Unit 1.5 & 2

6 types of proteins

6 types of proteins

structural, enzyme, hormone, contractile, immunological & transport

Polypeptides

unbranched chain of amino acids

condensation reaction (draw)

removal of water links monomers together to combine smaller organic molecules to form larger moleculeU

Proteins

single polypeptide or more than one polypeptide of amino acids linked together

Structure of an amino acid (draw)

an amino group, a carboxylic acid, and a R group (varies for each amino acid

amino acid condensation reaction

• linked by condensation reaction

• new bond called peptide

• dipeptide; 2 amino acids

• tripeptide: 3 amino acids

Number of amino acids

20

Synthesis of polypeptides

DNA provides info, transcribed into RNA, where the synthesis takes place in the ribosomes (translation)

Number of polypeptides in proteins

one or more

Polypeptide structures

• primary, secondary, tertiary, quaternary

• folding determined by amino acid sequence

• stabilized by intramolecular bonds between amino acids

Determinant of shape & function of protein

Order of amino acids

R group determines

types of bonds, interactions w/ other molecules, properties, function, structure

Conformation

three-dimensional shape of a proteinmolecule

Effect of gene mutation

changes protein's conformation, shape, loss of function

Primary structure

Simple linear sequence, defines all aspects of structure & function

Secondary structure

Folding chains on themselves (pleated sheet or alpha helix)

teritary structure

foils & coils to form complex 3d shape

Quarternary stucture

2 or more polypeptide chains held in a multi

Denaturation

Permanent loss of secondary, tertiary (sometimes quaternary) due to hydrogen bond disruption between R groups & amino groups

Cause of folding & touching of proteins

Ionic bonds between positively and negatively charged R groups

Genome

unique DNA content in every organism

Proteome

Unique set of proteins coded by genome

• varies because diff cells make diff proteins and depends on cell activity

gel electrophoresis

Process to separate proteins

Divisions of protein

globular & fibrous

Determinant of divisions of protein

solubility in water

Globular proteins

Complex polypeptide chains linked to other chains, soluble in water cause hydrophobic R groups fold into the core away from surrounding water

Role of Globular proteins

active in cell metabolism

Fibrous proteins

Long polypeptide chains with hydrophobic R groups exposed therefore insoluble in water

Role of fibrous proteins

structural parts: tendons, skin, collages, keratin

Rubisco

• globular enzyme

• active site catalyzing photosynthesis reaction that fixes CO2 from atmosphere

Insulin

• globular, hormone, 2 diff polupeptide chains

• produced by pancreas

• carried, dissolved in blood

• binds specifically & reversibly to insulin receptors causing absorption pf glucose to lower blood glucose conc

Immunoglobulin

Globular, Y shaped, antibodies to fight infections by recognizing and binding to antigen molecules

Rhodopsin

• globular, pigment protein

• retina rod cells become light-sensitive to serve a nerve impulse

Collagen

Fibrous, 3 diff polypeptide chains. structural protein, in muscles, tendons, ligaments to give tensile strength. In skin & bones to prevent tearing & fractures

Spider silk

Fibrous, structural protein, produced by spiders for webs, can be extended & resistant to breaking

Ways to denature proteins

higher temperatures, extreme pH of surrounding solution

3 properties of enzymes

substrate specific, optimum pH, optimum temperature

Why primary structures are not affected by denatueation

peptide bonds holding adjacent amino acids do not break

Reason for high fever danger

Some proteins start to denature, enzymes no longer function

Effect of temperature change on amino acids

Interaction between amino acids changed, affecting quaternary, tertiary & secondary

Effect of pH on amino acids

strong solutions can break bonds between non adjacent amino acids or between polypeptide chains

Coagulation: Structure when denatured

Hydrophilic attracts water molecules, hydrophobic portions unstable therefore associates with other hydrophobic molecules

Enzyme role

control metabolism of cell

• globular protein

Define Enzyme

biocatalyst that regulates the role of biochemical reactions without taking part

How is enzyme a catalyst

lowers minimum activation energy needed for reactants to react

Location of enzyme & substrate reactions

watery environment

Active site

location where substrate binds to enzyme to react

State of enzyme after reaction

unchanged & used again

Enzyme structure

large polypeptides with tertiary or quaternary structure, globular with specific active site

Induced fit

Once substrate binds to active site and during transition stage, enzyme changes slightly resulting in tighter binding

Role of induced fit

enzyme induces bond weakening within molecules thus reducing activation energy needed

Enzymatic reaction

1. attraction of substrate to enzyme (diff shapes)

2. conformational change reaction of substrate-enzyme complex

3. enzyme revers to original shape and products leave reaction

Active site structure

sequence of amino acids responsible for catalytic activity

Activation energy

minimum energy that reacting particles should possess for a reaction to make products

Collision theory

1. particles must collide to react together

2. need sufficient energy to break & form bonds

3. orientation (opposite charge molecules)

Exothermic or exergonic reation

product formation releases energy

Endothermic or endergonic

product formation associated with energy absorption (usually heat)

Causes of structural changes to active site

1. temperature

2. pH

3. Substrate concentration

4. Enzyme concentration

Effect of temperature on collision theory

• Low temp = slowly, collision low

• High temp = rapid, collision high, denature

Low Substrate concentration

• more substrate than enzyme

• low rate of reaction

High substrate concentration

• more collision chances

• rate of enzymatic reaction rises gradually

• increase halted when active sites occupied

Graph structure of optimal temperature & pH

• increases due to more collisions of heat

• peak reached

• drops due to denature of heat and pH

• increase, peak and drop with pH

Graph structure of substrate/enzyme concentration

1. increases because more collisions between substrate and active site

2. plateau phase because most active sites are occupied

Immbolisation of enzyme

process of attaching enzyme to a material to restrict movement

Permit of immboilisation of enzyme

• not present in final product

• doesn't restrict conc

• avoid adverse effects to human consumption

• higher conc of enzymes

• faster rate of reaction

• immediate separation from reaction mixture

• recycled

How to increase pH as dependent variable

• increase rate of reaction!

• increase enzyme conc

• increase temp

• longer time

Value of V(velocity) at start of reaction

Minimum since active sites are free

Amino acids

carbon center. monomers of proteins

Cell theory

1. All living organisms are composed of one or more cells.

2. The cell is the basic unit of structure and organization in organisms

3. Cells arise from pre-existing cells.

Louis Pasteur method & results

Heated broth with swan necks \n 1. Sealed & upright: no growth \n 2. Unsealed: microbial growth \n 3. Tilted: growth

Louis Pasteur Conclusion

Air carries microbes but non-living conditions do not make living things

Spontaneous generation

Living things arise from non-living aka abiogenesis

Biogenesis

cells formed from pre-existing cells

Miller Urey Method

Recreated early earth conditions:

• atmosphere (low oxygen, high radiation, gasses)

• heating of water vapor

• electrical storm shocks

Miller Urey Conclusion

Solution found organic molecules including amino acids found in living organisms

4 conditions for life to emerge & persist

1. Simple organic molecules (amino acids, fatty acids, carbohydrates)

2. Larger organic molecules must be assembled from simpler molecules (DNA, phospholipids)

3. Reproduction for replication

4. Biochemical reactions require set conditions therefore self-contained structures need membranes

endosymbiotic theory

Mitochondria (likely anaerobes) & chloroplasts (likely cyanobacteria) were prokaryotes taken by larger prokaryotes

evidence for endosymbiotic theory

In mitochondria & chloroplasts

• double membrane

• circular naked DNA like prokaryotes

• DNA as single chromosomes

• 70s ribosomes like prokaryotes

• binary fission like prokaryotes

• susceptible to some antibiotics

How do living organisms control composition?

complex web of chemical reactions

Metabolism

web of all enzyme

Why is life carbon

based

4 types of macromolecules

carbohydrates, lipids, proteins & nucleic acids

Lipids

• triglycerides, phospholipids, and steroids

• carbon compounds made by living organisms

• mostly or entirely hydrophobic

• 2-3 hydrocarbon chains or quadruple ring structure (steroids)

• stores energy for later use

triglyceride

• fatty acid tails are flexible

fatty acids

• carboxyl group: acidic and -COOH

• unbranched hydrocarbon

• type of lipid

• 3 fatty acids form a triglyceride

Macromolecules

organic compound made of smaller molecules

Role of macromolecules

build living cells & take part in biochemical reactions

glycerides

• lipids

• fatty acids linked to glycerol by condensation reaction

Composition of carbohydrates

carbon, hydrogen & oxygen

Role of starch

energy storage in plants

Color of iodine solution if starch present

blue

Color of biuret test for proteins

purple

Color of benedict solution for carbohydrates

orange or brick red

Structure of Alpha Glucose (draw)

H top, OH down

Structure of Beta glucose (Draw)

OH top, H down

Anabolism

• synthesis of complex molecules to simpler molecules

• requires energy input

Catabolism

• breakdown of complex into simpler molecules

• hydrolysis of macromolecules into monomers

Hydrolysis reaction

breaking chemical bonds by adding water molecules

Urea formula

CO(NH2)2

Use of urea

human body to excrete nitrogen because urea is non