AP BIO 100110 Macro Molecules Proteins

8/8/2019 AP BIO 100110 Macro Molecules Proteins

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Macromolecules: Focus onProteins

AP Biology


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Macromolecules: Focus on Proteins

ObjectiveStudents will demonstrate understanding ofprot

structure and folding by identifying chemicalproperties in paper models.

Do Now (linking your homework toyesterdays work)

Draw the general structure of an amino acipacket, pg 2)

(from HW): What are the 4 chemical types amino acids?

Thought Question (HARD): How can the str

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,S u n d a y 0 3 O cto b


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ObjectiveStudents will demonstrate understanding of

macromolecules by identifying chemical proppaper models.

Homework-Finish Macromolecules Packets #1 & 2-Look at amino acid structures (textbook o

google):

-What are the 4 chemical categories of AmAcid R-groups?

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Classwork-Notes on protein structure

Question for class:What are the building blocks (monomers) of pr

________________________?

-Work Time, packet #2

-Summary of Chemistry / Preview of Next

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Functional Groups

Functional groups are

the parts of moleculesinvolved in chemicalreactions

They Are thechemically reactivegroups of atoms

within an organicmolecule Give organic molecules

distinctive chemicalproperties

HO

O

CH

Estradiol

Female lion

Male lion.igure 4 9


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Six functional groups are important in thechemistry of life

Hydroxyl Carbonyl

Carboxyl

Amino

Sulfhydryl Phosphate


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Some important functional groups of orgacompounds

FUNCTIONALGROUP

STRUCTURE

( )may be written HO

YDROXYL CARBONYL CA

OH

( ),In a hydroxyl group OH ahydrogen atom is bonded to an,oxygen atom which in turn is

bonded to the carbon skeleton. (of the organic molecule Do

not confuse this functional,group with the hydroxide ion

OH.)

When an oxygen atom bonded to a carbon a

also bonded to a hydentire assembly of a

a arboxyl group (

C

O

.igure 4 10

Thearbonyl group( )CO consists of a

carbon atom joined to anoxygen atom by a double

.bond


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Some important functional groups of orgcompounds

,c et ic a ci d which sour tatste

AME OFCOMPOUNDS

Alcohols (their specific-names usually end inol

)

Ketonesif the carbonyl group iswithin a carbon skeleton

Aldehydesif the carbonyl groupis at the end of the carbon

skeleton

,arboxylic acids oacids

EXAMPLE

,ropanal an aldehyde

,cetone the simplest ketone

,thanol the alcoholpresent in alcoholic

beverages

H

H

H

H H

C C OH

H

H

H

HH

H

H

C C H

C

C C

C C C

O

H

H

H

H H

HO

H

.igure 4 10


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Some important functional groups of organcompounds

The min o gr oup (NH2)consists of a nitrogen atom

bonded to two hydrogen atoms.and to the carbon skeleton

MINO SULFHYDRYL PHOSPHATE

( )may be written HS

The ulfhydryl groupconsists of a sulfur atom

;bonded to an atom of hydrogen

resembles a hydroxyl group in.shape

In a hosphate grouatom is bonded to fou

one oxygen is bonded ;skeleton two oxygens

; charges abbreviated (group OPO32 ) is an

a phosphoric acid gro

).the two hydrogens

N

H

H

SH

.igure 4 10


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Our life is maintained by molecuOur life is maintained by molecunetwork systemsnetwork systems

Molecular networksystem in a cell

(From ExPASy Biochemical Pathways; http://www.expasy.org/cgi-bin/show_thumbnails.pl?2)


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Proteins play key roles in a livProteins play key roles in a livsystemsystem

Three examples of protein functions

Catalysis:Almost all chemical reactions in aliving cell are catalyzed by proteinenzymes.

Transport:Some proteins transports varioussubstances, such as oxygen, ions,and so on.

Information transfer:For example, hormones.

Alcodehoxidaldeketo

Haemoglobincarries oxygen

Insuamothe


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Amino acid: Basic unit of proteAmino acid: Basic unit of prote

COO-NH3

+ C

R

HAn amino acid

Different side chadetermin the prop

20 amino acids.Amino group Carboxylicacid group


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2020 Amino acidsAmino acids

Glycine (G)

Glutamic acid (E)Asparatic acid (D)

Methionine (M)

Threonine (T)Serine (S)Glutamine (Q)

ATryptophan (W)Phenylalanine (F)Proline (P)

Isoleucine (I)Valine (V)Alanine (A)

Lysine (K)

Tyrosine (Y)

Arginine (R)

White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic


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Proteins are linear polymers of amProteins are linear polymers of amacidsacids

R1

NH3 C CO

H

R2

NH C CO

H

R3

NH C CO

H

R2

NH3 C COO

H

R1

NH3 C COO

H

H2OH2O

Peptide bond Peptide bond

The amino acid se

called as primaryA A

FNG G

ST

S

DK

A carboxylic acid cowith an amino grourelease of a water


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Amino acid sequence is encodedAmino acid sequence is encodedDNA base sequence in a geneDNA base sequence in a gene

CGCGAATTCGCG

GCGCTTAAGCGC

DNA molecule

DNAsequ


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Second letterT C A G

Firstletter

T TTT Phe TCT Ser TAT Tyr TGT Cys

TTC TCC TAC TGC

TTA Leu TCA TAA Stop TGA Stop

TTG TCG TAG TGG Trp

C CTT Leu CCT Pro CAT His CGT Arg

CTC CCC CAC CGC

CTA CCA CAA Gln CGA CTG CCG CAG CGG

A ATT Ile ACT Thr AAT Asn AGT Ser

ATC ACC AAC AGC

ATA ACA AAA Lys AGA Arg

ATG Met ACG AAG AGG

G GTT Val GCT Ala GAT Asp GGT Gly

GTC GCC GAC GGC

GTA GCA GAA Glu GGA

GTG GCG GAG GGG

Amino acid sequence is encodedAmino acid sequence is encoded


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, , From Traphagen DiMarco and Sill


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Gene is proteins blueprint, genoGene is proteins blueprint, genois lifes blueprintis lifes blueprint

Gene

GenomeDNA

Protein

Gene Gene

Gene

GGene

GeneGene

GeneGeneGene

Gene

Protein Protein

ProteinProtein

Protein

ProteinProteinProtein P

P

Protein


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Gene is proteins blueprint, genoGene is proteins blueprint, genois lifes blueprintis lifes blueprint

Genome

Gene Gene

Gene

GGene

GeneGene

GeneGeneGene

Gene

Protein Protein

ProteinProtein

Protein

ProteinProteinProtein P

P

Protein

Glycolysis network


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3 billion base pair => 6 G letters&

1 letter => 1 byte

The whole genome can be recorded in just 10 CD-ROMs!

In 2003, Human genomeIn 2003, Human genomesequence was deciphered!sequence was deciphered! Genome is the complete set of genes of a living thing.

In 2003, the human genome sequencing was completed.

The human genome contains about 3 billion base pairs.

The number of genes is estimated to be between 20,000 t25,000.

The difference between the genome of human and that of

chimpanzee is only 1.23%!


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Each Protein has a unique structEach Protein has a unique struct

Amino acid sequence

NLKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVG

TIVTMEYRIDRVRLFVDKLDNIAEVPRVG

Folding!

i l i f i


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Basic structural units of proteinBasic structural units of proteinSecondary structureSecondary structure

-helix -s

Secondary structures, -helix and -sheet,have regular hydrogen-bonding patterns.


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Three-dimensional structure oThree-dimensional structure o

proteinsproteins

Tertiary structure

Quaternary str


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Hierarchical nature of proteinHierarchical nature of protein

structurestructure Primary structure (Amino acid sequence)

Secondary structure -helix, -sheet

Tertiary structure Three-dimensional struc

formed by assembly of secondary structure

Quaternary structure Structure formed by than one polypeptide chains


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Close relationship between protClose relationship between prot

structure and its functionstructure and its functionenzyme A

B

A

Binding to A

Digestion ofA!

enzyme

Matching theshape to A

Hormone receptor AExample of enzyme reaction

enzyme

substrates


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Protein structure prediction has remaProtein structure prediction has remaelusive over half a centuryelusive over half a century

Can we predict a protein structure fits amino acid sequence?

Now, impossible!


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SummarySummary Proteins are key players in our living systems. Proteins are polymers consisting of 20 kinds of amino

Each protein folds into a unique three-dimensional stdefined by its amino acid sequence.

Protein structure has a hierarchical nature.

Protein structure is closely related to its function.

Protein structure prediction is a grand challenge ofcomputational biology.

Documents

AP BIO 100110 Macro Molecules Proteins