CSF Macromolecules

phosphorylation

• a type of covalent enzyme modification where kinase adds a phosphate group to turn inactive glycogen phosphorylase b to active phosphorylase a

• to undo, phosphatase takes phosphate away

• REVERSIBLE

proteolytic cleavage

removal of part of the polypeptide chain, irreversible

ex: coagulation cascade (thickens blood in a cut), complement cascade (deactivates bacteria in blood)

zymogen

synthesized inactive enzyme that gets proteolytic cleavage to activate it

covalent modification

a way to regulate enzymes by covalently adding or removing a compound, reversible

protease

an enzyme that carries out proteolytic cleavage, cutting a protein up

robert hooke

1665 observed dead cork compartments and named them cells

anton van leeuwenhoek

1674 improved the microscope and observed single-celled organisms

motility proteins

contraction and movement, some enzymatic activity

amino acids

the monomers of proteins, only 20 kinds

L- vs D- amino acid

L-amino acid has the amino group on the LEFT

D-amino acid has the amino group on the RIGHT

all amino acids in the human body are L-amino acids

how to tell if an amino acid is hydrophobic or hydrophyllic

if the R group has an OH or SH it’s hydrophillic because it’s polar

Which of the non-polar amino acids is the only amino acid that does not have separate L and D isomers?

glycine because it’s R group is only an H, making it perfectly symmetrical and no difference when mirrored

polypeptides

the polymers of amino acids to make proteins

How are polypeptides formed?

amino acids are linked together by a dehydration/condensation reaction, a covalent C-N bond/peptide bond is formed

monomeric protein

a protein that consists of a single polypeptide strand

multimeric protein

consists of multiple polypeptides

dimer - two polypeptides

trimer - three polypeptides

primary structure

the amino acid sequence with covalent peptide bonds

secondary structure

alpha helices, beta sheets, and random coils made with hydrogen bonds between NH and CO in the backbone

tertiary structure

three dimensional folding of a polypeptide chain

• disulfide bonds

• hydrogen bonds

• ionic bonds

• van der waals

• hydrophobic interactions

quaternary structure

association of multiple polypeptides to form a multimeric protein, same kinds of bonds as tertiary

What direction are amino acid sequences synthesized in?

from the N terminus to the C terminus

proline

amino acid that can not form hydrogen bonds, disrupts alpha helix structures

motif

supersecondary structure composed of a few secondary structure elements like alpha helices and beta sheets

fibrous proteins

characterized by extensive regions of highly ordered, repetitive secondary structure

• structural proteins

• very rigid

• elasticity in one direction

• ex: fibroin, silk, beta sheets

• ex: keratin, hair, a helices

globular proteins

folded into a compact structure

• enzymes are globular

protein domains

local regions with a function, not always continuous in primary structure

nucleic acids

the polymers on nucleotides

What component of DNA and RNA is responsible for the “acidic“ part of nucleic acid?

the phosphate group, it has a negative charge on the O- due to releasing an H+, making the solution acidic

structure of a nucleic acid

structure of ATP

What direction are nucleotides synthesized?

5’ to 3’

phosphodiester bridge

covalent phosphodiester bond between the 5’ carbon of one nucleic acid to the 3’ carbon of another to create the sugar backbone

purine

double ring nucleic acid

• adenine

• guanine

pyrimidine

single ring nucleic acid

• cytosine

• thymine

• uracil

Why do purines bind to pyrimidines?

Complementary base pairing has A match up with T with two hydrogen bonds and G with C with three hydrogen bonds. The difference in size must be made equal so the strands can be antiparallel.

polysaccharide

long chain polymer of sugar and sugar derivatives, used for structure and to store energy

aldehyde

aldosugar with a terminal carbonyl group

ketone

ketosugar with an internal carbonyl group

Why are there two forms of glucose?

When making a ring there is a 50/50 change the hydroxyl group will end up on the bottom or the top, creating an alpha-D-glucose or a beta-D-glucose, both with vastly different physical and chemical characteristics.

alpha-D-glucose

hydroxyl group on the bottom, unit of starch and glycogen, energy storage

beta-D-glucose

hydroxyl group on the bottom, unit of cellulose, creates a non-digestible cell wall

glycosidic bond

a covalent bond between two monosaccharides, dehydration

• usually 1-4, but 1-6 can cause branching

starch

storage polysaccharide in plant cells

glycogen

storage polysaccharide in animal cells and bacteria

lipid

not a long polymer, hydrophobic, function for energy storage, membrane structure, or signal transmission

fatty acid

monomer of lipid, amphipathic, long hydrocarbon chain with a carboxyl group at the end

amphipathic

having both polar and nonpolar regions

saturated

unbent fatty acid chain, liquid at room temp

unsaturated

bent fatty acid due to a double bond between two Cs, solid at room temp

cis double bond

in an unsaturated fatty acid, bent on the same side

trans double bond

in an unsaturated fatty acid, bent on different sides

triacylglycerol

storage lipids

phospholipid

has a phosphate, important to membrane structure because they are amphipathic

glycolipid

contains a carbohydrate, r group is a sugar chain, outer monolayer of the plasma membrane

steroids

a lipid with a four ringed hydrocarbon skeleton, hormone

• no fatty acids

• nonpolar, very hydrophobic

• built off cholesterol

cellulose

a polysaccharide macromolecule, the linear polymer of the beta-D-glucose monomers

Why, when something is thermodynamically feasible, does it not always proceed?

Even when the delta G is negative, there is an activation energy barrier. Enzymes are needed to catalyze the reaction and provide an alternate path with a lower activation energy, causing the reaction to actually proceed.

How do enzymes affect reaction rate?

ribozymes

rare instance where an enzyme is not a protein but is made of RNA, cleaves tRNA

cofactors

non-protein component needed by an enzyme to carry out chemical function, usually to accept an electron

• prosthetic groups: metal ions or small organic compounds bound to enzyme

• coenzymes: small organic compounds derivatives of vitamins

the induced-fit model

an enzyme's active site is flexible and changes its shape slightly to form a tight, precise fit around a substrate

methods of substrate activation

1. bond distortion: makes the bond more susceptible to catalytic attack

2. proton transfer: increases reactivity of substrate

3. electron transfer: temporary covalent bonds between enzyme and substrate

irreversible inhibitors

covalently bind to an enzyme causing permanent loss of function

reversible inhibitors

noncovalently bind to enzymes and can dissociate, causing the enzyme to regain function

competitive inhibitor

binds to active site of enzyme, blocking the substrate

noncompetitive inhibitor

binds to nonactive site of enzyme, changing its shape so it can not bind with substrate

• makes an allosteric enzyme

phosphorylation