Scale of Cellular World

7/24/2019 Scale of Cellular World

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Object Real Size X 106

Water 0.28 nm 0.28 mm

Alanine 0.5 nm 0.5 mm

Diam. DNA 2.5 nm 2.5 mmHemoglobin 7.0 nm 7 mm

Ribosome 20 nm 2 cm

Polio Virus 30 nm 3 cmMitochondrion 1500 nm 1.5 m

E. coli 2000 nm 2 m

Liver cell 20,000 nm 20 m

Perspective:

Scale of the Cellular World


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pH is a measure of the acidity or basicity of an

aqueous solution

pH ~ -log[H+]

pH>7 is basic

pH


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Can you think of an

example in your body

where the pH is not

neutral (i.e., near pH7)??

Reflection


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Hydrogen bonds

Shared hydrogen between two molecules or parts

of a molecule

Non-covalent bonding

in biological systems


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Ionic/electrostatic interactions




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Hydrophobic interactions/forces




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Fig. Geckos climb on sheer

surfaces using van der Waals

forces between the surface

and microscopic projectionson their footpads

van der Waals Interactions




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IMPORTANT:

Approximate Bond Strengths


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Promotes assembly

Occurs spontaneously

Driven by interaction energy

Large number of small forces creates flexibility of

structures

Example: Membranes/lipid bilayer

Non-covalent Bonding Essential to Life


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Why are the

properties of

water soessential to life

as we know it?

Reflection


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Order of amino acids determined bynucleotide 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 semesterBottom line: DNA sequence linked to RNA

sequence linked to protein sequence

Proteins Composed of Amino Acids


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Amino Acid Structure


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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


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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

Properties of Side Chains Important
http://www.wiley.com/college/boyer/0470003790/animations/acideroids/acideroids.htmhttp://www.wiley.com/college/boyer/0470003790/animations/acideroids/acideroids.htm


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Amino

Acid

Structures


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Only imino acid:

Proline


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Amino

Acid

Structures

Annotated


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Why are the

properties of the

amino acid sidechains

important?

Reflection


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Proteins are polymers assembled from amino

acids units (IMPORTANT) Only 20 natural amino acids make up many 1000s

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


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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

PROTEIN STRUCTURE


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In the 1930s William Astbury studiedwool 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)

Patterns of Protein Structure


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Link to YouTube video about alpha helix

Identified by PaulingHistoric Article

Alpha Helical Structure
http://www.youtube.com/watch?NR=1&v=eUS6CEn4GSAhttp://www.youtube.com/watch?NR=1&v=eUS6CEn4GSA


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Backbone hydrogenbonding between

amino and carbonyl

separated by 4residues



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Backbone hydrogenbonding within the

same strand



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Can have interactionsof R groups (not shown

here in poly-Ala) to

stabilize helix



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Link to YouTube video about beta sheets

Backbone hydrogen bonding

between strands

Beta-Sheet Structure
http://www.youtube.com/watch?v=wM2LWCTWlrEhttp://www.youtube.com/watch?v=wM2LWCTWlrE


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Backbone hydrogen bondingbetween strands

Note interaction between R

groups (does this limit R size?)

Beta-Sheet Structure


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Orientation can be

anti-parallel

orparallel

b-Sheet Structure


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Beta-

SheetStructure


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Why do you think thatthe a-helix and b-sheet

are each referenced as

secondary structure?

How does the energy of

these structures compareto the energy of the

peptide bond?

Reflection


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What contribution doesthe side chain of each

amino acid make to

secondary structure?

Would you expect all

amino acids participatein secondary structure?

Reflection


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Primary Structure: Amino acid sequence

Secondary Structure:

a-helix/b-sheet

Tertiary Structure:

Folding into 3-dimensions

Quaternary Structure:

Assembly into higher oligomers

Levels of Protein Structure


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d l d ld


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Stabilizing energy for protein folding:

Primarily non-covalent interactions

Disulfide

bond

formation

(covalent

bond) can

stabilize

protein fold

Bonds Utilized in Protein Folding


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Link to another YouTube video about protein folding

Link to YouTube video about protein folding

Interactions occur rapidly and result in the folded structure

Process is dynamic AND Structure is dynamic

Bringing Alpha Helices/Beta Sheets

Together in a Folded Structure
http://www.youtube.com/watch?v=_xF96sNWnK4&NR=1http://www.youtube.com/watch?feature=fvwp&NR=1&v=fvBO3TqJ6FEhttp://www.youtube.com/watch?feature=fvwp&NR=1&v=fvBO3TqJ6FEhttp://www.youtube.com/watch?v=_xF96sNWnK4&NR=1


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Protein Folding Funnels

Energetic Pathways to Function


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Large energy penalty for loss of entropy think of it as loss of options for

different states so that the overall difference in energy betweenfolded/unfolded is small!




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VERY IMPORTANT: Energetic difference between folded and

unfolded proteins ~ equivalent to 1-2 non-covalent interactions




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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 afterprotein 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 Waals

Forces That Hold Proteins Together

h ld h


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PROTEINS ARE STABILIZED

GENERALLY

BY


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Can you imagine whymost living organismsare sensitive toelevated

temperature?

What would you

imagine wouldhappen to proteinstructure?

Reflection

Documents

Scale of Cellular World