IB Biology Proteins

What are proteins made of?

- amino acids form polypeptides
- polypeptides form ————

How many amino acids are there?

20 different amino acids

Structure of general amino acid

STUDY PICTURE
-amine NH2 and carboxylic group

How do amino acids differ from each other?

The R-group or side group/chain makes each amino acid different

What makes proteins different from other compounds?

They will contain nitrogen

How many different R groups are there?

20 different R groups, simple H or CH3 to complex ring structures

The R group charge

- can have a positive/negative charge
- can be polar or nonpolar
***** polarity dictates shape

How many amino acids are essential and nonessential?

- 8 are essential: you MUST get them thru diet by eating protein
- 12 are nonessential: you can make them from the other 8

Amino acids are linked together

- one at a time by ribosomes
- start w dipeptides and on up to polypeptides

How many possible sequences are there for protein?

- infinite
- amino acids can be linked together in any sequence, it gives a huge range of possible polypeptides

The amino acid sequence is ———— for by ————

Coded, DNA
- genes store info in the sequence of nucleotide bases

Since there are 20 dif amino acids, it is possible to have an ————

Incredible diversity of primary structures
- diversity of polypeptides within cells of dif types of organism is relatively low

Proteins can be

Single polypeptides or many polypeptides long

changing one amino acid

May completely alter protein
Ex. Substitution of one amino acid for another in hemoglobin causes sickle cell disease

Examples of proteins

Lysozyme, integrin, collagen, hemoglobin

Lysozyme

1 polypeptide
Enzyme in nasal mucous and tears
Kills bacteria by digesting peptidoglycan in cell walls

Integrin

2 polypeptides
membrane protein used to make connections inside and outside a cell

Collagen

3 polypeptides
Structural protein in tendons, ligaments, skin and blood vessel walls
Provides high tensile strength with limited stretching

Hemoglobin

4 polypeptides
Transport protein in red blood cells
Binds O2 in lungs and releases it in tissues that need it

How are proteins made? : Formation of a dipeptide and a polypeptide

- condensation reaction/ dehydration synthesis
- peptide bond forms between the carboxyl group of the 1st amino acid and the amine group of the second amino acid
- amine group (N terminal) at one end and a carboxylic group at the other end

polypeptides can be --------- in the same way as ----------- (----------)

hydrolysed, polysaccharides, (need to incubate w acids)

amino acid sequence determines

3-D conformation of protein as well as polypeptides that make up protein

Levels of protein structure or conformation

primary, secondary, tertiatery, quaternary

Levels of protein structure or conformation: Primary Structure

- the number and order of amino acids in a polypeptide chain
- N-C-C-N-C-C-N-C-C "backbone" to the chain
- --------- is always read from the N terminus to the COOH terminal

Levels of protein structure or conformation: Secondary Structure

- has atoms projecting from the N-C-C backbone
- O2 from carboxyl C=O and the H from the Amino N-H can form hydrogen bonds
- does NOT involve R-groups
3 forms of --------- : alpha helix, beta-pleated sheet, open loops
- only N, H, and O

Secondary Structure: Alpha helix

-3.6 amino acid per turn of helix
- basis of fibrous polymers
- discovered by Linus Pauling

Secondary Structure: Beta- pleated sheet

- stretched out in comparison to the alpha helix
- has twists that increase the strength and rigidity of the structure

Secondary Structure: Open loops

- loops that often connect the more alpha helices and pleated sheets
- are often important regions of proteins including the active sites of enzymes

Levels of protein structure or conformation: Tertiary Structure

- three dimensional conformation of a polypeptide, where it starts to take shape
- folds in polypeptide chain
- shape is maintained by intramolecular bonds
- hydrogen bonds, ionic bonds, disulfide bridges

R side chains have the ability to

form hydrogen bonds and ionic bonds

Disulfide bridges

- covalent bonds formed between 2 adjacent cysteine amino acids
- stabilizes the tertiary shape of a protein

Levels of protein structure or conformation: Quaternary Structure

- number of tertiary polypeptides joined together
ex hemoglobin

example of quaternary structure

hemoglobin
- composed of 4 dif polypeptide chains
- each chain forms a tertiary structure called a
heme group each w/ Fe 2+
- prosthetic groups
- proteins are often bound to inorganic
compounds/ elements

shape of protein determines

function

Two Classifications of proteins

fibrous and globular

Two Classifications of proteins: fibrous proteins

- water insoluble, long, narrow proteins
- structural- provide strength and support to tissues

examples of fibrous proteins

collagen:
- basis of the connective
- composed of 3 left handed helices
- most common protein in animals

keratin:
- common fibrous protein
- composed of 7 helices
- major protein in hair and nails structure

Two Classifications of proteins: globular proteins

- near soluble (colloids)
- more compact and rounded shape
- functional- pigments (myoglobin), transport (hemoglobin and lipoproteins), antibodies (immunoglobulins)

The Importance of polar and nonpolar amino acids

- in cell membrane proteins:
- nonpolar amino acids allow protein to pass thru cell membrane
- polar amino acids are in contact w water inside and outside the cell; allows polar molecules to pass thru cell membrane

Examples of Proteins

Hormones, Immunoglobulin, Rubisco, Collagen, Spider Silk, Rhodopsin, Hemoglobin, Amylase, Actin and Myosin and Enzymes

Hormones

Insulin
-51 amino acid polypeptide
-it is in all cells, especially muscle and liver

Hormones help

glucose enter cells
-helps the storage of glucose as the insoluble polymer glycogen

Immunoglobulin

-Antibodies
-Produced in an immune response to an infectious antigen
-Great variation in the heavy chains (allows a response to virtually any possible antigen surface)

Rubisco

Ribulose Biphosphate Carboxylase
- the most abundant protein on the planet
-most important enzyme in the world
- catalyzes the reaction that fixes CO2

Rubisco catalyze the reaction that ...

fixes carbon dioxide in the atmosphere

Collagen takes the form of

-Many forms of rope-like proteins
- forms a mesh of fibers in skin and blood vessels that resists tearing

Purpose of Collagen

-provides immense strength to ligaments and blood vessel walls
-prevents cracks and fractures in bones and teeth,

Purpose of Collagen

-provides immense strength to ligaments and blood vessel walls
-prevents cracks and fractures in bones and teeth

Rhodopsin

"Visual Purple" strongly absorbs green/blue light
-pigment in rod of retina sensitive to light

Hemoglobin

Transports O2 and CO2

Amylase

Helps digest Starches

Actin and Myosin

Proteins in muscle cells that interact to cause contractions

Enzymes

-large globular proteins often with prosthetic groups
-speed up chemical reactions

Denaturation

Changing proteins native conformation
Change shape= change in activity

How does denaturation happen?

1. High Temperature
2. Chemical agent (acid or base) change in pH
3. Organic Solvent

What is the end result of denaturation?

Proteins have complex shapes
-Can have areas that are polar or Nonpolar, therefore have varied functions in living things

Denaturation can be used for

Energy, but is not the first choice

Functions of Proteins

Catalysis, Muscle Contraction, Cytoskeletons, Tensile Strengthening, Blood Clotting, Transport of Nutrients and Gases, Cell Adhesion, Membrane Transport, Hormones, Receptors, Packing of DNA, Immunity

What kind of bonds form in the formation of proteins?

Peptide bonds

Proteins are made of how many amino acids

Thousands