Lecture 5_Proteins and nucleic acids.pdf

8/10/2019 Lecture 5_Proteins and nucleic acids.pdf

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Macromolecules Macromolecules are often polymers.

long molecule built by linking together small,similar subunits

Dehydration synthesis removes OH and H during

synthesis of a new molecule. Hydrolysis breaks a covalent bond by adding OH

and H.


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Proteins Structure:

Polypeptide chains

Consist of peptide bonds between 20 possible amino acidmonomersHave a 3 dimensional globular shape


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Proteins

Proteins are composed of 4 elements: carbon, hydrogen,oxygen and nitrogen. The basic unit is called an amino acidand it looks like this.

This is a 3-D image of a protein containing thousands ofamino acids connected together & folded to make thisdistinct shape.


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Functions of Proteins

Enzymes which accelerate specific chemicalreactions up to 10 billion times faster than they wouldspontaneously occur.

Structural materials, including keratin (the proteinfound in hair and nails) and collagen (the proteinfound in connective tissue).


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Specific binding, such as antibodies that bindspecifically to foreign substances to identify them tothe body's immune system.

Specific carriers, including membrane transportproteins that move substances across cell

membranes, and blood proteins, such ashemoglobin, that carry oxygen, iron, and othersubstances through the body.


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Contraction, such as actin and myosin fibers thatinteract in muscle tissue.

Signaling, including hormones such as insulin thatregulate sugar levels in blood.


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Proteins - C, H, O, N, S

H


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Amino Acids

contain an amino group (-NH 2), a carboxyl group (-COOH) and a hydrogen atom, all bonded to a centralcarbon atom

twenty common amino acids grouped into fiveclasses based on side groups

Non-polar amino acids polar uncharged amino acids charged amino acids aromatic amino acids special-function amino acids


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Structure of Amino Acid Monomers

Consist of an asymmetric carbon covalently

bonded to :

o Hydrogen

o Amino groupo Carboxyl (acid) groupo Variable R group specific to each amino acid


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Properties of Amino Acids Grouped by polarity

Variable R groups (side chains) confer different propertiesto each amino acid:

o polar, water soluble.

o non-polar, water insoluble

o positively charged

o negatively charged.


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Alanine(Ala) Leucine(Leu) Isoleucine(Ile) Phenylalanine(Phe) Tryptophan(Trp)

Tyrosine(Tyr)

Glutamine(Gln)

Asparagine(Asn)

Threonine(Thr)

Serine(Ser)

Glycine(Gly)

Glutamic

acid (Glu)

Aspartic

acid (Asp

Histidine

(His)

Lysine

(Lys)

Arginine

(Arg)

Charged

Polar uncharged

Nonpolar

NONAROMATIC AROMATIC

Valine(Val)

CH 3

C C

H O

CH C C

H O

C C

H O

CH

C C

H O

H C

C C C C

H O

NH C

C C

H O

OH

H C OH

C C

H O

C C

H O

C

NH2

O

CH 2

C C O

H O

OH

C

C C

H O

O

H

C C

H O

C C

H O

C O

C C

H O

NH C

C C

H O

C C

H O

C N

HC NH+

CH H

C C

H O

C

O

CH 3 CH 3

CH 3 CH 3 CH 3

CH 3 CH 2

CH 2

CH 2

CH 2

CH 2CH 2CH 2

NH2CH 3

CH 2

NH2

H3N+ H3N+ H3N+ H3N+ H3N+ H3N+ O

O

O

O

O

H3N+ H3N+ H3N+ H3N+ H3N+

O O

O O

O

O

O

CH 2

CH 2 CH 2 CH 2 CH 2

CH 2

CH 2

CH 2CH 2

CH 2

CH 2

NH2+

NH3+

O

H O

H3N+ H3N+ H3N+ H3N+ H3N+ H3N+ O

O

O

O

O


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Amino Acids

Peptide bond links two amino acids. A protein is composed of one or more long chains ofamino acids linked by peptide bonds ( polypeptides ).


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Protein Structure The shape of proteins is extremely important and can

determine the function Waters tendency to hydrophobically exclude nonpolarmolecules literally shoves the nonpolar portions of theprotein to the interior

Many shapes Primary the specific amino acid sequences Secondary formed by hydrogen bonding

Alpha helix coils Beta pleated sheet - foldbacks

motifs - folds or creases supersecondary structure


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Protein Structure

Tertiary - final folded shape of globular protein(3-dimensional shape) based on bonding ofside groups

Domains independent functional units of theprotein 100 200 amino acids long - encoded bya specific DNA sequence (exon)

Quaternary - forms when two or morepolypeptide chains associate to form afunctional protein


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N N N

H

H

H

H

H H

H C C C C C C N C C N C C C

O

O O

O H H

O H H

R

R

R R

R R

Motifs

Primary structure 1

2

3 helix

turn motif b motif

b pleated sheet

Secondarystructure

Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.


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Copyright The McGraw Hill Companies, Inc. Permission required for reproduction or display.

4

5

6

Tertiarystructure

Domains

Quaternarystructure

Domain 3Domain 2

Domain 1


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Primary Structureo Unique sequence of amino acids in a proteino Slight change in primary structure can alter functiono Determined by geneso Condensation synthesis reactions form the peptide bonds

between amino acids


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Secondary Structure

Repeated folding of proteins polypeptide backbone stabilized by H bonds between peptide linkages in the

proteins backbone 2 types:

alpha helix, beta pleated sheets


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Tertiary Structure

Irregular contortions of a protein due to bondingbetween R groups

Weak bonds :

o H bonding between polar side chainso ionic bonding between charged side chainso hydrophobic and van der Waals interactions

Strong bonds :o disulfide bridges form strong covalent linkages


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Quaternary Structure Results from interactions among 2 or more

polypeptides


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Factors That Determine ProteinConformation

Occurs during protein synthesis within cell Depends on physical conditions of environment

pH, temperature, salinity, etc. Change in environment may lead to denaturation of protein Denatured protein is biologically inactive

Can renature if primary structure is not lost


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Chaperone Proteins

Chaperone proteins are special proteins which helpnew proteins fold correctly.

o Chaperone deficiencies may play a role in facilitating certaindiseases.


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Unfolding Proteins

Denaturation refers to theprocess of changing aproteins shape; usually

rendered biologically inactive . Causes

pH

temperature Ionic concentration - salt-curing and pickling used topreserve food


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Nucleic AcidsNucleic acids make up DNA and RNA which

are gigantic molecules that carry yourhereditary information from generation togeneration and are used to make proteins

Nucleic acids are made up of lots of nucleotides(the smallest units) strung together. DNA takes theshape of a double helix.


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Nucleic Acid Structure

Nucleic acids are composedof long polymers of repeatingsubunits, nucleotides.

o five-carbon sugaro Phosphate groupo nitrogenous base

Purines double ringedo adenine and guanine

Pyrimidines single ringedo cytosine, thymine, and

uracil


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Nucleic Acids

Polymer of ribofuranosiderings linked by phosphate

ester groups. Each ribose is bonded toa base.

o Ribonucleic acid (RNA)o Deoxyribonucleic acid

(DNA)


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Two kinds:DNA:

o double strandedo can self replicate

o makes up genes which code for proteinso is passed from one generation to another

RNA:o single stranded o functions in actual synthesis of proteins coded for by

DNA

o is made from the DNA template molecule

Nucleic Acids - C, H, O, N, P


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Nucleotide Monomer Structure

Both DNA and RNA are composed of nucleotidemonomers.

Nucleotide = 5 carbon sugar, phosphate, andnitrogenous base

Deoxyribose in DNA Ribose in RNA


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Base Pairings


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Building the Polymer Phosphate group of one nucleotide forms strong

covalent bond with the #3 carbon of the sugar of theother nucleotide.


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Functions of Nucleotides

Monomers for Nucleic Acids Transfer chemical energy from one molecule to

another (e.g. ATP)


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Structure of DNA

b-D-2-deoxyribofuranose is the sugar.

Heterocyclic bases are cytosine, thymine(instead of uracil), adenine, and guanine.

Linked by phosphate ester groups to form theprimary structure.


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Structure of DNA


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DNA: Double helix

2 polynucleotide chainswound into the double helix

Base pairing betweenchains with H bonds

o A - T

o C - G


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Double Helix of DNA

Two complementarypolynucleotide chainsare coiled into a helix.

Described by Watsonand Crick, 1953.


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59

39

P

P

P

P

OH

5-carbonsugar

Nitrogenous base

Phosphate group

Phosphodiesterbonds

Adenine

O

O

O

O

Guanine

CCNN

N

C

H N

CCH

O

H

Cytosine

(both DNAand RNA)

Thymine(DNA only)

Uracil(RNA only)

HCCNC

HN

C

NH2

NN

CHOCC

NC

HN

CHH

OCCNC

HN

CO

HH3C

H

OCCNC

HN

CO

HHH

PURINES

P YRI

MIDINES

NH2

NH2


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Ribonucleosides

A b -D-ribofuranoside bonded to aheterocyclic base at the anomericcarbon.


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Ribonucleotides

Add phosphate at 5 carbon.


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Additional Nucleotides

Adenosine monophosphate (AMP), a regulatoryhormone.

Nicotinamide adenine dinucleotide (NAD), acoenzyme.

Adenosine triphosphate (ATP), an energy source.


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Summary of the OrganicMolecules:

Documents

Lecture 5_Proteins and nucleic acids.pdf