NOTE: NC IS A BOND BETWEEN 2 OPPOSITE CHARGES, NOT SHARED ELECTRONS.
DEFINE AMPHOTERIC MOLECULES.
ACT AS EITHER ACID OR BASE. WATER
ACIDITY IS MEASURE USING THE pH SCALE. FORMULA?
pH = -LOG [H+]
CHANGES IN THE pH AFFECT THE _____ STATE AND FUNCTION OF PROTEINS.
IONS
T OR F?
BUFFERS RESIST pH CHANGE.
TRUE
WHAT IS AN ISOMER?
SAME CHM FORMULA, DIFFERENTLY ARRANGED.
-OH
WHAT GROUP IS THIS?
HYDROXYL GROUP
-COOH
WHAT GROUP IS THIS?
CARBOXYL GROUP
CH3CH2OH
COMMONLY KNOWN AS WHAT?
ETHYL ALCOHOL (ethanol)....BEER!
NAME 4 MACROMOLECULES
PROTEINS
LIPIDS
POLYSACCRIDES
NUCLEIC ACIDS
C=O
WHAT GROUP IS THIS?
CARBONYL.
DO NOT MIX UP WITH COOH, CARBOXYL!!!
FRUCTOSE....KEYTOSE OR ALDOSE?
KETOSE.
C=O (CARBONYL IS LOCATED INSIDE AND NOT H CONNECTED.
GLUCOSE. ALDOSE OR KETOSE?
ALDOSE.
CARBONYL, C=O,TERMINAL CARBON LOCATED AT END WITH H ATTACHED.
SUGAR CAN BE LINEAR, BUT CAN FORM RING STRUCTURES CALLED _________
PYRANOSES
ASYMETRIC CARBONS BOND TO ______ DIFFERENT GROUPS
4
MOLECULES WITH ASYMETRIC CARBONS EXIST IN TWO FOEMS...NAME THEM
ENANTIOMERS AND STEROISOMERS
ENANTIOMER: is one of two stereoisomers that are mirror images of each other that are non-superposable (not identical), much as one's left and right hands are the same except for opposite orientation
HOW DO YOU TELL D OR L
LOOK AT HYDROXYL GROUP ON CARBON 2
SUGARS CAN BE JOINED TOGTHER HOW?
COLVALENT GLYCOSIDIC BONDS
C1 OF ONE SUGAR AND THE HYDROXYL GROUP OF ANOTHER.
GENERATING A -C-O-C- LINKAGE BETWEEN THE TWO.
SUCROSE IS COMPOSED OF WHAT
GLUCOSE AND FRUITCOSE.
G= 6C AND F=5C MOLECULE.
JOINED BY ALPHA 1,2 LINKAGE.
WHAT IS LACTOSE COMPOSED OF AND HOW IS IT BONDED?
GLUCOSE AND GLACTOSE
BETA (1,4) LINKAGE
WHAT SUGAR IS USED AS A SOURCE OF READILY AVAILABLE ENERGY
DISACCRIDES
DEFINE OLIGOSACCRIDES AND WHERE ARE THEY FOUND ?
A LINK OF SMALL SUGARS THAT FORM A CHAIN. FOUND ON CELL SURFACES, MAYBE USED IN CELL RECONGIZATION.
_________ is a plant product made of unbranched glucose polymers
Cellulose
MOST ANIMALS CANT DIGEST CELLOSE, WHY
because of b(1, 4) linkage
Madeof unbranched N-acetylglucosamine polymers
Chitin
Diverse group of non-polar molecules
LIPIDS
_______ _____ are unbranched hydrocarbons with one terminal carboxyl group; amphipathic
Fatty acids
LIPID TYPE......Solids at room temp
Saturated fatty acids
lack C=C double bonds
lack C=C double bonds
SATURATED OR UNSATURATED ?
SATURATED.
SOLID AT RT
_______ _______ _______ have one or more C=C double bonds and are liquid at room temp
Unsaturated fatty acids
In animals, fats are stored for energy in ______
adipocytes
________ are four-ringed animal lipids
(implicated in artherosclerosis)
STEROIDS
REMEMEBER THAT STEROIDS ARE LIPIDS!
Phospholipid phosphatidylcholine
NAME THE PARTS
NAME THE 9 PROTEIN FUNCTIONS
METABOLIC
STRUCTURE..CYTOSKELETON
REGULATORY...HORMONES
RECEPTORS...IN MEMBRANE
MOVEMENT..MOTORS (THINK CELL)
Ab
CLOTS...HELP FORM
ABSORB LIGHT
TRANSPORT.....MATERIALS
Amino acids are linked together by ______
bonds into ________ chains to make
proteins
peptide
polypeptide
BOND C-N
nPeptide bonds form between the------ & ------- OF participating
amino acids
alpha-carboxyl and alpha-amino
THINK C-N
WHEN AA IS POLAR HYDRO PHILLIC OR PHOBIC?
HYDROPHILLIC.
LOVES WATER
BOTH CHARGED AND UNCHARGED GROUPS
WHAT AA GROUP HAS SIDE CHAINS THAT FORM IONIC BONDS & INVOLED IN CHM RXNS ?
POLAR CHARGED
NAME THE POLAR CHARGED
HIS.....HISTIDINE
ASP...ASPARTIC ACID
LYS.....LYSINE
ARG......ARGININE
GLU....GLUTAMIC ACID
"HALAG"
WHAT AA GROUP FORMS H BONDS AND ASSOCIATE WITH WATER
P[OLAR UNCHARGED
NAME THE POLAR UNCHARGED AA
GLUTAMINE
ASPARAGINE
TYROSINE
THREONINE
SERINE
WHAT AA GROUPS ARE HYDROPHOBIC?
NONPOLAR
NAME THE NONPOLAR AA
"VAMPLIT"
VALINE
ALANINE
METHIONINE
PHENYLALANINE
LEUCINE
ISOLEUCINE
TRYPTOPHAN
NAME 3 AA WITH UNIQUE PROPERTIES
GLYCINE...SIMPLE H....PHILLIC OR PHOBIC
CYSTEINE.....SULFER ....POLAR UNCHARGED
PROLINE...PHOBIC..MAKES KINKS & FOLDS
WHEN YOU ADD 2 CYS TOGTHER...OX OR REDUX?
DEFINE PRIMARY STRUCTURE AND WHAT BOND TYPE
Sequence of amino acids in a polymer.
PEPTIDE BONDS
alpha-helix, beta-sheets, kinks, loops, turns
WHAT STRUCTURE TYPE ?
ALSO NAME THE BOND TYPE
SECONDARY
H BONDS
WHAT LEVEL OF STRUCTURE RESULTS FROM INTERACTIONS BETWEEN BACKBONE PORTIONS OF AJENCE OR NEARBY AA ?
SECONDARY
DEFINED AS THE ABSOLUTE SEQUENCE OF AA FROM AMINO END TO CARBOXYL END.
PRIMARY
PROTEIN FIBROUS, GLOBULAR, "PROTEIN MOTIFS"
WHAT LEVEL OF STRUCTURE ?
TERTIARY
SICKLE CELL WHAT AA IS SWAPED FOR WHAT
Normally a charged glutamine,
Switched to non-polar valine.
IN THE ALPHA HELIX, 360 DEGREE Turn for every ______ AA residues
3.6
IN A ALPHA HELIX, WHAT BOND FORMS BETWEEN THE AA'S?
HYDROGEN
Outer surface of water soluble proteins contains_______ AAs
POLAR
Common in globular proteins inside the cell...WHAT SECONDARY STRUCTURE TYPE ?
ALPHA HELIX
Fibrous proteins outside cell (connective tissues)
Resist shearing forces
Carbonyl and imine
WHAT SECONDARY STRUCTURE TYPE?
BETA PLEATED SHEETS
LABEL THE STRUCTURES
Ribonuclease asTertiary Structure
Green spirals..a-helices N-terminal to C-terminal direction
Red ribbons are b-pleated sheets
Blues tructures are disulfide bridges
Loops and turns connect overall structure
first globular protein whose tertiary structure was determined.
WHAT, WHO & WHEN?
MYOGLOBIN
1957
John Kendrew et al. at Cambridge University
MYOGLOBIN HAS _______ in hydrophobic pocket that
promotes O2 binding without oxidizing Fe
HEME
HOW WAS MYOLOBIN DISCOVERED?
nx-ray crystalography
T OR F MYOGLOBIN HAS 8 AA IN ALPHA HELIX FORM, NO BETA SHEETS OR DISULFIDE BRIDGES.
TRUE
NAME 3 Types of noncovalent bonds maintaining conformation of proteins.
VAN DER WAALS
HYDROGEN
IONIC
WHAT LEVEL OF STRUCTURE RESULTS FROM R GROUP INTERACTIONS BTWN MULTIPLE PROTEIN CHAINS (SUBUNITS) WHICH FORM A FUNCTIONAL PROTEIN UNIT?
QUATERNARY.
T OR F ?
Protein folding is a process that occurs in
orderly steps by self assembly
TRUE
_____ _______ occur when groups of proteins
associate to perform a specific function
Multiprotein complexes
________ structure applies to proteins with sub-units
Quarternary
acetylcholinesterase CLOSES DUE TO WHAT TWO AA'S?
tyrosine and phenylalanine
IN WHAT PROTEIN STRUCTURES DO YOU FIND DIMERS?
QUADS.
a dimer made from identical subunits
HEMOGLOBIN IS WHAT TYPE OF PROTEIN STRUCTURE
QUAD
T OR F ?
Knowledge of a protein’s amino acid sequence rarely allows for prediction of protein’s higher order structure
TRUE
Knowledge of a protein’s amino acid
sequence rarely allows for prediction of protein’s higher order structure...SO HOW DO YOU CHANGE IT?
Use site directed mutagenesis
Alterations in single amino acid
Must change the DNA that codes for protein
Current technology enables us to make artificial genes. HOW?
Code for proteins of specific amino acid sequences
Pyruvate Dehydrogenase is a Multiprotein Complex. what is its main function?
connect the glycolytic and TCA cycles which prevents product dilution
Nucleotides consist of a ______ carbon sugar (ribose in RNA), a phosphate group and a nitrogen base
5
what is connected in a 3’-5’ phosphodiester bond?
Links between 3’ hydroxyl group and
one sugar with the 5’ phosphate group of the adjoining sugar. Nucleotides joined to form a strand covalently.
Adenine and guanine
Purines or Pyrimidines Nitrogenous Bases?
FOUND IN DNA, RNA OR BOTH?
Found in both DNA and RNA.
NAME THE Pyrimidines Nitrogenous Bases?
FOUND IN DNA, RNA OR BOTH?
Cytosine and uracil in RNA
Cytosine and thymidine in DNA
T OR F?
RNA may have catalytic properties
TRUE.
THINK RIBOZYMES
_______is a ribonucleotide with three phosphates (high energy)
ATP
Different types of sub-units are capable of self-assembly.
WHAT EXPERIMENT PROVED THIS POINT?
1950s experiments show that TMV (Tobacco Mosaic virus)
particles are capable of self assembly.
T OR F
PROKARYOTIC Ribosomal sub-units ARE KNOWN TO assemble spontaneously IN A STEP WISE MANOR?
TRUE.
Components of the mature eukaryotic ribosomal sub-units require accessory proteins to assemble.
THINK CHAPERONES.
OBJECTIVE OF A CHAPERONE?
GIVE ONE EXAMPLE!
Help proteins reach proper folded state.
Helps move across membranes
Helps with heat shock
E.coli GroEL protein is essential for the proper folding of other cellular proteins
IN AD, The ϒ-secretase can act at either of the two
cleavage sites of the APP, resulting in two different results.
NAME THEM AND WHAT WHICH IS BAD.
AB40 AND AB 42
Aβ 42 difference is that it has a tendency to spontaneously refold into different confirmations that contain more β-pleated
sheets, and this is where the problem arises.
DEFINE PROTEOME
THE ENTIRE INVENTORY OF PROTEINS THAT IS PRODUCED BY AN ORGANISM. ALSO APPLIES TO THE INVENTORY OF ALL THE PROTIENS PRESENT IN A CELL, TISSUE OR ORGANELLE.
DEFINE SITE-DIRECTED MUTAGENESIS
A TECHNIQUE TO MODIFY A GENE IN A PREDETERMINED WAY SO AS TO PRODUCE A PROTEIN WITH A SPECIFICALLY ALTER AA SEQUENCE.
ON A 2D GEL RUN WHAT ARE THE TWO UNITS OF MEASUREMENT?
kDA.....1.6605402E-24
pI...... isoelectric point.
PRINCIPAL ANIMAL ENERGY STORAGE PRODUCT ESPECIALLY IN LIVER AND MUSCLE
glycogen
principal higher plant energy storage product with amylopectin
Alpha-amylose
principal higher plant energy storage product with alpha amylose
amylopectin
mainly structural; nutrient it can break it down… Mammals who use as a food source lack enzymes to digest it but have rumen.
Highly insoluble
cellulose
structural, possibly some minor barrier functions
peptidoglycan
structural extremely important in development.
Two alternating sugars usually one is an amino sugar
beta 1-4 and beta 1-4 or beta 1-3.
NO BRANCHING
glycosaminoglycan
(GAGs)
where would you find glycosaminoglycans?
extracellular material and spaces and around cells and connective tissue.
name for products that added sugar component of D-glucose