Online Biochem

What is the angle of a sp3 bond?

109.5

What are the major elements in living organisms?

H,C,N,O,Na,P,S,Cl,K,Ca

What are the angles in a sp2 bond?

120

What shape are sp2 bonds?

Planar trigonal

What the angles in a sp bond?

180

Stereoisomer

Same composition but a different configuration

Configurational isomer

Different arrangements of groups around a chiral center, a single bond must break

Enantiomers

Mirror images, can never be rotated to get the other enantiomer (a bond must break)

Confromations

From rotation around a single bond

Eclipsed

Higher energy, less stable

Staggered

Lower energy, more stable

Configuration

Fixed arrangement of atoms directed by the bonds of a molecule

Biochemical reactions

Matter and energy exhanged

Catabolism

Converting energy to be used

Why does energy need to be convereted?

To do work and anabolism

Phototroph

Uses sunlight as energy

Chemotroph

Energy from chemical molecules

Lithotroph

Inorganic molecules used as fuel

Organotroph

Organic molecules are used as fuel

Autotroph

Fix CO2 to get carbon

Heterotroph

Use organic molecules to get carbon

Energy

The capacity to do work

What is the first law of thermodynamics

Energy is constant, never created or destroyed, only changes forms

What is the second law of thermodynamics?

Energy is transferred to increase entropy

What is gibbs free energy equation?

G=H-TS or DG=-RTln(keq)

Enthalpy

Total energy in a system

Free energy

Energy available to do work

Spontaneous

Negative DG, exergonic, DH<TS, energy released, products more stable than reactants

Nonspontaneous

Endergonic, positive DG, products less stable than reactants

Equilibrium

No net change between products and reactants, no work is done

What is the equation to find the equilibrium constant?

K=[P]/[R]

Le Chateliers principle

When equilibrium is disturbed, the system will correct this change and move back to equilibrium

Draw the structure of an amino acid

Zwitterion

Has a positive and a negative charge

Why does binding need energy input?

Due to loss of entropy

Sulfhydryl

Very reactive, forms disulfide bonds in extracellular conditions

Where do disulfide bonds form?

In extracellular conditions (oxidizing), inside of cells it is reducing

Glycine

Not chiral, important for folding

Proline

Cyclic, conformationally restricted

What are the types of secondary structures of proteins?

Helix, beta sheet, and loop

How do peptide bonds form?

Condensation reaction

Peptide bond

Unbranched, planar, no rotation, must be cis or trans

Is cis or trans favored for a peptide bond?

Trans, except when proline is the terminal amino acid

Phi

Bond between N and the alpha C

Psi

Between carbonyl carbon and alpha carbon

How are phi bonds measured?

Look down the bond from the N to the terminal alpha carbon, then measure the angle between the carbonyl carbons

How are psi bonds measured?

Look down N to the terminal alpha carbon, measure the angles between the Ns

Ramachadran plot

Areas of dihedral angles that phi/psi that are allowed for regular proteins, have minimized steric clashses

What allows secondary structures to form?

Multiple bonds in a row being in the same plot area, polar groups forming H-bonds

Helix

carbonyl of x bonds with the amino group of x+4, 3.6 residues per turn, side chains point out

Beta sheet

Multiple beta strands joined through H-bonds, side chains perpendicular to H-bonds, can be parallel anti parallel or both, sides of sheets have different properties

Loop

Can be any combination of plot areas, connect secondary structures, many small and polar residues, form active sites, flexible, proline and glycine here often

How are peptide bonds named?

Cis (0) and trans (180)

Alcohol dehydrogenase

Enzyme that is important in energy metabolism

Primary structure

Amino acid sequence

What geometry does an alpha carbon have?

Tetrahedral

What geometry does a carbonyl carbon have?

Trigonal

What atoms connect to form a peptide bond?

Carbonyl carbon and nitrogen

Imino acid

R group connects with N and carbonyl C, no h to h bond with, breaks alpha helixes