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BCHM 270- All Questions100% Solved with Verified Solutions
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Protein structure (primary) - Answer - Linear sequence of amino acids with the absence of R group interactions, connected by strong peptide bonds (require strong acids/bases, heat, and/or enzymes to bond) which have partial double bond character due to resonance, almost always in a trans conform...

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BCHM 270- All Questions100% Solved with
Verified Solutions
Protein structure (primary) - Answer - Linear sequence of amino acids with the absence
of R group interactions, connected by strong peptide bonds (require strong acids/bases,
heat, and/or enzymes to bond) which have partial double bond character due to
resonance, almost always in a trans conformation
- Once the bond is formed, the carbonyl and amino groups are uncharged and cannot
ionize, so the only charged groups are the N-terminus, C-terminus, and R groups of
ionizable side chains


Protein structure (secondary) - Answer Alpha-helices: right handed spiral including a
coiled backbone core (stabilized by hydrogen bonds formed between the carbonyl
oxygen of the first residue and an amine hydrogen four residues away) decorated by
side chains pointing outward
- Amino acids with similar side chains tend to group together on the same side of the
helix
- Helix breakers: amino acids that break the helix
> Proline: rigid
> Charged amino acids: ionic repulsion disrupts helix
> Bulky amino acids: steric hindrance disrupts helix


Beta sheets: multiple segments of beta strands held together by hydrogen bonds with a
fully extended backbone and side chains above and below the strands - strands can be
parallel or antiparallel to each other


Motifs: combinations of alpha helices and beta sheets forming supersecondary
structures

,Protein structure (tertiary) - Answer Folding of domains together to form a 3D structure
stabilized by disulfide bonds, hydrogen bonds between side chains with FON groups,
and ionic interactions between charged side chains


Protein structure (quaternary) - Answer Binding of 2+ identical/different protein
subunits together, stabilized by noncovalent interactions and sometimes disulfide bonds


Post-translational modifications - Answer - Disulfide bonds: cysteine thiol group forms a
covalent disulfide bond with other cysteines (thiol must be oxidized on both cysteines),
helps stabilize protein
- Glycosylation: carbohydrate is added, either to amie group in asparagine (N-linked) or
to the hydroxyl group in serine/threonine (O-linked)
- Phosphorylation: phosphate added to the hydroxyl group in serine, threonine and
tyrosine to change the function or activate a protein - added by kinases and removed by
phosphatases


Protein shapes - Answer - Globular proteins: roughly spherical, with hydrophobic cores
and hydrophilic exteriors; some contain quaternary structure - serve as molecular
transporters, storage proteins, enzymes, etc
- Fibrous proteins: long chains of multimers running parallel to each other and often
twisted together; often stabilized by disulfide bridges - play a structural role in the body


Hemeproteins - Answer Globular family of proteins that contain heme as a tightly bound
prosthetic group (not a protein)
- has many functions depending on the protein it is bound to: it can be an electron
carrier, held remove hydrogen peroxide, and reversibly bind to oxygen


Myoglobin (Mb) - Answer Heme protein: oxygen carrier to heart and skeletal muscle
- Single peptide chain that is mostly an alpha helix, interior is nonpolar and exterior is
polar

,- Heme binds to a pocket lined with nonpolar amino acids - distal His binds to Fe of
heme and distal His stabilizes binding of oxygen to Fe of heme
- Each Mb can reversibly bind to a single oxygen - the amount of oxygen bound to Mb in
the blood is represented by percentage leading to a hyperbolic binding curve
- Mb always binds oxygen with the same affinity, so it is usually 90% saturated


Hemoglobin (Hb) - Answer Heme protein: oxygen carrier in red blood cells, transports
oxygen from lungs to capillaries
- Consists of a dimer of dimers, aB dimer is held together by strong hydrophobic
interacts and two aB dimers are held together by weak hydrogen bonds and ionic
interactions
- Each Hb can reversibly bind to 4 oxygens (1 per subunit) - the Hb binding curve is
sigmoidal and shows subunit cooperativity (the binding of oxygen to one subunit
increases the affinity of the remaining subunits in the tetramer)
- Cooperative binding allows for complete saturation of oxygen in the lungs


Collagen - Answer Fibrous
- most abundant protein in the body, contributes to structural integrity of the body
- Organized into four major classes according to their protein isoforms (functionally
similar, but slightly different structure)
- Primary structure is a repeating Gly-X-Y sequence (X and Y could be one of many amino
acids), often including hydroxyproline and hydroxylisine post-translationsal
modifications
- Proline residues cause left handed helices, and three left handed helices form a
subunit - three subunits form a coiled coil, of which many form fibrils and many fibrils
form fibers


Restriction Endonucleases - Answer Enzymes naturally produced by bacteria which
cleave double-stranded DNA at 4-6 bp palindromes to produce "restriction fragments" -
scientists can use these enzymes for DNA cloning. Cuts are done to generate a 3' end

, with a hydroxy terminus and a 5' end phosphate on the other end. Cuts can be "sticky"
(staggered) or "blunt" (ends will not hydrogen bond with each other)


Nomenclature of enzymes:
- First letter is the genus of the bacterium
- Next 2 letters are the species of the bacterium
- Number is the order in which the enzyme was discovered per organism


PCR - Answer Used to amplify a select DNA sequence in order to compare genes, detect
sequences, or for forensic analysis. DNA is heated to 95°C to denature the strands, then
cooled to 55-60°C so complementary primers can anneal, then increased to 65°C so Taq
DNA polymerase can synthesize complementary strands.


Allele-specific PCR can determine single-nucleotide polymorphisms (SNP) by putting
primers for wild/mutant alleles and then determining the length of promoted DNA using
gel electrophoresis


Gel Electrophoresis - Answer Method used to separate molecules by size (done by
separating by charge) - often done with restriction digest fragments and PCR products in
order to visualize them. Samples are placed on agarose/polyacrylamide gels and then an
electric field is applied. The larger the molecule, the less distance it will travel. The gel is
stained with fluorescent ethidium bromide in order to visualize the distance of the
molecules.


DNA Probes - Answer Single stranded DNA labelled with radioisotopes or fluorescent
dye, complementary to target DNA. They are bound to the target DNA (hybridization) in
order to identify target sequences.

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