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CELL BIOLOGY
BIOL 3320
Lecture 1 Outline + Notes
PROTEINS
I
...
They fit
together like wheels; they build, destroy, repair, and edit; they stretch like rubber; they are
sturdy as concrete
...


Why begin with proteins?
1
...

2
...
Support
b
...
Movement
d
...
Metabolic regulation (enzymes)
f
...
Coordination and control

B
...

A proteins function is determined by its folded shape in three dimensions
...

Proteins can assume almost unlimited numbers of different shapes
yielding theoretically an unlimited number of different functions
...

The unlimited number of shapes derives from the large number of ways 20
AAs can be strung together to form different sequences
...


Amino acids
A
...

Central α-carbon connected via 4 covalent bonds to:
a
...

Carboxyl group
c
...

R group (side chain)- one of 20 possible molecular groups

2
...


B
...


Peptide Bonds
1
...

Peptide bond has a partial double bond character due to electron resonance
between the carbonyl group and the peptide bond; makes the peptide bond
rigid and bonded groups planar
...

However, the groups bonded to the α-carbon rotate freely, giving the
attached R group the mobility to interact with other molecules (e
...
, water,
other parts of the protein, etc
...

Peptide backbone— the peptide bond and associated groups — allow for
both structural rigidity (stability) and mobility
...

Definitions
...

A few amino acids (2 - about 50): peptide
b
...

c
...

(2)
Subunits may be held together by noncovalent bonds
(common) or by covalent bonds (less common)
...

A
...

4 classes
a
...

(1)
Important: These 5 amino acids are the main determinants
of the overall charge of a protein, which strongly affects the
proteins shape, and hence, its function
...

Polar uncharged (5) (partial charge on R group): Ser, Thr, Gln,
and Asn
...

Nonpolar (11): Ala, Val, Leu, Ile, Met, Phe, Trp, Gly, Pro, Cys,
Tyr
...
Ser, Thr, and Tyr
frequently become phosphorylated (become activated and
able to do many things)
...

Other (special):
(1)
Gly: small R group (a H-atom) allows it to fit in tight
places where proteins come in close contact (e
...
, triple
helix of collagen)
...

(2)
Pro: The ring structure puts a kink/bend into the peptide
backbone
...

 Interchain bond- two separate chains
 Intrachain bond- on the same chain
 Not found in the cytosol (reducing environment)
3

Disulfide bonds do not change the conformation of the protein, but instead act as atomic
staples to reinforce the structure
...
Also,
disulfide bonds are only present in an oxidizing environment (outside of the cell, perinuclear
space or ER lumen)
...


B
...

Hydrophobic (e
...
, nonpolar, uncharged) AAs occupy the folded interior
of proteins to minimize contact with water
...

Folded surface of proteins contains mostly charged and polar AAs
...

Secondary structures, which form early in the folding process (MOTIF),
enable the polar polypeptide backbone to penetrate the hydrophobic core
of the protein
...

Loops (e
...
, random coils) that lack secondary structure are generally
located on the surface of the protein
...
The rER and the Golgi help fold secretory proteins that are made
for export, in addition to ER resident chaperones
...
The final three-dimensional
shape of the protein is still specified by its amino acid sequence, chaperones simply make the
folding process more reliable and faster
...


Bonds in Proteins
A
...

Noncovalent
1
...

Hydrogen bonds (H-bonds) (Very Important)
3
...

Hydrophobic interactions

Polar AA’s can be in the hydrophobic core of the protein, but not too many
...

4

IV
...

Four Levels of Protein
1
...

Secondary: Simple, frequently-used patterns (recognizable shapes) into
which parts of a polypeptide are folded
...

a
...

-sheet
(1)
comprised of -strands
(2)
antiparallel vs
...
This links the
carbonyl group of one peptide bond to the amino group of
another
...
6 amino acids
...
Relative
to beta sheets, alpha helices are generally longer due to
their coiled structure and H bond formations
...
The R groups of
an alpha helix project out radially while the R groups of a
beta sheet project out perpendicularly, above and below
...
Thus, proteins can contain more than one
secondary structure
...

Beta sheets can orient themselves parallel, relative to each other, causing them to
have longer loops with less hydrogen bonds, making the orientation higher in free
energy
...
In addition, secondary structures are formed to hide the polar
backbone in the hydrophobic core
...
Loops, on
the other hand, connect domains on the protein’s surface and are not considered
secondary structures
...

*peptides are too short to have secondary structures*

5

c
...


Loops: Chain of residues of variable length and shape that connect
adjacent secondary elements (not ordered AA’s pro gly {specific
for antigen})
(1)
Hairpin loops connect two adjacent antiparallel -strands
...
g
...
Can serve as recognition site
...


*In order to determine the direction of the polypeptide
you must first locate the “lollypop head” carbonyl group
...
*
3
...

a
...
Specifically a sequence
...


In other proteins, Alpha helices wrap around each other to form a particularly stable
structure, known as a coiled-coil
...
Long rodlike coiled-coils often provide
the structural framework for many elongated proteins
...

Domains: Part of a protein
that folds independently of other
parts
...

May contain one or several motifs
...

(a)
fibrous (rod-like) - myosin monomeric “tail”
...

(2)
Functional domains: part of a protein that performs a
specific function
...

[Domains sometimes are encoded by separate parts of genes, known as exons
...
]
4
...

a
...
g
...
g
...

7

Review Questions
Why begin the course with the study of proteins?
How can proteins posses such a wide variety of functions?
How can a polypeptide be both rigid and flexible at the same time?
What are the 5 charged AAs names, symbols, charges, structures, and additional information?
What are the 4 polar AAs names, symbols, charges, structures, and additional information?
What are the 11 nonpolar AAs names, symbols, charges, structures and additional information?
What is the acronym for nonpolar AAs?
List the noted information for collagen
...

What is a domain?

8



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