Biochem Summer exam 2

Non-essential amino acids

have shorter pathways

Essential amino acids

usually bigger and have complex biosynthesis pathways

amino acid structure

alpha carbon, alpha carboxyl, alpha amine, hydrogen, and R group

19 amino acids have

chiral center

glycine

smallest amino acid, no chiral center

amino acid configuration, life

life uses L configuration (except glycine since it’s not chiral)

Peptidoglycan is made from

D-form alanine (

aspartic acid

important component of alpha helix

OH side group containing amino acids (targets of kinesis)

serine, threonine, and tyrosine

pi (isoelectric point)

overall charge of amino acid is zero, no net charge

amino acid breakdown first step

deamination (take amide group off of alpha carbon

protein functions

catalysis

signaling

structure

energy/gradient generation

amino acids are broken down into intermediates that can be made into glucose

glucogenic

amino acids are broken down into acetyl-CoA

ketogenic

cross-linking peptide bridges of peptidoglycan

see amino acids, predomiantly D-alanine

neurotransmitter precursor amino acid

Tyrosine

amino acid (protein) kinases target

Hydroxyl group (OH) of tyrosine, threonine, and serine

peptide bond

forms from dehydration synthesis, has partial double bond character (1.5)

aspartic acid and glutamic acid

are made from citric acid cycle intermediates from trans amination reactions (easy to make)

primary sequnce

amino acid sequence/order

primary sequence

starts at amino terminus, ends at carboxyl

cis/trans config

R-groups of consecutive amino acids in a protein are usually oriented on opposite sides of the polypeptide chain (trans)

Phi

a rotatable bond (φ or Phi) between the α-amine and α-carbon following the peptide bond

Psi

a rotatable bond (ψ or Psi) between the α-carbon and α-carboxyl preceding the next peptide bond,

Hydropathy scores rate the relative hydrophobicity/hydrophilicity of each

High positive values indicate high hydrophobicity whereas high negative values correspond to high hydrophilicity

non-covalent interactions (stabilize tertiary structure

hydrogen bonds(most Important) , van der waals, ionic bonds

disulfide bond (covalent

a strong, covalent chemical link between the sulfur atoms of two cysteine amino acids within a protein

protein folding funnel

bottom is native state

diagram with many local minima a folding protein can “fall into” and become trapped, thus explaining misfolding

Leventhal’s Paradox

proteins cannot fold into their functional shapes through a purely random search. If a protein sampled every possible shape, it would take longer than the age of the universe to find its correct configuration

Cumulative Selection Theory

proposes that only problematic portions of misfolded proteins are unfolded and then re-folded, NOT the whole protein

chaperonins

class of proteins assisting folding/ provide a lidded chamber within which folding occurs

Proteasomes

cellular structures involved in degradation of damaged/ misfolded proteins

ubiquitin

Degradation is targeted on proteins flagged by being bound to

There are 4 major secondary structural elements

well-defined = a-helix, b-sheets,

not well-defined = loops, and turns

Tertiary Structure

arises from the process known as folding and is determined ultimately by the amino acid sequence of the protein

Loops and turns connect

give rise to tertiary structure. They often connect different secondary structures

a-helices and b-sheets to each other

prions

misfolded protein that acts infectiously

mad cow (bovine spongiform encephalopathy

prions (holes in brain) misfolded protein cause cell death

amyloids

-improperly folded protein aggregates, insoluble, leads to plaque that kills cell

Scrapie

a fatal, degenerative prion disease affecting the central nervous system of sheep

globular

soluble/spherical

fibrous proteins

karatin, collagen (strong structural

can have fibrous and globular parts

proteins

pure and pyrimidine biosynthesis similarities

both regulated by feedback inhibitionb

pure and pyrimidine biosynthesis differences

purines are bigger/take more atoms

purine bifurcates, pyrimidine linear

purine starts with PRP/pyrimidine PRP comes at end

nucleoside vs nucleotide

Nucleosides contain only sugar and a base whereas Nucleotides contain sugar, base and a phosphate group as well

Hypoxanthine (Xanthine Oxidase) and Guanine (Guanase) are Converted to Xanthine

Xanthine is Converted to Uric Acid by Xanthine Oxidase

Uric Acid Crystals are the Cause of Gout

Deficiency of the Guanine/Hypxanthine Enzyme, HGPRT, Causes Lesch-Nyhan Syndrome

severe intellectual disability, and movement problems

a rare inherited disorder caused by a deficiency of the enzyme HGPRT, leading to the overproduction of uric acid and severe neurological abnormalities. Its hallmark features include compulsive self-injurious behavior (such as lip and finger biting), severe intellectual disability, and movement problems

nucleotide reductase ultimate/local electron donor

ultimate ADPH

local thyroxine

purine biosynthesis

good regulatory enzyme attributes

large neg delta g step early in the pathway

committed step

most important monosacharride

glucose

glucase

converts starch into glucose

fructose

aldehyde

ribose

all oh to right

galactose

same middle

sugar configuration

D

glyceraldehyde

lactose

galactose and glucose

maltose

two glucose

sucrose

glucose and fructose

polysaccharides

one reducing end

cellulose subunit

glucose

beta 1,4

glycogen main chain

alpha 1,4

glycogen branched point

alpha 1,6

Chitin

N-acetylglucosamine units joined by β-1,4

lectin

proteins that bind carbohydrates specifically

Part of innate immune system

Glycoproteins - proteins linked to oligosaccharides

N-linked - joined to asparagine in protein - E.R. and Golgi apparatus

      O-Linked - joined to serine/threonine in protein - Golgi apparatus

oligosaccharide

contains several different sugars

sphingosines

sphingolipid backbone,found in brain(good). bond allows tight packing

glycogen

non reducing ends are where glucose is added

Heparin helps prevent clotting of blood by

inhibiting conversion of fibrinogen to fibrin

The repeating disaccharide of 2-Osulfated iduronic acid and 6-O-sulfated, N-sulfated glucosamine, occupies about 85% of the molecule and make heparin the molecule with the highest negative charge density known

Hyaluronic acid

glycosaminoglycan in connective, epithelial, and nerve tissues that lacks sulfate

tissue repair, joint lube

double bonds

cis