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Chapt. 3Proteins pgs. 3642

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Add many AA in this fashion to form a protein. Peptide Links ... Example: enzyme binding sites, substrate binding sites. Protein Structure ... – PowerPoint PPT presentation

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Title: Chapt. 3Proteins pgs. 3642


1
Chapt. 3-Proteins pgs. 36-42
  • Make up 50 dry weight of any organism.
  • Roles
  • Enzymes. Assist in chemical reactions
  • Defense. Immune system
  • Structural roles
  • Keratin
  • Muscles
  • Cytoskeleton
  • - Chemical messengers. Hormones

2
Proteins Made up of Amino Acids
  • All proteins have a similar basic structure.
    They are all composed of small units called amino
    acids (AA).
  • Stick a bunch of AA together and make a protein.
  • So whats an amino acid?

3
Amino Acids
  • A molecule composed of 4 pieces all covalently
    bonded to a central C atom
  • 1. An amino group (NH2)
  • 2. A carboxyl group (COOH)
  • 3. An H atom
  • 4. An R group
  • Text pg. 36-37
  • If it has these 4 traits, its an AA!!

4
Amino Acids
  • There are 20 common AA used in making proteins in
    living organisms
  • R groups account for the differences
  • R may be small- CH3
  • OR, R may be a large aromatic ring
  • R groups define the behavior of an AA
  • Text pg 37

5
R Groups in AA
  • Nonpolar R groups -CH3 or -CH2
  • Polar-Uncharged R groups usually with an -OH or
    O
  • Polar-Charged R groups posses acidic (-) or
    basic () groups such as -COOH or -NH
  • Aromatic R groups contain a carbon ring
  • Text pg. 37

6
R Groups in AA define the protein structure
function
  • The chemical behavior of a protein is determined
    by the AA properties…
  • Whether the AA are polar or charged or aromatic.

7
How to make a protein?
  • Proteins are simply chains of AA stuck together
  • 2 AA link together via a peptide bond to form a
    polypeptide
  • Add many AA in this fashion to form a protein

8
Peptide Links
  • Covalent bonds between the -COOH of one AA and
    the -NH2 on another
  • Text pg. 38
  • Numerous peptide links will form longer and
    longer polypeptides

9
Quiz
  • How many different Amino acids are there?
  • How do we link together 2 AA ?
  • How can we form different types of proteins?

10
Protein Structure
  • Proteins rarely exist as long straight chains of
    AA
  • AA1-AA2-AA3-AA4-AA5-AA6
  • Functional proteins are more commonly formed into
    folded, globular structures
  • Text pg. 39

11
Levels of Protein Structure
  • Primary (10) Structure The AA linear sequence.
    The chain of AA...
  • Ala-Gly-Ser-Val-Thr
  • Text pg. 39

12
Protein Structure
  • 20 Structure Hydrogen bonding may occur between
    different AA in the same chain …
  • Leading to a coiled alpha (a) helix structure….
  • OR, Hydrogen bonding may occur between different
    AA in neighboring chains.
  • Leading to a pleated sheet (b) structure.
  • Text pg. 39

13
Protein 20 Folding a-Helix
  • The alpha helix resembles a ribbon of amino acids
    wrapped around a tube to form a stair case like
    structure. Here is pictured a ribbon and ball and
    stick diagram of a model alpha helix. This
    structure is very stable, yet flexible and is
    often seen in parts of a protein that may need to
    bend or move.

14
Protein 20 Folding b-Sheet
  • In the beta sheet, two planes of amino acids
    will form, lining up in such a fashion so that
    hydrogen bonds can form between facing amino
    acids in each sheet. The beta pleated sheet or
    beta sheet is different than the alpha helix in
    that far distant amino acids in the protein can
    come togeher to form this structure. Also, the
    structure tends to be rigid and less flexible.

15
Motifs
  • Supersecondary protein structures
  • in which multiple a helices and b sheets combine
    to form complex, characteristic folds.
  • example a b a

16
Supersecondary Protein Structures 2 Transmembrane
proteins
17
Domains
  • Definite 3D regions along a polypeptide with a
    precise function
  • Example enzyme binding sites, substrate binding
    sites

18
Protein Structure
  • Tertiary (30) Structure The tightly folded
    structure in which motifs and polar/nonpolar
    groups all take on a 3D shape.
  • Text pg 40

19
Protein Structure
  • Quaternary (40) Structure Several 30 polypeptide
    chains link together to form complete
    multi-subunit protein
  • I.e. Hemoglobin is composed of 4 separate chains
  • Text pg. 39, 41

20
Protein Folding An Analogy
30
20
10
21
How do Proteins fold correctly?
  • As proteins are produced, they may take on any
    number of different shapes…but only one is
    correct.
  • Other proteins, termed Chaperones, help in the
    correct folding process

22
Molecular Chaperones
  • Molecular chaperones are proteins that are
    grouped together into highly conserved families.
    By binding to incompletely-folded target
    proteins, molecular chaperones help them to
    complete folding, assemble into correct
    structures, or translocate across an
    intracellular membranes.
  • Therefore, molecular chaperones play pivotal
    roles in normal protein metabolism in an
    environment that is so densely packed with
    macromolecules that unchaperoned processes are
    virtually impossible.
  • Under suboptimal conditions, such as encountered
    when applying mild heat to cells, the proteins
    will misfold and aggregate. Cells respond to such
    stress by increasing the expression of a subset
    of genes encoding the so-called heat shock
    proteins. Not surprisingly the majority of heat
    shock proteins are molecular chaperones.
  •  

23
Heat Shock leads to Unfolding Proteins
  • When proteins are exposed to dramatic
    environmental changes, they will unfold.
  • A term for unfolded proteins is denatured
    proteins
  • If we cook or change pH or salt levels, we
    denature proteins.

24
When yeast cells are given a mild heat shock,
some proteins unfold and aggregate, such as the
molecular chaperone (Hsp104). We investigated the
subcellular distribution of Hsp104 in normal and
heat shocked cells. Hsp104 relocalizes in
response to heat shock into irregular foci that
disappear upon recovery at optimal temperatures.
We have tagged Hsp104 with a fluorescent protein
(GFP) so that its subcellular responses to
various physiological conditions can be observed.
A) After mild heat shock, Hsp104 redistributes
into irregularly-shaped foci, presumably
aggregates of heat-damaged protein. B) After 1h
recovery, Hsp104 is again uniformly distributed.
http//bioinfo.med.utoronto.ca/Brochure/JG.html
25
Nucleic Acids
  • Information storage molecules
  • Cells receive instructions from nucleic acids
    about which proteins to make
  • Nucleic acids come in two types
  • DNA
  • RNA

26
DNA/RNA Structure
  • Both similar…composed of a long sequence of small
    molecules..
  • Termed nucleotides.
  • Many small nucleotides linked together form a
    large DNA or RNA macromolecule.

27
Nucleotides
  • Composed of only 3 parts
  • 1) 5C sugar
  • 2) Phosphate group
  • 3) Ring-shaped Nitrogen base
  • Text pg. 47

28
Nucleotides build Nucleic Acids
  • Individual nucleotides link together by the PO4
    of one linking to the sugar of another.
  • This linkage is a dehydration reaction...
  • And is termed a phosphodiester linkage

http//krupp.wcc.hawaii.edu/BIOL100/present/molege
ne/sld008.htm
29
Nucleotides contain information. How?
  • Of the 3 ingredients in a nucleotide, only the
    N-bases show any real variety
  • It is these N-bases that account for all the
    information in living organisms
  • And yet, there are only 5 different types of
    N-bases…..

30
Nitrogen-Bases
  • Adenine
  • Guanine
  • Cytosine
  • Thymine
  • Uracil

Uracil
31
Just 5 different N-bases determine all of life on
earth!
32
2 Types of Nucleic Acid RNA DNA
  • Differ in a few essential ways
  • Text pg. 48

33
DNA
  • Exists as long double linear sequence
  • Two long polymers of DNA wind around each other
    to form a helical structure
  • Termed a double helix…a twisted ladder
  • The two strands run in opposite directions…..
    they are antiparallel

34
DNA
  • Uses A,T,C G bases only
  • Text pg 47

35
DNA
  • The 5-C sugar in DNA is ribose with one missing O
    atom on Carbon 2
  • deoxy-ribose

36
What holds DNA antiparallel strands together??
  • H-bonds between nitrogen bases on opposite
    strands
  • There is room between DNA strands for 3 carbon
    ring structures…
  • So… purines (A,G) align with pyrimidines (C, T)
    in a precise way
  • This is known as..Complementary pairing
  • A-T and C-G always pair up
  • Text pg. 47

37
RNA
  • Usually single-stranded
  • Uses Uracil as a substitute for Thymine
  • RNA uses U,A,G C

38
RNA
  • Sugar component is 5C Ribose
  • Ribose has an -OH group on Carbon 2

39
The Central Dogma of Biology
  • DNA makes RNA makes Protein
  • DNA --gt RNA --gt Protein
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