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Unit I: What Makes a Cell (Chapters 1-3)

Introduction to Cells / The study of cells

Molecules of Life and Bioenergetics


Physiology in Focus: Metabolic Disorders

Proteins see Revised Chapter 3 Key Terms/Concept Sheet on ELMS!!!


Exam 1: Monday 2/13/17

Format: Multiple Choice, Short Answer, Matching


Study Materials:
Lecture Slides
Chapter Key Terms/Concept Sheets
Practice Problems (similar types of questions will be on exam)
Chapter 3 Questions/Objectives

I. What are the factors that determine the structure and


shape of proteins?

II. How is protein structure related to protein function?

III. What do proteins do?

a) binding
I
Disruption of a proteins environment can unfold (denature) the
protein, but it will refold spontaneously once the disruptor is
removed

urea disrupts noncovalent interactions within proteins

Other denaturation agents: pH, high temperature, salt concentration


Figure 3-6a Molecular Biology of the Cell ( Garland Science 2008)
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II Tertiary structures can form DOMAINS
within a protein
Protein domain:
3D Structural unit of a protein with uniquely defined binding/functional
properties that often act independently of the rest of the protein

Three tertiary structures within


this protein form 3 separate
Domains
Different domains of a protein often
II have different functions

Catalytic domain
Inhibits host cell protein
synthesis

Receptor binding
domain (attaches to cell
surface)

Hydrophobic domain
(Inserts into membranes)
Diptheria Toxin
3 functional domains
II
Protein Domains
- can also be described according their structure

Alpha helical domains


Coiled-coiled domains
Beta-sheet domains
Random coil domains (no secondary structure)
Interactions between secondary structures
II can form functional protein DOMAINS

Alpha helices can wrap around one another to form coiled-coils


Coiled coil alpha helices held
together by stripe of hydophobic
amino acid R groups (red)

Single alpha helix

Figure 3-9 Molecular Biology of the Cell ( Garland Science 2008)


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II Similar domains which occur in many related proteins are
called sometimes called motifs e.g. a DNA-binding motif

Common ribbon structure


Red = Drosophila
proteins backbone

Green = yeast
proteins
backbone

These two DNA-binding proteins are separated by a billion years of evolution,


yet share the same DNA-binding motif composed of three alpha helices
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Todays Questions/Objectives

I. What are the factors that determine the structure and


shape of proteins?

II. How is protein structure related to protein function?

III. What do proteins do?

a) binding

b) distinct functional classes


IIIa Proteins Interact with other
Molecules
A proteins physical interaction with other
molecules determines its biological properties.
All proteins bind to other molecules
Ions, small organic molecles
Other biomolecules (lipids, nucleic acids, ligands
carbohydrates)
other proteins

Because ligand binding is achieved by noncovalent


bonds, it is reversible.
IIIa
Protein-ligand Interactions
Can be weak and short-lived
Can be tight and stable

Are ALWAYS specific

A given protein is usually only capable of interacting with only a few


other molecules out of the thousands of different types in its
environment.
IIIa Ligand Binding sites are 3 dimensional

The amino acids that contribute to binding a ligand are often


quite far apart on a proteins primary sequence but come
together when the protein folds.

Hence the importance


of correct folding
for protein function

Figure 3-37a Molecular Biology of the Cell ( Garland Science 2008)


IIIa Close-up view of a binding site

ligand

Figure 3-37b Molecular Biology of the Cell ( Garland Science 2008)


IIIa A proteins structure and binding properties can be
altered by covalent modifications

Covalent modifications: covalent linkages between a


protein and some other molecule.
Our focus:
Phosphate groups
Acetyl Groups
Ubiquitin
IIIa Covalent modifications to proteins:
Phosphorylation
Transfer of phosphate groups to a protein
3 Target amino acids: Ser, Thr, Tyr

The presence of a phosphate group Phosphate groups are


only added to these 3
on a protein enables new amino acids:
electrostatic attractions/repulsions.

This can cause changes in a proteins:


Conformation/Shape
Localization in the cell
Binding properties

Change in protein function


IIIa Covalent modifications to proteins:
Acetylation
Transfer of acetyl groups
Target amino acid: Lysine (LYS)

Acetylases

Deacetylases

Removes the electrostatic property of the Lys R group


IIIa Covalent modifications to proteins:
Ubiquitylation
Transfer of the ubiquitin protein
Ubiquitin Target amino acid: Lysine (LYS)
Small cytosolic protein (76 amino acids)
Covalently attached to proteins (reversible)
Serves as a tag that can either:
mark proteins for degradation, or
direct proteins to specific locations in the cell
Isopeptide
bond: formed
between the
COOH terminus
of ubiquitin and
the lysine R
group of the
protein target
IIIa
Ubiquitylation of Proteins occurs at lysine amino acids

protein
protein

Lysine
Lysine
Ub
Ub
Lysine

Ub
monoubiquitylation
polyubiquitylation Lysine

Ub

Directs Protein degradation

Directs Protein localization in the cell


IIIa Many proteins are covalently modified in
multiple ways at multiple sites

A proteins function/behavior can be regulated by different combinations of modifications.

Figure 3-81c Molecular Biology of the Cell ( Garland Science 2008)

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