rate of Chemical Reaction

Equilibria

Precise self-replication and assembly

Evolution

Low Density of Ice

Ice cap on large or moving bodies of water

Temperature of water below ice is buffered from subzero air

Water doesn't freeze through

High Specific Heat of water

Terrestrial Animals

Internal water buffers extremes of temperature

Imprecise Self-replication

Cell Mitosis

Segregating subcellular structures into daughter cells

Central Dogma

Replication, Transcription, Translation

Complexity and Organization

Structural Hierarchy: Molecules to Cells

Level 4: The cell and its organelles

Level 3: Supramolecular Complex

Cell wall

Plasma Membrane

Chromatin

Level 2: Macromolecule

Cell Wall --> Cellulose

Plasma Membrane --> Protein

Chromatin --> DNA

Level 1: Monomeric Units

Cellulose --> Sugars

Protein --> Amino Acids

DNA --> Nucleotides

Tissue Specific Expression of Genes

Genomic DNA

~3000 are expressed in all cells

20,000 to 24,000 genes

Microscopic Motion

Dynein

Macroscopic Motion

Muscle, Bone, Sinew

Biological Polymers

Separation from, but response to environment

Compartmentalization of functions

Selective Permeability

Membranes are Complex

Peripheral

Integral

Fluid Mosaic Model

Fat Soluble Materials

Signaling Lipids

Receptors

Membranes

Lipid barriers between aqueous compartments

Phosphoglycerides

Phosphate

Glycerol

Water

Water as a Solvent

Noncovalent Bonds

Ionic Interaction

Hydrophobic Interaction

Van der Waals Interaction

Dipole-Dipole Interaction

Ion-dipole Interactions

Hydrogen Bonds

Key to Interactions of Biological Molecules

Good Solvent, Bad Solvent

Ice Floats

Polar, Dipole

Biological Molecules and Digestion

Biological Macromolecules

Polymers

Cholesterol

Sphingolipids

Phosphoacylglycerol

Lard - TAGs in animals - saturated FAs

Oils - TAGs in plants - unsaturated FAs

Storage in Adipose

FAs esterified to glycerol

Fatty Acids

Polysaccharides

hemiacetals and acetals

Glycosidic bonds

Monosaccharides

Nucleic Acids

Phosphodiester

Ribophosphate backbone

Nucleotides

Amino Acids

R= side chains

20 common acids

folded complex structures

3 or 4 degrees structures

Chaos to order to chaos

Complex Molecules

Lipids

Glycogen

Work in Body

Coordinated synthesis and Degradation

Dysequilibrium

Muscle Contraction

Plants

Photosynthesis

Glucose

Starch

Ate and Digested

Anabolism

Catabolism

Animals

Organs of Digestive System

Key Concepts

Pancreas

Synthesis of digestive enzymes

Pro-peptidases/ Peptidases

Pro-elastase/ Elastase

Chymotrypsinogen/ Chymotrypsin

Trypsinogen/ Trypsin

Triacyglycerol

Pancreatic Lipase

Hormones

Bile acid synethesis

Bile Salts

Enzymer

Harvesting

Small Intestine

Adsorption of small molecules

Transporters

Intestinal lining

Digestion of Fats

Pancreatic Lipase (+Colipase)

Bile Acids

Liver

Pancreatic Enzymes

Zymogens

Neutralization

Stomach

Zymogen/Protease

Activation by acid

Protease- Enzyme that hydrolyses peptide bonds (Pepsin)

Zymogen- Inactive precursor protease (Pepsinogen)

Hydrolyze peptide bonds

Pepsinogen/Pepsin

Acidic Conditions

Strong Acid

Activates pepsinogen to pepsin in stomach

Unfolds proteins

Acidifies chewed food entering stomach

Completely dissociates

Cells in stomach lining secrete HCl

Stomach lining epithelium is protected from acid by mucins

Secreted after meal is eaten

Peptide bonds

Amides

Stable polymers folded into complex structures

Purpose

Digestion of Proteins

Homogenization

Acid

Mouth

Saliva

Enzymes

Amylase

Proteins

Mucopolysaccharides

Antimicrobials

Enzymes that degrade or poison microbes

Teeth

Chewing

The text explores the biological perspective of chemical bonding, focusing on both covalent and noncovalent interactions. Covalent bonds are examined in terms of bond dissociation energy, highlighting their strength and stability.