This site is 100% ad supported. Please add an exception to adblock for this site.

Biochem 1 2


undefined, object
copy deck
What's the Central Dogma of Molecular Biology?
(transcription) (translation)
Total # of genes estimated at ___________.
Genome is the ____________ component of an organism, while the Proteome is the __________ component.
How many more proteins than genes?
3x more proteins than genes
sequence of bases is _______% the same in all people
_____% of the genome codes for the production of proteins.
less than 2%
repeated sequences that do not code for proteins (junk DNA) makes up _____% of the genome
at least 50%
Name 3 methods of achieving diversity in the genome (and give examples for each).
1) mRNA editing (ApoB)
2) splicing (alcohol dehydrogenase)
3) post-translational modification
___________ of the same enzyme perform different kinetics of the same basic function. These are generated by _________________.
alternate mRNA splicing
What causes 15% of all genetic diseases? Give example.
defects in mRNA splicing
What are the levels of protein structure?
1. primary (aa sequence)
2. secondary (alpha helix, beta sheet)
3. tertiary (fully folded peptide)
4. quaternary (homo/hetero subunit interactions or holoenzyme)
5. multiprotein machines
Give an example of a multi-protein machine. Tell how it works.
pyruvate dehydrogenase (PDH)

changes pyruvate (from glycolysis)
to acetyl CoA for the TCA cycle

PDH is made of 60 polypeptides (5000 kDa!)
Proteins can function as enzyme. Give example.
DNA polymerase
Give example of protein functioning as structural.
Give example of toxin protein.
Give example of protein functioning as receptor.
insulin receptor
Give example of protein functioning as contractile.
Give example of protein functioning as a carrier.
Give example of protein functioning as protective.
Give example of protein functioning as a ligand.
Give example of protein functioning as a transporter.
ATP pump, cisplatin for Ca
Which protein copies DNA prior to cell division? What type of protein is it?
DNA polymerase
How does Botox work?
2 polypeptide chains

light chain protease cleaves SNARE complex, preventing release of ACh vesicles.

heavy chain binds to cholinergic cell surface glycoproteins
Which muscles is Botox usually injected into to prevent formation of ___________ lines?
corrugator muscles and procerus muscle
glabellar lines
What's a common cancer therapeutic? How can it be neutralized?
(kills cells that replicate too rapidly)

can be neutralized by glutathione and transporter pump
The level of a protein is determined by its rate of both ___________ and __________.
synthesis and degradation
DNA polymerase functions as an _________.
How does B-thalassemia occur?
pre-mRNA splicing defects
Explain how the multidrug resistance protein works in regards to cancer chemotherapeutics.
Cisplatin causes DNA crosslinks, preventing cancer cells from replicating.
The multidrug resistance comes from the transporter pump using glutathione to take cisplatin out.
What's the orientation of DNA synthesis?
5' to 3'
With bioinformatics, what is still the last step?
confirmation by experimentation
Proteins only contain the ___ isomer of amino acids.
What does Zwitterionic mean?
Within the molecule, there are + and - charges, but the net is neutral at pH 7.
Describe the amino acid. Which one is the simplest aa?
alpha carbon
amino group (NH3+)
carboxyl group (COO-)
variable R group

glycine: R group is H
Name the non-polar amino acids.
What's another name for non-polar?
VALINE (branched isopropyl)
Name the polar amino acids.
HAVE -OH (targets for phosphorylation and glycosylation)

Name the basic amino acids. Which charge do they have at pH 7?

Name the acidic amino acids. What charge do they have at pH 7?

Name the uncharged polar amino acids. What's another name for them?
carboxiamide amino acids

Explain the effect of pH on the ionization of an unsubstituted amino acid.

What happens if you lower/raise pH?
isoelectric point is pH 7 (Zwitterionic form)

lower pH, protonate COOH, so now the aa is +

raise pH, deprotonate NH2, so now the aa is -
In terms of pKa values, which groups are "neutral," acting as acid/base catalysts?
histidine and cysteine
In terms of pKa values, which aa's are acidic? Are these pKa values high or low?
LOW (the aa's are - charged)

In terms of pKa values, which aa's are basic? Are these pKa values high or low?
HIGH (the aa's are + charged except for tyr)

Given a polypeptide has 4 lysine residues, what is its charge at pH 7?
at pH 12?
(lysine is basic, +, has high pKa)
so at pH 7 (neutral), it's POSITIVE (basic)
at pH 12, you're deprotonating, making it more Neutral.
Name the acidic amino acids.
What's the charge at neutral pH?
Name the basic amino acids.
What's the charge at neutral pH?
Which amino acid is really an imino acid?
proline (has a ring)
How does penicillin work?
inhibits synthesis of bacterial cell wall peptidoglycan at the active site SERINE
Tell me about cysteine residues. What molecule do they help stabilize?
SH groups oxidize to S-S making inter/intramolecular disulfide covalent bonds.

insulin (polypeptide hormone)
What's the 21st amino acid? What's it's codon?
selenocysteine (sec)
UGA (usually a stop codon)

acts as an acidic aa b/c has low pKa
How can you use aa's as indicators of disease?
look at serum levels as compared to normal ranges
Low tyrosine levels are indicative of what disease?
Phenylketonuria (PKU)

phenylalanine to tyrosine by phenylalanine hydroxylase. These kids have autosomal recessive deficiency in phenylalanine hydroxylase.
Preventable by LOW PHE DIET.
What's a peptide bond? How do you break it?
alpha carboxyl & alpha amino
(amide bond)
It's how you link aa's. Requires energy.

Water hydrolyzes the bond to give you free aa's again.
What's the favored stereochemistry of the peptide bond?
trans. less steric hinderence.
Which aa is basic, aromatic, and polar?
_______ bonds are rigid and do not rotate.
_______ bonds can rotate the rigid amide planes.
peptide rigid
phi and psy bonds can rotate
AAs are always written ______ terminus to _______ terminus.
+H3N to COO-
What is a D aa analog that acts as an antibiotic? How?

In bacterial, 5 gly residues are added to D-ala by glycopeptide tranpeptidase= cell wall. (inhibited by penicillin)

Cycloserine is D-ala analog, so it acts as antibiotic.
Valine is _______ aa.
Serine is _______ aa.
polar (-OH)
Tryptophan is ______ aa.
(b/c turkey smells good, haha)
Lysine is ______ aa.
Aspartate is ________ aa.
Cysteine has a _____ group on it.
thiol (sulphur)
What has protein and RNA components?
What is the signal for import into the ER lumen?
Which form of ribonuclease is active? Why?
native with S-S b/c the denatured polypeptide has SH groups. The biological activity depends on the 3D structure.
What dictates conformation of protein?
primary sequence
What happens in spongiform encephalopathies? Give 2 examples of these diseases.
prion diseases, conformational change from alpha helices to beta sheets. Proteins aggregate.

examples: Creutzfeld-Jacob, Mad Cow
How do distant active site residues get close to each other?
What are 3 ways to attack the bacterial cell wall?
1) lysozyme cleaves NAM-NAG
2) penicillin blocks glycopeptide transpeptidase
3) D-cycloserine (seromycin) acts as a D-ala analog to gly residues don't attach
What's a zymogen?
inactive precursors for proteolytic enzymes
How are zymogens and insulin activated?
proteolytic processing

-chymotrypsinogen (inactive in pancreas)
-trypsin cleaves it, making 2 S-S bonds
-autocatalyzes to alpha chymotrypsin (active) with 3 chains
How are HIV gp120 and glycogenin modified?
(add sugar residues)
What are the 2 types of glycosylation and on which aa's does each type happen?
1) N-linked (asn-asparagine)
2) O-linked (serine, threonine, tyrosine)
What's the functional structure of collagen?
quaternary structure
(NOT alpha helix)
What's the alpha chain of collagen made of? (sequence)
What's a post-transl modification that's the suicide mechanism for methyltransferases?
methylation of active site Cys (so now G=C doesn't base pair pair)
What's the post-transl mod of histones to control chromatin structure? On which residues does this happen?
lysine residues
decrease affinity of histone for DNA
What's the post-transl mod for insertion of proteins into membranes? Which residues are a target? Give an example.
cysteine residues

S-Palmitoylcysteine gets palmitic acid at the thioester. Anchors it into membrane by attachment of lipid groups.
How does apo enzyme differ from holo enzyme? What's an example?
2 alpha subunits, 2 beta subunits
Hemoglobin with heme bound
apo globin without heme bound.

So they require non-proteinaceous groups bound for function.
Proteins are targeted to organelle locations by signals in their ____ sequence.
_____________ directs proteins to their ultimate destination. How?

In ER, mannose residues are added,
phosphorylated in Golgi,
the M6P residue targets to lysosome.
What's the targeting sequence for lysosomes?
M6P (mannose 6 phosphate)
What's the targeting sequence for mitochondria? Give an example.
positively charged amphipathic alpha helix

influenza virus PBI-F2 (kills immune cells to ensure virus survival)
As a protein crosses the membrane, that stretch of aa's are ___________. Therefore, we can do ____________ plots to predict trans-membrane regions of polypeptides.
hydropathy plots
What's the molecular basis for prion disease?
conformational change of normal protein causes aggregation

alpha to beta
chaperones (GroES-GroEL) don't work
What does bioinformatics do? What's the last step always?
-identify genes, protein coding sequences
-predict function, structure
-trace evoluationary development
What are the 2 categories of homologs?
1) orthologs (same structure & fcn, different species)
2) paralogs (same structure, different function)
What is active site conservation?
different proteins with same catalytic functions

Both chymotrypsin and subtilisin have catalytic triad ser-his-asp at active sites.
What's a technique for primary structure determination?
Edman Degradation (N-terminal aa sequencing)

use phenyl isothiocyanate to cleave PTH-N terminal aa.
What's a technique for secondary structure determination?
circular dichroism

spectroscopic measurement of elipticity/absorbance of polarized light.

(alpha helix high peak, beta sheet lower peak)
3 things about alpha helix:
1) all R groups point out, H bonds at 1 and 4 parallel to axis
2) there are 3.6 residues per turn
3) there is a net dipole moment - --> +
NEGATIVE TO POSITIVE (how optimistic!)
How do you determine the mass of a protein from the aa's?
# aa's x 110 = mass of protein
Give 2 examples of all alpha helical proteins
hemoglobin and myoglobin
What is a "helix breaker" ? Why? What is it found in?
PROLINE b/c always steric hinderance
collagen alpha chains
2 things about Beta sheets
1) R groups protrude above and below strand
2) H bonding of all C=O & N-H bonds
What causes reverse turns in beta sheets?
Forces that define protein structure...
which are involved in hydroxylation of proline?
covalent bonds
forces that define protein structure...
which are involved in collagen triple helix?
hydrogen bonding
forces that define protein structure...
which are involved in leucine zipper? What drives the leucine zipper?
hydrophobic interactions (dimerization with another leucine zipper - oligomerization)

increase in entropy (S) drives hydrophobic interactions (-delta G)
What is an acceptor in hydrogen bonds in proteins?
What's the weakest of the bonds?
van der waals
Many proteins ___________ into a quaternary structure.
Do enzymes work in isolation? What are they part of? Give an example.
multi-protein machines
(pyruvate dehydrogenase)
What does gel filtration do?
Separates based on size
(big stuff goes faster b/c small stuff enters beads)
What does ion exchange do? How?
Separates based on charge
Based on % of charged aa's
(basic: lys,
acid: asp)

(same chg goes thru faster b/c repelled)
What does protein electrophoresis do?
separates based on MW and mass

little stuff goes faster.

denatures proteins, reducing agent, makes them all - so they migrate to +
What's an ELISA?
detects ANTIBODY in sample

Ag coat well, add serum to see if it has Ab, add enzyme-linked Ab, add color, color is proportional to amount of serum Ab.
For HIV, must confirm with WB.
What does mass spectrometry do?
gives exact mass of polypeptide

small ions fly faster thru field
What's another name for multi-enzyme machines?
What's an example of a homodimer?
DNA polymerase clamp (2 identical subunits)
Tell the 4 post-trans mods done to collagen.
1) hydroxylation of proline to hydroxyproline for more H bonding potential
2) lysine residues are hydroxylated, then glycosylated in Golgi
3) interstrand covalent crosslinks S-S at C terminus
4) collagenase cuts off globular ends --> fibril
What is osteogenesis imperfecta?
mutations produce shortened collagen chains that "poison" triple helix stability

aa substitutions destabilize intrastrand bonding
Give an example of a multi-subunit enzyme.
RNA polymerase (hetero-oligomerization of 4 different subunits)
Give an example of a multifunctional enzyme.
DNA polymerase III
(hetero-oligomerization of 10 subunits)
alpha: DNA synthesis 5' to 3'
beta: clamp
gamma: clamp loader
epsilon: 3' to 5' exonuclease
Give 2 examples of a multi-protein machine.
20S proteosome

pyruvate dehydrogenase (60 polypeptides!)
What's Xeroderma Pigmentosum?
Autosomal Recessive sensitivity to UV rays

defect in nucleotide excision repair mechanisms
How does emphysema occur in 2-5% of cases?
mutations in alpha 1-antitrypsin, so elastin gets degraded by elastase.
How does phosphorylation work? Which are the most often targeted aa's?
serine, threonine, tyrosine (b/c have -OH)

terminal gamma phosphate gets used. Activates enzyme.
Can remove PO4 with protein phosphatase to deactivate.
Name the aromatic amino acids.
have polycyclic aromatic ring

What is the structure of influenza PBI-F2 protein? Where is it targeted to?
+ charged alpha helical (arg and lys residues)
targeted to mitochondria
What's a technique for quaternary structure determination?
genetic and biochemical screen to detect protein-protein interactions

x-ray diffraction and electron microscopy
The immunoglobulin (IgG) molecule is mostly _________ (structural). It has ______ chains, linked by _________.
beta sheet
2 light chains, 2 heavy chains
disulfide bond
Why do you need vitamin C to prevent scurvy?
vitamin C (ascorbic acid) hydrolyzes proline to hydroxyproline, needed for the collagen chain stability
What's the targeting sequence for nucleus?
lysine residues
In gluconeogenesis, what's required as a prosthetic group? How does it function?

in pyruvate carboxylase, changes pyruvate to oxaloacetate (happens on lysine residues)
How do you break IgG into its subunits?
proteolysis by papain breaks domains into Fab and Fc
Insulin functions as a _________.
mRNA to RNA occurs in ___________. Process called ________.
What's Maple Syrup Urine disease?
patient makes too much valine
What's a Western Blot?
detects presence of ANTIGEN in sample

gel, transfer, react w/ Ab, film, protein band
What degrades structural elastin? What degrades that? What disease does this lead to?
ALPHA1-ANTITRYPSIN (anti-elastase, prevents elastin degradation)

Defects in alpha1-antitrypsin (or smoking) lead to EMPHYSEMA.
How do you get a protein degraded in a proteasome? What's a target for this on the polypeptide?
(ubiquitin gets added at the C terminus)
lysine residues are targets
How can you measure increases in protein purity?
increase in specific activity
What's a technique for tertiary structure determination?
x-ray diffraction
(crystalize the protein)

Which proteins cause a big multi-drug resistance problem? How do they work?
transporters (ATP-dependent small molecule pumps)
Increase efflux of drug from the cell.
Proteins proceed through partially folded intermediates aided by _____________.
Hsp 70 (small)
Hsp 60 (big)
What is a mixed beta sheet?
parallel and anti-parallel
Which aa's are targets for modification by phosphorylation/glycosylation? Why?
polar aa's: serine & threonine
b/c have -OH groups
Which of these proteins would go to ER lumen?

a) N-tyr-glu-asp-C
b) N-lys-val-ser-C
c) N-trp-cys-glu-C
d) N-ala-tyr-ser-C
b) N-lys-val-ser-C

N-basic-hydrophobic (nonpolar)-polar-C
Making mRNA occurs in __________. Process is called ________.
Myosin is a ____________ protein.

Deck Info