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Beyond Midterm


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What are the 4 catagories of amino acids?
1) Non-polar, aliphatic R groups
2) Polar, uncharged R groups
3) Aromatic R groups
4) Charged (+/-) R groups
What is the primary structure of a protein?
-when amino acids are joind in a precise linear sequence
What are some characteristics of a peptide bond?
-shorter (1.3A) than the C-N single bond in a normal amine (1.49A)

-There is an electric dipole from the carbonyl oxygen (weakly negative) to the amide nitrogen (weakly positive).

-There is no free rotation about the
peptide bond! Sharing the P electrons can only happen when the carbonyl O and amide N are coplanar, which constrains the peptide bond that joins them.
What are the 2 commonly occurring secondary structures?
-alpha helix

-beta strand
What are the 3 interactions which help stabilize the alpha helix? (ie: keeps it compact?)
1) H-bonds (b/w NH-OC)

2) hydrophobic interactions (keeps the CH groups in the middle, R-groups on the outside)

3) van der Waals forces(lots of low energy, attractive forces b/w atoms that are close together. Contribute to the general helix stability)
What is an amphipathic protein?
-a protein with a hydrophobic side and a hydrophilic side
What is a beta turn?
-a long Beta polypeptide turns 180 and goes in the opposite direction from which it came
-result is 2 antiparrallel strands

**180 kink is caused by H-bond between N of first amino residue and O of fourth amino residue. Causes 90 degree turn in 2 and 3 residues**

**first amino residue in the turn is most likely a glycine residue**
What is the simple definition of tertiary structure?
-the overall placement of atoms in a protein
Approximately how many residues are there per turn in an alpha helix?
-approx 4 residues/turn. 3.6 to be exact
What is a coiled coil motif?
-a protein that contains 2 alpha helices that wrap around each other
What are the 3 classes of tertiary structures?
1) Fibrous Protein (eg: alpha keratin, collagen, fibroin)

2)*Globular Protein (eg: myoglobin)

3) Transmembrane Protein (eg: ion channels)
What is a heme group?
-an iron protoporphyrin ring
-ring runs off of 4 N that all connect to a centre Fe
-helps bind oxygen

*Usually sits in the hydrophobic pocket of the protein*
What are Supersecondary Motifs/Structures?
-stable formations of 2 or more secondary structure elements in sequence
What are domains?
-globular structures that retain their structure and function even when separated from the rest of the protein

-domains are joined together by flicker regions
What are the 4 categories of Protein Domains?
1)All alpha: domains consists almost entirely of alpha helices and loops

2)All beta: domains contain only beta sheets and loops

3)alpha/beta: regions of a helix and beta strand alternate in the domain

4)alpha+beta: domains consit of mostly separate clusters of alpha helices and beta sheets
What is a homodimer?
-protein that is composed of 2 or more identical subunits
What is a heterodimer?
-a protein that contains 2 or more sub units that are NOT identical
What is an icosahedral protein?
-a protein with 12 corners and 20 faces
What is a quartenary stucture?
-a bunch of tertiary structures joined together
What's the function of myoglobin?
-a monomeric protein that facilitates oxygen storage in peripheral tissue (muscle) of vertebrates

-contains 8 helices and a heme group
2)Native Conformation
1)Precise orientation of each residue and R-group in the polypeptide chain

2)Each protein folds into a single low energy structure
What are salt bridges?
-an ionic interaction between oppositely charged R-groups

-H-bonds come hand in hand with salt bridges
Define denaturation
-disruption of native conformation of a protein, resulting in loss of biological function

-heat and chemicals are common ways to unfold proteins (urea and guanidinium chloride)
What 2 chemicals are used to unfold proteins?
1) Urea
2) Guanidinium chloride
Proteins fold cooperatively... What does this mean?
-the folding in proteins fold cascadingly, the first fold helps the second and so on...

-like dominoes
What are some characteristics of protein folding?
-makes protein most stable (lowest energy state)
-most proteins fold spontaneously
-folding is rapid (<1sec)

**If G = H than lots of spontaneous folding, vice versa**
What are prion diseases?
-causes protein folding defects
-f'd up protein hangs out in nervous tissues and f's up transmission
-eg: mad cow disease
What are molecular chaperones?
-proteins that speed up the process of protein folding

-Consists of GroEL(the container part) and GroES(the lid part)
What's the difference between the R and T state of hemoglobin?
-R is the Relaxed state of Hb (ie: oxyHb)
-T is the Tense state of Hb (ie: deoxyHb)
-T/R equilibrium is controlled by the binding of molecules to either the T or R state

**if T and R are in equilibrium, it is known as an allosteric equilibrium**
What is an allosteric Protein?
-a protein (generally with multiple subunits) with multiple ligand binding sites, such that ligand binding at one site affects ligand binding at another

*allosteric activators and inhibitors for Hb are oxygen and Bisphospho-D-Glycerate(BPG) respectively*
What is a Ligand?
-a small molecule that binds specifically to a larger one; for example, a hormone is the ligand for its specific protein receptor
How Hb bind to BPG?
-pos charged R-groups from the Hb polypeptide make SALT BRIDGES with the neg charged phosphates of BPG

*being so, BPG fits into central cavity only in the T-state*
What happens when oxygen binds to one Hb subunit?
-structural changes are transmitted to other subunits in the Hb tetramer

-when oxygen binds to one Hb subunit, salt bridges at the interface b/w subunits break and the dimers rotate about 15deg. Therefore the central cavity in an R-state Hb is SMALLER then the T-state Hb
What are enzymes?
-globular proteins that act as biological catalysts
-can undergoe conformational changes during substrate binding or catalyses
-can change shape to fit substrate

What is a substrate?
-a reactant for an enzyme
-enzymes are specific towards substrate
What is an active site of an enzyme?
-the active site is where substrate binding and chemistry take place
What 3 events happen at the active site?
1) Substrate(s) binds (R-groups make favorable site to attach)

2) Chemistry occurs (usually adding or removing a proton)

3) Product(s) released
How does substrate binding occur?
-via weak non-covalent interactions:
1) vdW forces favored by complementary surface shape of the substrate and the enzyme active site

2) polar groups of substrate make Hbonds with polar R-groups at the active site

3) may form salt bridges b/w opposite charged R-group of enzyme and substrate
What are Ribozymes?
-RNA-containing enzymes
How are enzymes classified?
-based on the the type of chemical conversion they catalyze

-they mostly act on small metabolites (ie:sugars, fats, NA, AA) via breakdown of nutrients and in the synthesis of cellular precursors
How do enzymes catalyze a reaction?
-lowers the activation energy of a reaction by:

1) Substrate binding
2) Transition state binding
What's the difference between nucleophiles and electrophiles?
-Electrophiles are electron poor (pos)therefor ALWAYS LOOKING FOR ELECTRONS

-Nucleophiles are electron rich (neg)therefor DON'T REALLY CARE

**nucleophiles ATTACK electrophiles!**
What do Serine proteases do?
-cleaves peptide bonds into protein substrates
-in other words, breaks peptide bonds to separate the chain

**3 residues are always found at the active sites of serine proteinases, they are: Asp, His, and Ser**
Besides enzymes, what else can contribute to catalysis?
-acids and bases

-acid: a covalent bond may break more easily if a nearby atom is protonated

-base: can remove a proton from a water molecule or a substrate or a reactive amino acid reidue at the active site
What is the rate limiting step?
-the intermediate which requires the highest activation energy (ie: slowest proceeding step)
How effective are enzyme catalysts?
-very effective

-can boost rate by factors of 10^5 to 10^17
What is binding energy?
-energy derived from enzyme-substrate interactions
-binging energy is a major source of free energy used by enzymes to lower the activation energies of reactions
What are fatty acids?
-used as energy storing lipids
-are hydrocarbon derivatives
How does the number of double bonds affect the lipids melting point?
-more double bonds decreases the the lipids melting point
How does the number of carbons in the chain affect the lipids melting point?
-more carbons increases the melting point
What are lipases?
-enzymes that catalyze the hydrolysis of stored triacylglycerols, releasing fatty acids for export to sites where they are needed as fuel
What are storage lipids?
-non-polar lipids
-stores energy
*triacylglycerols(AKA triacylglycerol)*
What are the 5 types of structural membrane lipids?
1)Glycerophospholipid: 2 fatty acids and PO4 joined by glycerol

2)Galactolipids (sulfolipids): found in plant cells. Glycerol and galactose

3)Archaebacterial ether lipids: found in organisms in extreme conditions

4)Sphingolipids: don't have glycerol, sphingosine, fatty acid and variable

5)Sterols:has 4 fused rings as steroid nucleus. Includes cholesterol
What is phopholipases function?
-hydrolyzes the ester bonds of membrane lipids. Usually attacks the glycerol core
What are Eicosanoids?
-important for metabolism
-Prostaglandin(regs cAMP)
-Thromboxangs (blood platelets)
-Leukotrienes (white blood cells)

*that's all you need to know about them*
What are the 3 functions of lipids?
1)Energy Storage

2)Membrane Structure

3)Active Roles: signals, cofactors and pigments
What are active lipids?
**main thing to know is that they carry intracellular signals (ie: hormones bind to surface, lipids carry the signal), cofactors, and help pigment**

-Carry messages b/w cells: Eicosanoids
-Carry messages b/w tissue: Steroid
-Dissolves fat soluble vitamins so that they can function
What are the functions of fat soluble vitamins D, A, E, and K?
D- found in skin, involved with calcium metabolism

A- Regulation of epithelial cells(Detanoic). Visual pigment (Retinol)

E- biological antioxident

K- needed for prothromidine to convert fibrinogen to fibrin
What are the 3 ways that lipid membrane layers can arrange themselves?
1) Micelles

2) Bilayers

3) Liposome
What's the difference b/w integral and peripheral proteins?
-integral go through the membrane
-peripheral just hang out around the membrane
What are the functions of a biological membrane?

2)organize complex reaction seqyences

3)Maintains bio-electricity
What is flippase?
-an enzyme which helps a phospholipid flip-flop in the bi-layer

-polar canal, so phospholipid sticks it's head in and flips
What is co-transport?
-the movement of 2 different ions at the same time through protein
-2 Types:
1)Symport- both in same dir
2)Antiport- opposite dir
What is Bacteriorhodopsin?
-a membrane spanning protein
-single polypeptide chain
-folds into 7 hyrdrophobic alpha helices which traverses the lipid bilayers
-a light driven proton pump
-hydrophobic interactions b/w nonpolar AA and the acyl groups keeps it in the membrane
What is glycophorin?
-from human erythrocytes
-has 1 hyrdorphobic part in membrane as opposed to bacteriorhodopsins 7
-carbowyl terminus not always on inside
What are the 3 ways of attaching proteins to lipids in the membrane?
1)carboxyl to amine = amide bond

2)carboxyl to alcolhol = ester

3)cysteine linked bond
What is a nucleoside?
-an amino base and pentose
-For purines, give the 'osine' suffix
-for pyrimidines, give the 'dine' suffix
What is a nucleotide?
-composed of amino base, pentose sugar and phosphate backbone

-for purines and pyrimidines, add '...ylate' suffix
What are the purines?
What are the pyrimidines?
What are Tautomers?
-alternate structures that differ only in the location of their H-atoms
What are restriction endonucleases?
-produced by baceria
-used to prevent entry of foreign DNA
-foreign DNA is destroyed
-host cell is NOT degraded
-break DNA at palindrome sequences
How does DNA fingerprinting work?
-based on DNA sequence polymorphisms that occur in every DNA
-breaks the DNA at that point
-therefore DNA fragments will be different from one person to the next
-match'em up afterwords.
What are the steps involved in the chymotrypsin reaction?
1)chymotrypsin moves around as free enzyme

2)Substrate attaches, now an ES complex

3)Acylation occurs, breaking of bonds. Bonds broken and 1/2 of substrate takes off, now an acyl enzyme intermediate

4)Second half of substrate is prepared to go, deacylation

5)second half of substrate takes off, second product

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