Proteins

Multipurpose molecules

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2008-2009

Proteins

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Proteins
Most structurally & functionally diverse group Function: involved in almost everything

enzymes (pepsin, DNA polymerase) structure (keratin, collagen) carriers & transport (hemoglobin, aquaporin) cell communication signals (insulin & other hormones) receptors defense (antibodies) movement (actin & myosin) storage (bean seed proteins)

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Proteins Structure

H2O

monomer = amino acids

20 different amino acids

polymer = polypeptide
protein can be one or more polypeptide

chains folded & bonded together large & complex molecules complex 3-D shape
hemoglobin Rubisco growth hormones

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Amino acids Structure

central carbon amino group carboxyl group (acid) R group (side chain)

H O H | || C COH N | H R
Oh, I get it! amino = NH2 acid = COOH

variable group different for each amino acid

confers unique chemical

properties to each amino acid

like 20 different letters of an
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alphabet can make many words (proteins)

Effect of different R groups: Nonpolar amino acids nonpolar & hydrophobic

Why are these nonpolar & hydrophobic?

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Effect of different R groups: Polar amino acids polar or charged & hydrophilic

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Why are these polar & hydrophillic?

Ionizing in cellular waters

H+ donors

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Ionizing in cellular waters

H+ acceptors

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Sulfur containing amino acids

Form disulfide bridges

covalent cross links betweens sulfhydryls stabilizes 3-D structure

H-S S-H
You wondered why perms smell like rotten eggs?

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Building proteins Peptide bonds

covalent bond between NH2 (amine) of one amino acid & COOH (carboxyl) of another CN bond

H2O

dehydration synthesis

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peptide bond

Building proteins Polypeptide chains have direction

N-terminus = NH2 end C-terminus = COOH end repeated sequence (N-C-C) is the polypeptide backbone

can only grow in one direction

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Protein structure & function Function depends on structure

3-D structure
twisted, folded, coiled into unique shape

pepsin

hemoglobin
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collagen

Primary (1) structure Order of amino acids in chain

amino acid sequence determined by gene (DNA) slight change in amino acid sequence can affect proteins structure & its function

even just one amino acid change

can make all the difference!

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lysozyme: enzyme in tears & mucus that kills bacteria

Sickle cell anemia

Just 1 out of 146 amino acids!

Im hydrophilic!
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But Im hydrophobic!

Secondary (2) structure Local folding

folding along short sections of polypeptide interactions between adjacent amino acids

H bonds weak bonds

between R groups

forms sections of 3-D structure

-helix -pleated sheet

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Secondary (2) structure

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Tertiary (3) structure Whole molecule folding

interactions between distant amino acids

hydrophobic interactions

cytoplasm is
water-based nonpolar amino acids cluster away from water H bonds & ionic bonds disulfide bridges
covalent bonds between
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sulfurs in sulfhydryls (SH) anchors 3-D shape

Quaternary (4) structure

More than one polypeptide chain bonded
together

only then does polypeptide become functional protein

hydrophobic interactions

AP Biology = skin & tendons collagen

hemoglobin

Protein structure (review)

R groups hydrophobic interactions disulfide bridges (H & ionic bonds)

amino acid sequence peptide bonds determined by DNA

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4
2
R groups H bonds

multiple polypeptides hydrophobic interactions

Protein denaturation Unfolding a protein

In Biology, size doesnt matter, SHAPE matters!

conditions that disrupt H bonds, ionic bonds, disulfide bridges

temperature pH salinity

alter 2 & 3 structure

alter 3-D shape

destroys functionality
some proteins can return to their functional shape

after denaturation, many cannot

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EAT
Lets build X some

Proteins!

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2008-2009

Ghosts of Lectures Past (storage)

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2007-2008

Chaperonin proteins
Guide protein folding

provide shelter for folding polypeptides keep the new protein segregated from cytoplasmic influences

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Protein models
Protein structure visualized by
X-ray crystallography extrapolating from amino acid sequence computer modelling

lysozyme
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Nucleic acids

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2006-2007

Nucleic Acids
Information storage

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2006-2007

Nucleic Acids

Function:

genetic material
stores information genes blueprint for building proteins

DNA RNA proteins

DNA

transfers information blueprint for new cells blueprint for next generation

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T G T C A G G A C A

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C

A T

Nucleic Acids Examples:

RNA (ribonucleic acid)

single helix

DNA (deoxyribonucleic acid)

double helix

Structure:

monomers = nucleotides

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DNA

RNA

Nucleotides 3 parts
nitrogen base (C-N ring) pentose sugar (5C)

ribose in RNA deoxyribose in DNA

Nitrogen base Im the A,T,C,G or U part!

phosphate (PO4) group

Are nucleic acids charged molecules?

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Types of nucleotides 2 types of nucleotides

different nitrogen bases purines

Purine = AG Pure silver!

double ring N base

adenine (A) guanine (G)

pyrimidines
single ring N base cytosine (C) thymine (T) uracil (U)

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Nucleic polymer Backbone

sugar to PO4 bond phosphodiester bond

new base added to sugar of

previous base polymer grows in one direction

N bases hang off the sugar-phosphate backbone

Dangling bases? Why is this important?

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Pairing of nucleotides Nucleotides bond between

DNA strands
H bonds purine :: pyrimidine A :: T

2 H bonds

G :: C
3 H bonds

Matching bases? Why is this important?

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DNA molecule Double helix

H bonds between bases join the 2 strands

A :: T C :: G

H bonds? Why is this important?

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Copying DNA Replication

2 strands of DNA helix are complementary

have one, can build other have one, can rebuild the

whole

Matching halves? Why is this a good system?

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When does a cell copy DNA? When in the life of a cell does DNA have
to be copied?

cell reproduction
mitosis

gamete production
meiosis

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DNA replication
It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.
James Watson Francis Crick 1953

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Watson and Crick and others

1953 | 1962

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Maurice Wilkins and

1953 | 1962

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Rosalind Franklin (1920-1958)

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Interesting note
Ratio of A-T::G-C
affects stability of DNA molecule

2 H bonds vs. 3 H bonds biotech procedures

more G-C =

need higher T to separate strands

high T organisms
many G-C

parasites
many A-T (dont know why)

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Another interesting note ATP

Adenosine triphosphate

modified nucleotide adenine (AMP) + Pi + Pi

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HELIXHELIX

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Macromolecule Review

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2006-2007

Carbohydrates Structure / monomer

monosaccharide

Function
energy raw materials energy storage structural compounds

glycosidic bond

Examples

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glucose, starch, cellulose, glycogen

Lipids Structure / building block

glycerol, fatty acid, cholesterol, H-C chains

Function
energy storage membranes hormones

Examples

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ester bond (in a fat)

fat, phospholipids, steroids

Proteins Structure / monomer

amino acids levels of structure

Function
enzymes transport signals

defense u structure u receptors

u

peptide bond

Examples

digestive enzymes, membrane channels, insulin hormone, actin

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Nucleic acids Structure / monomer

nucleotide
information storage & transfer DNA, RNA

Function

Examples

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phosphodiester bond

Lets build some DNA, baby!

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Ghosts of Lectures Past (storage)

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2007-2008

Building the polymer

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RNA & DNA RNA

single nucleotide chain

double nucleotide chain
N bases bond in pairs

DNA

across chains

spiraled in a double helix

double helix 1st proposed as structure of DNA

in 1953 by James Watson & Francis Crick (just celebrated 50th anniversary in 2003!)
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Information polymer Function

series of bases encodes information

like the letters of a book

stored information is passed from parent to offspring

need to copy accurately

stored information = genes

genetic information
Passing on information? Why is this important?

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