Biochemistry Class 1

What are four types of macromolecules?

Proteins, carbohydrates, lipids, and neucleic acids

How are macromolecules made?

Via polymerization reactions using polymerases (aka condensation reaction, dehydration synthesis reactions)

Adds them together via removal of water

Makes polymers out of monomers

What are acidic amino acids?

Aspartate, glutamate

What are basic amino acids?

Lysine, arginine, histidine (kinda)

What are polar amino acids?

Serine, threonine, asparagine, glutamine, tyrosine, cysteine

What are the non-polar amino acids?

Glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tryptophan

What are neutral amino acids?

Serine, threonine, asparagine, glutamine, cysteine, tyrosine

Histidine can be

pKa of amino acid R groups and charge at physiological temperature

1 and 3 letter abreviations

How is a peptide bond formed?

Amino group attacks carboxylic acid group → loose a water

What direction are proteins synthesized in?

N → C

What is primary structure? Secondary? Tertiary? Quaternary?

1. sequence of amino acids

2. interactions between the backbone (alpha helix, beta sheet)

   1. hydrogen bonds

3. interactions between R groups

   1. non covalent bonds

   2. covalent disulfide bridge

4. more than one peptide whose side chains interact

What is hydrolysis?

Use a water to break a molecule

What is the monomer of carbohydrates? Formula?

Monosaccharides

CnH2nOn

What is glucose structure?

What is fructose structure?

What is galactose structure?

What is ribose structure?

see image

What is deoxyribose sugar?

see image

What is maltose made of?

Two glucoses

What is sucrose made of?

Glucose + fructose

What is lactose made of?

Glucose + galactose

What is glycogen?

Chain of glucose for storage in animals

Humans can digest it

Polar, so it carries water with it

What is starch?

Chain of glucose for storage in plants

Humans can digest it

What is cellulose?

Plant structure

Not digestable by humans

How are carbs primarily used?

Energy, cell surface markers, adhesion (in unicellular organisms mainly)

What are fatty acids?

Hydrocarbon with an acid on the end

What are properties of saturated vs unsaturated fatty acids?

Saturated: solid at room temp

Unsaturated: liquid at room temp

What are triglycerides?

Three fatty acids attached to glycerol via dehydration synthesis

How fats are stored

What are phospholipids?

Two fatty acids and a phosphate group bound to glycerol

Phospholipid is polar

What are terpenes?

Made of isoprene units (at least two)

Precursor to cholesterol, steroids, ear wax

Precursor to vitamin A (a terpenoid)

What is isoprene?

Monomer of a terpene

How are terpenes named?

The number of sets of two isoprene units they have

Called a terpenoid if something else is added to it

What are cholesterols?

3 six carbon rings and 1 five carbon ring

Used in membranes, bile salts

Precursor to vitamin D and steroids

What are monomers of lipids?

Hydrocarbons

What is gibbs free energy?

delta G = delta H - T(delta S)

G = gibbs free energy

H = enthalpy = potential energy

T(delta S) = kinetic energy

When is a reaction spontaneous?

Negative delta G

Kinetic energy must be greater than potential energy

When is a reaction at equilibrium? In terms of free energy

Delta G = 0

Why are endergonic reactions sometimes coupled to exergonic ones?

The exergonic reaction releases energy the endergonic one can use

What is delta G of ATP hydrolysis? kcal/mol

-12 kcal/mol

What is kinetics?

How fast a reaction proceeds

How is reaction rate and energy of activation related?

Inverse of one another

What is delta G on an RCD?

Energy difference between reactants and products

Constant for a given reaction

What is the rate determining step in a reaction?

Reactants → transition state

How do catalysts work?

Stabilize transition state, thus lowering its energy

Reduce energy of activation

What are three characteristics of enzymes?

Increase rate of reaction

Not used up by reaction

Specific for a particular reaction

How are enzymes activated/deactivated?

Phosphorylation (#1 way to regulate them)

Allosteric regulation (#2 way)

What kind of feedback is most common in the body?

Negative/inhibition feedback

How is positive feedback used?

Neurons firing

Birthing

Both have external regulators (action potential, baby is birthed)

How does the V vs S plot look when S « E, S = E, S » E

S « E: linear

S = E: parabolic and levels off

S » E: levels off

What is V max? What does it depend on?

Max velocity of an enzyme

Depends on enzyme concentration and which enzyme is being used

What is Km? How does it relate to enzyme affinity?

Substrate concentration needed to reach ½ V max

Enzymes with higher affinity have lower Km

What are types of enzyme inhibition?

Competitive: binds at active site and blocks substrate

Non-competitive: bind at allosteric site of enzyme

Uncompetitive: binds to allosteric site of enzyme-substrate complex

Mixed: bind to allosteric site of enzyme alone or enzyme-substrate complex

How do mixed inhibitors affect V vs S?

V max decreases

Km varies

What is V vs S of uncompetitive inhibition?

Shifts left and down

Km decreases

V max decreases

What is V vs S of non-competitive inhibitor?

Curve shifts down

Km is constant

V max decreases

What is V vs S of competitive inhibition?

Curve shifted right

V max stays the same

Km increases

What causes changes in Km?

Affecting the ability of substrate to bind to the enzyme (ex: competitive inhibitor, uncompetitive)

What causes change in V max?

Allosteric regulation (non-competitive and uncompetitive0

What is an LB plot?

1/V vs 1/S

Y-intercept: 1/V max

X-intercept: -1/Km

What does competitive inhibition look like on an LB plot?

V-max same = y-intercept the same

Km increases = x-intercept approaches zero

What does non-competitive inhibition look like on an LB plot?

V max decreases = y-intercept is further from zero

Km constant = x- intercept is constant

What does uncompetitive inhibition look like on an LB plot?

V max decreases = y-intercept goes further from zero

Km decreases = x-intercept goes further from zero