Proteins 2.4.1 Amino acids are linked together by condensation to form polypeptides - PowerPoint Presentation

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Proteins

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2.4.1 Amino acids are linked together by condensation to form polypeptides

Polypeptides

are chains of amino acids linked together by condensation reactions

the main, or only, component in proteinsSome proteins are composed of only one polypeptide chain, while others are made of 2 or more

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Polypeptides can contain any number of amino acids (typically called

oligopeptides

if less than 20)

Insulin- two polypeptides; one with 21 aa, the other with 30 aaTitin (a large polypeptide in muscle protein) contains 34,350 aa

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Polypeptides are formed by condensation reactions

The amine group of one amino acid combines with the carboxyl group of the other amino acid; water is eliminated

The new bond formed between the two amino acids is called a

peptide bond

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S 2.4.1 Drawing molecular diagrams to show the formation of a peptide bond

2 amino acids are linked by a condensation reaction

Peptide bonds are the same, no matter what the R group is

Show the formation of peptide bonds

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2.4.2 There are 20 different amino acids in polypeptides synthesized in ribosomes.

Polypeptides synthesized in ribosomes can be made using 20 different amino acids.

Ribosomes- cell part where RNA codes for

proteins…translation

Because of the differences in R groups, the 20 amino acids are chemically diverse

Some proteins contain amino acids that are not the 20 produced on ribosomes.

This is due to an amino acid being modified after the polypeptide has been synthesized.

Example: Collagen

Collagen polypeptides made by ribosomes contain

proline

at many positions, but some of these are converted to

hydroxyproline

, making collagen more stable.

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Amino acids and origins: patterns, trends, and discrepancies.

Most but not all organisms assemble polypeptides from the same amino acids.

This trend is not due to chance, but why is it?

Several hypotheses:These 20 aa were produced by chemical processes before the origin of life, so all organisms used them and continue to use them

They are the ideal amino acids for making a wide range of proteins, so natural selection will favor organisms that use them and not others

All life evolved from a single ancestral species, which used all 20 aa.

Some species have been found to use codons that normally signal to stop the amino acid sequence to encode an extra non-standard aa. To learn more, click on the link below:

http://jnci.oxfordjournals.org/content/96/7/504.full

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2.4.3 amino acids can be linked together in any sequence giving a huge range of possible polypeptides.

Amino acids can be linked together in any way, peptide bonds can be formed between any two amino acids, so any sequence is possible.

The number of possible amino acid sequences can be calculated:

For a polypeptide with n amino acids, there are 20n

possible sequences

Example:

Dipeptides- 2 amino acids (n=2) 20

2

= 400 possible dipeptides

3 amino acids (n = 3) 20

3

= 8,000 possible sequences

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Complete the following table:

Number of amino acids

Number of possible

amino acid sequences

1

20

1

2

20

2

400

3

8,000

4

20

6

10.24 trillion

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The number of aa in a polypeptide can be from 20 to tens of thousands

Of a polypeptide has 400 amino acids, there are 20

400

possible aa sequencesCalculatorIf we add all of the possible sequences together the number of potential polypeptides is effectively infinite.

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2.4.4 The amino acid sequence of polypeptides is coded for by genes.

A cell must have the information to make all of these polypeptides (a typical cell produces thousands of different sequences)

The amino acid sequence is stored in coded form in a gene

A gene is a segment of DNARemember, DNA is composed of nucleotides, each of which contain a nitrogen base

3 nitrogen bases of a gene are needed to code for each amino acid

The sequence of bases that code for a polypeptide-

open reading frame

DNA strand is longer than the

aa sequence

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2.4.5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

Proteins may be

A single polypeptide

Many polypeptides linked togetherExamples

Integrin- membrane protein

2 polypeptides, each having a hydrophobic portion imbedded in the membrane

Collagen-

3 long polypeptides wound together to form a rope like protein

 great tensile strength, while allowing it to stretch

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2.4.6 The amino acid sequence determines the three-dimensional conformation of a protein.

The conformation of a protein is its 3-D structure, which is determined by the amino acid sequence of a protein and its constituent polypeptides.

Some proteins (fibrous proteins) are elongated with a repeating structure

Some proteins are globular, with an intricate shape, including parts that are helical or sheet like

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In globular proteins, the polypeptides gradually fold up as they are made to develop the final conformation. This is stabilized by bonds between the R groups of the amino acids that have been brought together by the folding.

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Protein structure

Primary structure- the linear sequence of amino acids in a polypeptide chain.

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Protein structure

Secondary structure- 3D structure of regions of a protein chain

alpha-helixes

beta-pleated sheets. These are stabilized by hydrogen bonds between backbone atoms

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Alpha-helixes-

secondary structure in which proteins

are coiled like a loose spring

.

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Beta-pleated sheets- individual protein chains are folded so that they lie along side each other. Every other protein chain is aligned in an opposite direction.

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Tertiary Structure

Geometric shape of a single polypeptide, consisting of one or more secondary structures

Stabilized by non-covalent interactions between side chains (R groups)

Low energy state

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Quarternary

Structure

The clustering of several polypeptide chains to fit a final specific shape.

Not every protein has quaternary structure.

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A2.4.1 Denaturation of proteins by heat or by deviation from pH from the optimum.

The 3-D structure of proteins is stabilized by bonds or interactions between R groups of amino acids within the molecule.

These bonds are relatively weak and can be broken, resulting in a change in conformation of protein



denaturation

Bonding interactions within tertiary structure of a protein

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Heat causes denaturation

Heat causes molecule to vibrate, breaking bonds (hydrogen bonds and non-polar hydrophobic interactions), allowing the proteins to unravel or change shape

http://

www.sumanasinc.com/webcontent/animations/content/proteinstructure.html

Different proteins tolerate different temperatures

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Extremes of pH can cause denaturation

Acids and bases can disrupt intermolecular bonds between side chains in a protein, changing the 3-D conformation

Milk in stomach acids?

Hair straighteners? Cheese production? Heat sanitation?

how are these things affected by denaturation of proteins?

http://highered.mheducation.com/sites/0072943696/student_view0/chapter2/animation__

protein_denaturation.html

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2.4.7 Living organisms synthesize many different proteins with a wide range of functions

Function

Description

Key examples *

Catalysis

Speed up or enable specific

chemical reactions

Rubisco

Muscle contractions

Actin and myosin

together cause muscle contractions used in locomotion and transport around the body

Cytoskeletons

Tubulin is the subunit

of microtubules, which give animal cells their shape and pull on chromosomes during mitosis

Tensile

strengthening

Fibrous

proteins give tensile strength needed in skin, tendons, ligaments, and blood vessel walls

collagen

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2.4.7 Living organisms synthesize many different proteins with a wide range of functions

Function

Description

Key Examples

Blood clotting

Plasma proteins act as clotting

factors that cause blood to turn from liquid to gel in wounds

Transport of nutrients

and gasses

Proteins in blood help transport oxygen, carbon dioxide,

iron, and lipids

Cell adhesion

Membrane

proteins cause adjacent animal cells to stick to each other within tissues

Membrane transport

Membrane proteins

are used for facilitated diffusion and active transport, also for electron transport during cellular respiration and photosynthesis

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2.4.7 Living organisms synthesize many different proteins with a wide range of functions

Function

Description

Key

examples

Hormones

Some

hormones are proteins (insulin), but hormones are chemically very diverse

insulin

Receptors

Binding

sites for hormones,

neutotransmitters

, tastes and smells, and light receptors

rhodopsin

Packing of DNA

Histones are associated with DNA in eukaryotes and help chromosomes

to condense during mitosis

Immunity

This is the most diverse group of proteins, as cells ca

n make huge numbers of antibodies

immunoglobins

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A2.4.2

Rubisco

, insulin,

immunoglobins, rhodopsin, collagen, and spider silk as examples of the range of protein functionsRubisco

Ribulose

biphosphate

carboxylase

Enzyme that

catalyses

the reaction that fixes carbon dioxide from the atmosphere

Provides the source of carbon from which all carbon compounds required by living organisms are produced

Found in high concentrations in leaves and algal cells

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Insulin

Hormone- signals cells to absorb glucose and help reduce glucose concentration of the blood

These cells have receptor proteins on their surface to which insulin can (reversibly) bind to

Secreted by  (beta) cells in the pancreas and transported by the blood

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Immunoglobulin

Antibodies

2 arms, with sites at the tips that bind to antigens (a molecule on a pathogen which provides an immune response) on bacteria or other pathogen

The other parts of the immunoglobulin cause a response (such as acting as a marker to macrophages to engulf a pathogen)

The body can produce a huge range of immunoglobulins, each with a different type of binding site, which is the basis of specific immunity to disease

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Rhodopsin-

Pigment that absorbs light

Membrane protein of rod cells of the retina (the light sensitive region in the back of the eye)

Rhodopsin consists of the opsin polypeptide surrounding the light sensitive retinal molecule

When the retinal molecule absorbs a single photon of light it changes shape, which causes the

opsin

to change causing the rod cell to send nerve impulses to the brain

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Collagen

Many different forms, all are ropelike made of 3 polypeptides wound together

About 25% of all proteins in human body.

Forms mesh of fibers in skin and blood vessel walls that resist tearingProvides strength to tendons, ligaments, skin, and blood vessel wallsForms parts of teeth and bones, helps to prevent cracks and fractures

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Spider silk

There are many different types of silk with different functions

Dragline silk is stronger than steel and tougher than Kevlar, used to make spokes of spider web and lifelines from which spiders hang

When first made, it contains regions where the polypeptide forms parallel arraysOther regions form a disordered tangle, but when stretched the polypeptide gradually extends, making the silk extensible and very resistant to breaking

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2.4.8 Every individual has a unique proteome

Genome

a

ll of the genes of a cell, a tissue, or an organismDetermines what proteins an organism can produceEnvironmental factorsEnvironment influences what proteins an organism needs to produce and in what

quanitity

Proteome-

all of the proteins produced by a cell, tissue, or an organism

A function of both the genome and the environment to which the organism is exposed- variable (over time) and unique to every individual