Chapt. 3-Proteinspgs. 36-42

• Make up ~50 dry weight of any organism.

• Roles:– Enzymes. Assist in

chemical reactions– Defense. Immune system

– Structural roles: Keratin

MusclesCytoskeleton

- Chemical messengers. Hormones

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 what’s an amino acid?

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 atom4. An R group

• Text pg. 36-37• If it has these 4 traits, it’s an

AA!!

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

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

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.

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

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

Quiz

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

proteins?

Protein Structure

• Proteins rarely exist as long straight chains of AAAA1-AA2-AA3-AA4-AA5-AA6

• Functional proteins are more commonly formed into folded, globular structures

• Text pg. 39

Levels of Protein Structure

• Primary (10) Structure : The AA linear sequence. The chain of AA...

Ala-Gly-Ser-Val-Thr

• Text pg. 39

Protein Structure

• 20 Structure: Hydrogen bonding may occur between different AA in the same chain …– Leading to a coiled alpha (α) helix structure….

• OR, Hydrogen bonding may occur between different AA in neighboring chains.– Leading to a pleated sheet (β) structure.

• Text pg. 39

Protein 20 Foldingα-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.

Protein 20 Foldingβ-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.

Motifs

• Supersecondaryprotein structuresin which multiple αhelices and β sheets combine to form complex, characteristic folds.

• example: α β α

Supersecondary Protein Structures2 Transmembraneproteins

Domains

• Definite 3D regions along a polypeptide with a precise function

• Example: enzyme binding sites, substrate binding sites

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

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

Protein FoldingAn Analogy

10

20

30

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

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.

Heat Shock leads to Unfolding Proteins

• When proteins are exposed to dramatic environmental changes, they will unfold.

• A term for unfolded proteins is denaturedproteins

• If we cook or change pH or salt levels, we denature proteins.

When yeast cells are given a mild heat shock, some proteins unfold and aggregate, such as the molecular chaperone (Hsp104). We investigated the subcellulardistribution 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

Nucleic Acids• Information storage

molecules• Cells receive

instructions from nucleic acids about which proteins to make

• Nucleic acids come in two types:

DNARNA

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.

Nucleotides

• Composed of only 3 parts:1) 5C sugar2) Phosphate group3) Ring-shaped Nitrogen base

• Text pg. 47

1

2

3

Nucleotides build Nucleic Acids

• Individual nucleotides link together by the PO4of 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/molegene/sld008.htm

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…..

Nitrogen-Bases

Adenine

Guanine

Cytosine

Thymine

Uracil Uracil

Just 5 different N-basesdetermine all of life on earth!

2 Types of Nucleic Acid:RNA & DNA

• Differ in a few essential ways:

• Text pg. 48

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

DNA

Uses A,T,C & G bases only Text pg 47

DNA

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

• = deoxy-ribose

What holds DNA antiparallelstrands 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

RNA• Usually single-

stranded• Uses Uracil as a

substitute for Thymine• RNA uses U,A,G & C

RNA• Sugar component is

5C Ribose• Ribose has an -OH

group on Carbon #2

The Central Dogmaof Biology

• DNA makes RNA makes Protein• DNA --> RNA --> Protein