ADP/ADT

Four levels of protein structure

Primary, secondary, tertiary, quaternary

Primary structure

Linear arrangement of amino acids in a protein due to peptide bonds

Primary structure example

Gly – Ala – Ala – His – Lys – Tyr – Gly – Val – Ser

Amino acids and protein conservation

Amino acids important to protein structure and function are conserved across species

Homologs

Multiple versions of a particular protein that have highly conserved regions important for function

Motifs

Clusters of conserved residues

Motif function

Motifs carry out a particular function or form a particular structure that is important for the conserved protein

Amino acid side-chain categories

Small hydrophobic; large hydrophobic; polar; positive charge; negative charge

Secondary structure

Local structure/folding due to peptide backbone interactions

Alpha-helix

Carbonyl oxygen in the backbone of one amino acid forms a hydrogen bond with the amide in the peptide backbone of the 4th amino acid down

Alpha-helix stability

Each hydrogen bond is relatively weak by itself; the sum

of the hydrogen bonds in a helix makes it stable

Alpha-helix formation

The propensity of a peptide to form an α-helix depends on amino acid sequence

Beta-sheet

Carbonyl oxygens and amides form hydrogen bonds

Beta-sheet arrangement

β-sheets can be antiparallel or parallel

Beta-sheet formation

The propensity of a peptide to form a β-sheet depends on its amino acid sequence

Tertiary structure

Overall folding due to interactions of secondary structures and side chains

What drives overall protein folding

Hydrogen bonds between side chains

hydrophobic interactions

ionic bonds between side chains

van der Waals interactions between side chains

disulfide bonds between side chains

Hydrogen bonds in tertiary structure

Hydrogen bonds can form between side chains

Hydrophobic interactions

Drive oily or hydrophobic side chains into the interior between side chains and away from water

Ionic bonds in tertiary structure

Ionic bonds form between side chains

Van der Waals interactions

Van der Waals interactions occur between side chains

Disulfide bonds

Disulfide bonds form between side chains

Tertiary structure interactions

Hydrogen bonding; ionic bonding; disulfide bonds; hydrophobic interactions

Effect of amino acid sequence changes

Changes in amino acid sequence can affect tertiary structure

Quaternary structure

Overall folding and association of multiple protein chains due to interactions among multiple protein chains

Quaternary structure formation

Interactions between multiple polypeptide chains produce quaternary structure

Protein structure clicker question

Ionic bonding between the side chains of glutamate and lysine residues on the same polypeptide chain is included in tertiary structure

Cells and energy

Cells take energy from their environment

Phototrophs

Use energy from the sun with CO2 and H2O to produce sugar and O2

Sugar and oxygen

Sugar + O2 → CO2 + H2O + energy; this is described as combustion

Actual combustion

Highly irreversible and releases most energy as heat

Cellular metabolism

Cells are much more efficient than actual combustion and shuttle energy through complex series of enzymatic reactions

Metabolism and cell growth

Stoichiometry and thermodynamics can be applied to metabolism of cell growth

ATP

Adenosine triphosphate

Endergonic reactions

Many reactions inside a cell are endergonic (ΔG > 0)

ATP function

Energy is stored and transferred in ATP

ATP structure

Contains ribose

Metabolic reaction coupling

Cells couple free energy from ATP hydrolysis to energetically unfavorable reactions

Enzyme coupling

An enzyme couples the two reactions by catalyzing transfer of the phosphoryl group of one directly to the other

ATP hydrolysis

ATP + H2O → ADP + Pi; ΔG° = -7.3 kcal/mol

ADP hydrolysis

ADP + H2O → AMP + Pi; ΔG° = -7.3 kcal/mol

Redox

NAD can exist in oxidized and reduced forms

NAD reduction and oxidation

Reduction involves +2H; oxidation involves -2H

NAD components

NAD contains ribose

NAD

Nicotinamide adenine dinucleotide

NADP

NAD with a phosphate group

NADH and NADPH

NADPH and NADH supply hydrogen in biosynthetic reactions

NADH function in respiratory chain

Electrons and protons carried by NADH are transferred to oxygen by compounds that make up the respiratory chain

Energy from NADH transfer

Transfer of electrons and protons from NADH to oxygen releases enough energy to create up to 3 ATP molecules

NADH

Reduced form of NAD

NAD

Oxidized form of NAD

Anaerobic glucose catabolism

Glycolysis followed by fermentation

Glycolysis alternative name

Embden-Meyerhof-Parnas (EMP) pathway

Fermentation products

Ethanol

Glycolysis

Converts glucose into two C3 units

Glycolysis reactions

10 enzyme-catalyzed reactions

Glycolysis Stage I

Hexose sugar is cleaved into 2 triose molecules and consumes 2 ATP

Glycolysis Stage II

Each of the 2 trioses per glucose is converted to pyruvate and produces 4 ATP

Glycolysis overall reaction

C6H12O6 + 2 NAD+ + 2 ADP + 2 Pi → 2 C3H4O3 + 2 NADH + 2 ATP + 2 H+

Glycolysis products per glucose

2 pyruvates

Glycolysis ATP accounting

Stage I consumes 2 ATP and Stage II produces 4 ATP

Anaerobic metabolism

Does not use oxygen

Anaerobic fermentation

Occurs after glycolysis

Anaerobic metabolism of pyruvate

Produces alcohol or lactic acid

ATP from fermentation

Fermentation itself produces zero ATP

NADH during fermentation

2 NADH are consumed

ATP source during fermentation

Organisms that undergo fermentation get all their ATP from glycolysis

NAD+ regeneration

Anaerobic metabolism produces the NAD+ needed for glycolysis

Fermentation enzymes shown

Pyruvate decarboxylase and alcohol dehydrogenase