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Perspective:

Scale of the Cellular World

Object

Real Size

X 10 6

Water

0.28 nm 0.5 nm

0.28 mm 0.5 mm

Alanine

Diam. DNA

2.5 nm

2.5 mm

Hemoglobin Ribosome Polio Virus Mitochondrion E. coli Liver cell

7.0 nm 20 nm 30 nm 1500 nm 2000 nm 20,000 nm

7 mm

2 cm

3 cm

1.5 m

2 m

20 m

pH

pH is a measure of the acidity or basicity of an

aqueous solution

a measure of the acidity or basicity of an aqueous solution • pH ~ -log[H +

pH ~ -log[H + ]

pH>7 is basic

pH<7 is acidic

pH influences most biological processes and is

usually near 7 (“neutral”) in living cells

Reflection

Can you think of an example in your body where the pH is not

neutral (i.e., near pH

7)??

Reflection • Can you think of an example in your body where the pH is not

Non-covalent bonding in biological systems

Hydrogen “bonds”

Shared hydrogen between two molecules or parts of a molecule

• Hydrogen “bonds” – Shared hydrogen between two molecules or parts of a molecule
in biological systems • Hydrogen “bonds” – Shared hydrogen between two molecules or parts of a

Non-covalent bonding in biological systems

Ionic/electrostatic interactions

Non-covalent bonding in biological systems • Ionic/electrostatic interactions
Non-covalent bonding in biological systems • Ionic/electrostatic interactions

Non-covalent bonding in biological systems

Hydrophobic interactions/forces

Non-covalent bonding in biological systems • Hydrophobic interactions/forces

Non-covalent bonding in biological systems

van der Waals Interactions

in biological systems • van der Waals Interactions Fig. Geckos climb on sheer surfaces using van

Fig. Geckos climb on sheer

surfaces using van der Waals

forces between the surface and microscopic projections on their footpads

climb on sheer surfaces using van der Waals forces between the surface and microscopic projections on

IMPORTANT:

Approximate Bond Strengths

IMPORTANT: Approximate Bond Strengths

Non-covalent Bonding Essential to Life

Promotes assembly

Occurs spontaneously

Driven by interaction energy

Large number of small forces creates flexibility of structures

Example: Membranes/lipid bilayer

energy • Large number of small forces creates flexibility of structures • Example: Membranes/lipid bilayer

Reflection

Why are the

properties of water so essential to life as we know it?

Reflection • Why are the properties of water so essential to life as we know it?

Proteins Composed of Amino Acids

Order of amino acids determined by

nucleotide sequence in DNA

Corollary Proteins are manifestation of DNA sequence

Intermediary process to copy DNA

(transcription) and assemble amino acids (translation)

More on these processes later in semester

Bottom line: DNA sequence linked to RNA

sequence linked to protein sequence

Amino Acid Structure

Amino Acid Structure

Properties of Side Chains Important

Multiple types Acidic (glutamic acid, Glu, E)

Basic (lysine, Lys, K)

Polar (serine, Ser, S)

Apolar/hydrophobic (tryptophan, Trp, W)

H (glycine, Gly, G)

Know these properties of the side chains!!

Assigned one structure in each category to be

able to recognize

Properties of Side Chains Important

Multiple types Acidic (glutamic acid, Glu, E)

Basic (lysine, Lys, K)

Polar (serine, Ser, S)

Apolar/hydrophobic (tryptophan, Trp, W)

H (glycine, Gly, G)

• Game (Lame Game??): Link to the game
• Game (Lame Game??): Link to the game

Amino

Acid

Structures

Proline

Only imino acid:

Proline • Only imino acid:

Amino

Acid

Structures

Annotated

Reflection

Why are the

properties of the amino acid side chains important?

Reflection • Why are the properties of the amino acid side chains important?

PROTEIN STRUCTURE

Proteins are polymers assembled from amino

acids “units” (IMPORTANT)

Only 20 natural amino acids make up many 1000’s of proteins

Linked by peptide bonds to form a polymer

Structure designated in two different ways

Peptide bonds and amino acid core form the “backbone” Each amino acid provides a unique side chain

PROTEIN STRUCTURE

Proteins are “written” from N-terminus to C- terminus aa sequence is PRIMARY STRUCTURE

Actually synthesized in that orientation

Always written in this orientation

Often written as a sequence of 1- or 3-letter

abbreviations:

GKPEESWEG

GlyLysProGluGluSerTrpGluGly

this orientation – Often written as a sequence of 1- or 3-letter abbreviations: GKPEESWEG GlyLysProGluGluSerTrpGluGly

Patterns of Protein Structure

In the 1930’s William Astbury studied

Structure • In the 1930’s William Astbury studied wool and hair using X-ray fiber diffraction (similar

wool and hair using X-ray fiber diffraction (similar to DNA studies)

Data showed coiled molecular structure

that he called “alpha” (later to become a- helix)

When heated or stretched, another pattern

was observed that he called “beta” (later to

become b-structure or b-sheet)

Alpha Helical Structure

Alpha Helical Structure Identified by Pauling Historic Article Link to YouTube video about alpha helix

Identified by Pauling

Historic Article

Alpha Helical Structure Identified by Pauling Historic Article Link to YouTube video about alpha helix

Alpha Helical Structure

Alpha Helical Structure Backbone hydrogen bonding between amino and carbonyl separated by 4 residues Link to

Backbone hydrogen

bonding between

amino and carbonyl separated by 4

Backbone hydrogen bonding between amino and carbonyl separated by 4 residues Link to YouTube video about

residues

Alpha Helical Structure

Alpha Helical Structure Backbone hydrogen bonding within the same strand Link to YouTube video about alpha

Backbone hydrogen

bonding within the same strand

Alpha Helical Structure Backbone hydrogen bonding within the same strand Link to YouTube video about alpha

Alpha Helical Structure

Alpha Helical Structure Can have interactions of R groups (not shown here in poly-Ala) to stabilize

Can have interactions

of R groups (not shown here in poly-Ala) to

stabilize helix

Can have interactions of R groups (not shown here in poly-Ala) to stabilize helix Link to

Beta-Sheet Structure

Backbone hydrogen bonding

between strands

Beta-Sheet Structure Backbone hydrogen bonding between strands Link to YouTube video about beta sheets
Beta-Sheet Structure Backbone hydrogen bonding between strands Link to YouTube video about beta sheets

Beta-Sheet Structure

Backbone hydrogen bonding

between strands

Note interaction between R

groups (does this limit R size?)

Structure Backbone hydrogen bonding between strands Note interaction between R groups (does this limit R size?)
Structure Backbone hydrogen bonding between strands Note interaction between R groups (does this limit R size?)

b-Sheet Structure

Orientation can be anti-parallel or

parallel

Beta-

Sheet

Structure

Reflection

Why do you think that

the a-helix and b-sheet

are each referenced as

“secondary structure”?

How does the energy of

these structures compare

to the energy of the

peptide bond?

as “secondary structure”? • How does the energy of these structures compare to the energy of
as “secondary structure”? • How does the energy of these structures compare to the energy of

Reflection

What contribution does

the side chain of each

amino acid make to

secondary structure? Would you expect all

amino acids participate

in secondary structure?

of each amino acid make to secondary structure? • Would you expect all amino acids participate
of each amino acid make to secondary structure? • Would you expect all amino acids participate

Levels of Protein Structure

Primary Structure: Amino acid sequence

Secondary Structure:

Structure: Amino acid sequence • Secondary Structure: – a -helix/ b -sheet • Tertiary Structure: –

a-helix/b-sheet

Tertiary Structure:

Folding into 3-dimensions

Quaternary Structure:

Assembly into higher oligomers

• Tertiary Structure: – Folding into 3-dimensions • Quaternary Structure: – Assembly into higher oligomers

PROTEIN FOLDING

Amino acid sequence of a protein

not functional without folding

acid sequence of a protein not functional without folding • 3-D structure is the active form

3-D structure is the active form of a protein

Non-covalent bonds between side chains (and peptide backbone interactions) create the “folded” form of the protein (IMPORTANT)

Folded form exhibits a biological activity

Folding of amino acid sequence based on DNA sequence is path to FUNCTION!

Bonds Utilized in Protein Folding

bond
bond

Disulfide

formation

(covalent

bond) can

stabilize protein fold

Stabilizing energy for protein folding:

Primarily non-covalent interactions

Bringing Alpha Helices/Beta Sheets Together in a Folded Structure

Interactions occur rapidly and result in the folded structure

•Process is dynamic

AND

and result in the folded structure •Process is dynamic AND •Structure is dynamic Link to YouTube

•Structure is dynamic

structure •Process is dynamic AND •Structure is dynamic Link to YouTube video about protein folding Link

Protein Folding Funnels Energetic Pathways to Function

Protein Folding Funnels Energetic Pathways to Function
Protein Folding Funnels Energetic Pathways to Function

Protein Folding Funnels Energetic Pathways to Function

Large energy penalty for loss of entropy think of it as loss of options for different states so that the overall difference in energy between folded/unfolded is small!

Protein Folding Funnels Energetic Pathways to Function

VERY IMPORTANT: Energetic difference between folded and unfolded proteins ~ equivalent to 1-2 non-covalent interactions

Forces That Hold Proteins Together

Covalent (primary structure)

Single bonds: C-H, C-C, C-N, C-O ~90 kcal/mole

Covalent (secondary and tertiary structure)

Disulfide: S-S, ~60 kcal/mole

Form after protein is folded by non-covalent bonding

Can be intramolecular or between separate chains

Most often found in excreted proteins (for extra stability)

Noncovalent (generally < 5 kcal/mole)

H-bonds (NOTE: Primary for secondary structure)

Hydrophobic

Ionic

van der Waal’s

Forces That Hold Proteins Together

Covalent (primary structure)

Single bonds: C-H, C-C, C-N, C-O ~90 kcal/mole

Covalent (secondary and tertiary structure)

Disulfide: S-S, ~60 kcal/mole

Form after protein is folded by non-covalent bonding

Can be intramolecular or between separate chains

Most often found in excreted proteins (for extra stability)

• Noncovalent (generally < 5 kcal/mole) – H-bonds (NOTE: Primary for secondary structure) – Hydrophobic
• Noncovalent (generally < 5 kcal/mole)
– H-bonds (NOTE: Primary for secondary structure)
– Hydrophobic
PROTEINS ARE STABILIZED
GENERALLY
– Ionic
BY <2 NON-COVALENT BONDS
– van der Waal’s

Reflection

Can you imagine why most living organisms are sensitive to elevated temperature?

What would you

imagine would happen to protein structure?

living organisms are sensitive to elevated temperature? • What would you imagine would happen to protein