chapters 4 & 5 carbon and macromolecules · 5 6 h oh 4c 6ch 2 oh ch 2 oh 5c h oh c h oh h 2 c 1...

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Chapters 4 & 5

Carbon

and

Macromolecules


CARBON

Atomic #: 6

1st level: 2

2nd Level: 4

# of bonds able to form – 4

- allows the formation of numerous different

compounds

- compounds that contain carbon are called

ORGANIC except for a few very common ones

such as CO and CO2


• The bonding versatility of carbon

– Allows it to form many diverse molecules,

including carbon skeletons

(a) Methane

(b) Ethane

(c) Ethene

(ethylene)

Molecular

Formula

Structural

Formula

Ball-and-

Stick Model

Space-

Filling

Model

H

H

H

H

H

H

H

H

H

H

H H

HH

C

C C

C C

CH4

C2H

6

C2H4

Name and

Comments

Figure 4.3 A-C


• The electron configuration of carbon

– Gives it covalent compatibility with many

different elements

H O N C

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

Figure 4.4


BOND TYPES

Covalent

• single - hydrogen, carbon, nitrogen and

hydroxyl

• double - oxygen, carbon, nitrogen

• triple - carbon, nitrogen

• C-H - hydrocarbon - non-polar

• C-O - polar

• C-N- slightly polar


Molecular Diversity Arising from Carbon Skeleton Variation

• Carbon chains

– Form the skeletons of most organic molecules

– Vary in length and shape

H

HH

H

H

H H H

H

H

H

H H H

H H H

H H

H

H

H

H

H

H

HH

H

H H H H

H H

H H

H H H H

H H

H H

HH

HH

H

H

H

C C C C C

C C C C C C C

CCCCCCCC

C

CC

C

C

C

C

CC

C

C

C

H

H

H

HH

H

H

(a) Length

(b) Branching

(c) Double bonds

(d) Rings

Ethane Propane

Butane 2-methylpropane

(commonly called isobutane)

1-Butene 2-Butene

Cyclohexane Benzene

H H H HH

Figure 4.5 A-D


Carbon: Base of All Biological Molecules

Difference between biological molecules

1) Structure:

Isomers: same chemical formula but different structure

Structual: C4H10

Butane

Isobutane (2-methylpropane)

Geometric: Ethene - cis and trans

- cis and trans:

L vs. D.

- left verses Right


• Three types of isomers are

– Structural

– Geometric

– Enantiomers

H H H H HH

H H H H HH

HHH

HH

H

H

H

H

HHH

H

H

H

H

CO2H

CH3

NH2

C

CO2H

HCH3

NH2

X X

X

X

C C C C C

CC

C C C

C C C C

C

(a) Structural isomers

(b) Geometric isomers

(c) Enantiomers

H

Figure 4.7 A-C


• Enantiomers

– Are important in the pharmaceutical industry

L-Dopa

(effective against

Parkinson’s disease)

D-Dopa

(biologically

inactive)Figure 4.8


2) Functional Groups

- different chemical attachments on hydrocarbons that change the reactivity

TYPES PAGE 54

a. Hydroxyl - OH - not hydroxide

alcohols

ethane vs. ethanol

b. Carbonyl - C=O

aldehydes - on end

ketones - in middle of chain


c. Carboxyl - -COOH

carboxylic acid

- weak acids

d. Amino - -NH2

nitrogen containing

amino acids

e. Sufhydryl Group - SHthiols

stabilize proteins – disulfide bridges

f. Phosphate - PO4


– Give organic molecules distinctive chemical

properties

CH3

OH

HO

O

CH3

CH3

OH

Estradiol

Testosterone

Female lion

Male lionFigure 4.9


• Some important functional groups of organic

compounds

FUNCTIONAL

GROUP

STRUCTURE

(may be written HO )

HYDROXYL CARBONYL CARBOXYL

OH

In a hydroxyl group (—OH),

a hydrogen 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 is double-

bonded to a carbon atom that is

also bonded to a hydroxyl group,

the entire assembly of atoms is

called a carboxyl group (—

COOH).

C

O O

C

OH

Figure 4.10

The carbonyl group

( CO) consists of a

carbon atom joined to

an oxygen atom by a

double bond.



compounds

Acetic acid, which gives vinegar

its sour tatste

NAME OF

COMPOUNDS

Alcohols (their specific

names usually end in -ol)

Ketones if the carbonyl group is

within a carbon skeleton

Aldehydes if the carbonyl group

is at the end of the carbon

skeleton

Carboxylic acids, or organic

acids

EXAMPLE

Propanal, an aldehyde

Acetone, the simplest ketone

Ethanol, the alcohol

present 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 OH

O

H

H

H H

HO

H

Figure 4.10



compounds

FUNCTIONAL

PROPERTIES

Is polar as a result of the

electronegative oxygen atom

drawing electrons toward

itself.

Attracts water molecules,

helping dissolve organic

compounds such as sugars

(see Figure 5.3).

A ketone and an

aldehyde may be

structural isomers with

different properties, as

is the case for acetone

and propanal.

Has acidic properties because

it is a source of hydrogen ions.

The covalent bond between

oxygen and hydrogen is so polar

that hydrogen ions (H+) tend to

dissociate reversibly; for

example,

In cells, found in the ionic

form, which is called a

carboxylate group.

H

H

C

H

H

C

O

OH

H

H

C

O

C

O

+ H+

Figure 4.10



compounds

The amino group (—NH2)

consists of a nitrogen atom

bonded to two hydrogen

atoms and to the carbon

skeleton.

AMINO SULFHYDRYL PHOSPHATE

(may be written HS )

The sulfhydryl group

consists of a sulfur atom

bonded to an atom of

hydrogen; resembles a

hydroxyl group in shape.

In a phosphate group, a

phosphorus atom is bonded to four

oxygen atoms; one oxygen is

bonded to the carbon skeleton; two

oxygens carry negative charges;

abbreviated P . The phosphate

group (—OPO32–) is an ionized

form of a phosphoric acid group (—

OPO3H2; note the two hydrogens).

N

H

H

SH

O P

O

OH

OH

Figure 4.10


Monomers Vs. Polymers

most biological molecules are polymers

Monomer - one part

Polymer - many repeating repeating parts

Macromolecules - combination of polymers


BUILDING of POLYMERS

• Polymerization reaction: 2 units form one larger unit

• KEY EX: Protein synthesis

Condensation Reaction or Dehydration Synthesis

• bond is formed by the removal of a water

• two hydroxyl groups - one molecule loses OH and one

loses an H

• results in a bond based on the remaining O and the H and

the OH combine to form water

• Requires energy and a catalyst


The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by condensation

reactions called dehydration reactions

(a) Dehydration reaction in the synthesis of a polymer

HO H1 2 3 HO

HO H1 2 3 4

H

H2O

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a water

molecule, forming a new bond

Figure 5.2A


BREAKING UP IS HARD TO DO

• Hydrolysis Reaction - addition of water to break a

polymer chain

• Also requires energy and enzymes - but generally

gives off more energy than it uses


• Polymers can disassemble by Hydrolysis

(b) Hydrolysis of a polymer

HO 1 2 3 H

HO H1 2 3 4

H2O

HHO

Hydrolysis adds a water

molecule, breaking a bond

Figure 5.2B


Dehydration Synthesis and Hydrolysis

Build - anabolic - requires energy

• Break - catabolic - releases energy

• NOTE: COMBINATION OF MONOMERS IN DIFFERENT

QUANTITIES AND PATTERNS RESULTS IN A WIDE

VARIETY OF MOLECULES

eg. Alphabet


Four Major Biological Molecules

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic Acids


CARBOHYDRATES

Elements: CHO and sometimes N

• FUNCTION:

• Energy

• Structure

• Protection

• Storage


Types of Carbohydrates

1. Sugars: simplest

Monomers: monosaccharides

Most common glucose : C6H12O6

Classification:

Monosaccharides: one sugar unit

Ex. Glucose - storage of solar energy via photosynthesis

Characteristics:

Two types of carbonyls:

aldehyde - carbonyl on end

ex. Glucose

ketone - carbonyl in middle

ex. fructose

carbonyl affects ring formation

placement of hydroxyl groups give different properties

Glucose and fructose


• Examples of monosaccharides

Triose sugars

(C3H6O3)

Pentose sugars

(C5H10O5)

Hexose sugars

(C6H12O6)

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

HO C H

H C OH

H C OH

H C OH

H C OH

HO C H

HO C H

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

C OC O

H C OH

H C OH

H C OH

HO C H

H C OH

C O

H

H

H

H H H

H

H H H H

H

H H

C C C C

OOOO

Ald

os

es

Glyceraldehyde

Ribose

Glucose Galactose

Dihydroxyacetone

Ribulose

Ke

tos

es

FructoseFigure 5.3


• Monosaccharides

– May be linear

– Can form rings

H

H C OH

HO C H

H C OH

H C OH

H C

O

C

H

1

2

3

4

5

6

H

OH

4C

6CH2OH 6CH2OH

5C

H

OH

C

H OH

H

2 C

1C

H

O

H

OH

4C

5C

3 C

H

H

OH

OH

H

2C

1 C

OH

H

CH2OH

H

H

OHHO

H

OH

OH

H5

3 2

4

(a) Linear and ring forms. Chemical equilibrium between the linear and ring

structures greatly favors the formation of rings. To form the glucose ring,

carbon 1 bonds to the oxygen attached to carbon 5.

OH3

O H OO

6

1

Figure 5.4


Glucose + Fructose = Sucrose


Dissacharides

formation of a 2 sugar unit by dehydration

synthesis

• glu + glu = maltose

• glu + galac = lactose

• glu + fruc = sucrose


https://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwjZgt7Dv6HTAhWQZiYKHYK2DEoQjRwIBw&url=https://en.wikipedia.org/wiki/Fructose&bvm=bv.152180690,d.eWE&psig=AFQjCNGu1fokS9yU6SwD49LQPX9fYlF1PA&ust=1492175083188473


• Examples of disaccharides

Dehydration reaction

in the synthesis of

maltose. The bonding

of two glucose units

forms maltose. The

glycosidic link joins

the number 1 carbon

of one glucose to the

number 4 carbon of

the second glucose.

Joining the glucose

monomers in a

different way would

result in a different

disaccharide.

Dehydration reaction

in the synthesis of

sucrose. Sucrose is

a disaccharide formed

from glucose and fructose.

Notice that fructose,

though a hexose like

glucose, forms a

five-sided ring.

(a)

(b)

H

HO

H

H

OH H

OH

O H

OH

CH2OH

H

HO

H

H

OH H

OH

O H

OH

CH2OH

H

O

H

H

OH H

OH

OH

OH

CH2OH

H

H2O

H2O

H

H

O

H

HOH

OH

OH

CH2OH

CH2OH HO

OHH

CH2OH

H

OH H

H

HO

OHH

CH2OH

H

OH H

O

O H

OHH

CH2OH

H

OH H

O

HOH

CH2OH

H HO

O

CH2OH

H

H

OH

O

O

1 2

1 4

1–4

glycosidic

linkage

1–2

glycosidic

linkage

Glucose

Glucose Glucose

Fructose

Maltose

Sucrose

OH

H

H

Figure 5.5


Polysaccharides: many sugar units

Chains of glucose

Type of polysaccharide dependent on the type of

glucose

alpha glucose

beta glucose

– differ in orientation of the hydroxyl group on

the number 1 carbon

alpha - down

beta - up


STORAGE POLYSACCHARIDES

1. Starch - storage in plants - as granuals in organelles called plastids

glucose monomers

linked together making an alpha 1-4 glucosidic linkages

two forms of starch

amalose - unbranched chains

amylopectin - branched - branches from the sixth glucose

- branches about every 30 units

2. Glycogen - storage in animals - storage in liver and muscle cells

alpha 1-4 linkage

extensivly branched

about every 10 units


Starch

– Is the major storage form of glucose in plants

Chloroplast Starch

Amylose Amylopectin

1 m

(a) Starch: a plant polysaccharideFigure 5.6


• Starch molecules in a bean embryo


• Glycogen

– Consists of glucose monomers

– Is the major storage form of glucose in animalsMitochondria Giycogen

granules

0.5 m

(b) Glycogen: an animal polysaccharide

Glycogen

Figure 5.6


Structural Polysaccharides

provide protection and support

1. Cellulose - long unbranched, straight

chains beta 1-4 linkages

makes for alternating bonds

makes for a very rigid structure

makes up cell walls

enzymes that break alpha bonds can't break

beta bonds


Cellulose vs. Starch

– Cellulose has different glycosidic linkages than

starch

(c) Cellulose: 1– 4 linkage of glucose monomers

H O

O

CH2O

H

HOH H

H

OH

OHH

H

HO

4

C

C

C

C

C

C

H

H

H

HO

OH

H

OH

OH

OH

H

O

CH2O

H

H

HH

OH

OHH

H

HO

4OH

CH2O

HO

OH

OH

HO

41

O

CH2O

HO

OH

OH

O

CH2O

HO

OH

OH

CH2O

HO

OH

OH

O O

CH2O

HO

OH

OH

HO4

O1

OH

O

OH OHO

CH2O

HO

OH

O OH

O

OH

OH

(a) and glucose ring structures

(b) Starch: 1– 4 linkage of glucose monomers

1

glucose glucose

CH2O

H

CH2O

H

1 4 41 1

Figure 5.7 A–C


Cellulose

Plant cells

0.5 m

Cell walls

Cellulose microfibrils

in a plant cell wall Microfibril

CH2OH

CH2OH

OH

O

H

O

OOH

OCH2OH

O

O

OH

OCH2OH OH

OH OHO

O

CH2OH

O

OO

HCH2OH

OO

O

H

O

O

CH2OHOH

CH2OHOH

OOH OH OH OH

O

OH OH

CH2OH

CH2OH

OHO

OH CH2OH

O

O

OH CH2OH

OH

Glucose

monomer

O

O

O

O

O

O

Parallel cellulose molecules are

held together by hydrogen

bonds between hydroxyl

groups attached to carbon

atoms 3 and 6.

About 80 cellulose

molecules associate

to form a microfibril, the

main architectural unit

of the plant cell wall.

A cellulose molecule

is an unbranched

glucose polymer.

OH

OH

O

OOH

Cellulose

molecules

Figure 5.8

– Is a major component of the tough walls that

enclose plant cells


• Cellulose is difficult to digest

– Cows have microbes in their stomachs to

facilitate this process – mutualism

Figure 5.9


Structural Polysaccharides

2. Chitin - structure of arthropod exoskeletons

and cell walls of fungus

differs: glucose with a nitrogen compound

attached


• Chitin, another important structural

polysaccharide

– Is found in the exoskeleton of arthropods

– Can be used as surgical thread

(a) The structure of the

chitin monomer.

O

CH2O

H

OHH

H OH

H

NH

C

CH3

O

H

H

(b) Chitin forms the exoskeleton

of arthropods. This cicada

is molting, shedding its old

exoskeleton and emerging

in adult form.

(c) Chitin is used to make a

strong and flexible surgical

thread that decomposes after

the wound or incision heals.

OH

Figure 5.10 A–C


• What is a carbohydrate? Video

https://www.youtube.com/watch?v=wxzc_2c6GMg


LIPIDS

CHOP - mostly HYDROPHOBIC

- MOSTLY hydrocarbons

NET affect - NON-POLAR

Types: fats, phospholipids, steroids, waxes


Function:

energy storage

Protection and insulation

Ex: Blubber

structure

chemical communication

repel water


FATS AND OILS

Structure - two parts

1. glycerol - three carbon chain with three hydroxyls

2. fatty acid - long chain of hydrocabons with a carboxyl head

• carboxyl head combines with hydroxyl of glycerol by dehydration synthesis so 3 fatty acids combine with the glycerols = triglycerol or triglyceride

• The massive amounts of hydrocarbons in the tail make fats NONPOLAR


Fats and Oils

Constructed from a glycerol and three fatty acids

Result = TRIGLYCERIDE


FATS vs. OILS

• FATS - animal derived - solid at room temp

• OILS - mostly plant derived - liquid at room temp

• crucial difference?

• bonding in the fatty acids


Saturation vs. Unsaturation

Saturated - all carbon bonds are single bonded -

all possible hydrogens

• straight chains

• atherosclerosis

Unsaturated - carbons may have double bonds

• - causes a bend in the chain

• - chains can't stack as neatly


• Saturated fatty acids

– Have the maximum number of hydrogen atoms

possible

– Have no double bonds

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12


• Unsaturated fatty acids

– Have one or more double bonds

(b) Unsaturated fat and fatty acidcis double bond

causes bending

Oleic acid

Figure 5.12


PARTIALLY HYDROGENATED OILS

BAD BAD BAD BAD BAD

WHAT IS FAT? Video

https://www.youtube.com/watch?v=QhUrc4BnPgg


ENERGY Content of Fats and Oils

9 Cal/g

• - carbs: 4 Cal/g

• - protein: 4 Cal/g

• - alcohol: 7 Cal/g


PHOSPHOLIPIDS

Function: STRUCTURE - cell membranes

Composition:

Hydrophilic head:

phosphate joined to glycerol

POLAR

- joins with other polar molecules - choline

Hydrophobic tail:

two chains not three


• Phospholipid structure - amphipathic

– Both hydrophilic and hydrophobic

CH2

O

PO O

O

CH2CHCH2

OO

C O C O

Phosphate

Glycerol

(a) Structural formula (b) Space-filling model

Fatty acids

(c) Phospholipid

symbol

Hydrophilic

head

Hydrophobic

tails

–

CH2 Choline+

Figure 5.13

N(CH3)3


Reaction with water

heads out tails in

2 structures

1. micelle

2. liposome

- cell membrane – PHOSPHOLIPID BILAYER


Phospholipids in Water


• The structure of phospholipids

– Results in a bilayer arrangement found in cell

membranes

Hydrophilic

head

WATER

WATER

Hydrophobic

tail

Figure 5.14


Steroids

four fused rings

• examples:

• testosterone

• estrogen

• cholesterol - stabilize cell membranes

– Understanding Cholesterol

– Coconut Oil

http://www.youtube.com/watch?v=wnK1Kv3XkZI

http://www.youtube.com/watch?v=ZZOR-Qd3QSg


• One steroid, cholesterol

– Is found in cell membranes

– Is a precursor for some hormones

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15


PROTEINS: molecular tools of cells

Function: PAGE 68

• support

• storage

• Transport

• Communication

• Movement

• Protection

• *****CATALYST*******


• An overview of protein functions

Table 5.1


• Enzymes

– Are a type of protein that acts as a catalyst,

speeding up chemical reactions

Substrate

(sucrose)

Enzyme

(sucrase)

Glucose

OH

H O

H2O

Fructose

3 Substrate is converted

to products.

1 Active site is available for

a molecule of substrate, the

reactant on which the enzyme acts.

Substrate binds to

enzyme. 22

4 Products are released.

Figure 5.16


Structure of a Protein

POLYPEPTIDE - chain of amino acids

• amino acid - monomer

Four parts of amino acid

1. alpha carbon

2. carboxyl group

3. amino group

- carboxyl and amino change with pH of environment

- very acidic: amino and carboxyl have H+

- as increase in pH # of H + decreases so H+ dissociate

- until reaches no H+ on amino or carboxyl

- point in between where amino group is positively charged and carboxyl is negatively charged is called the ZWITTERION


Zwitterion


Amino Acid Structure (cont.)

4. functional group - DISTINGUISHES ONE AA

FROM ANOTHER - a.k.a. R group - gives

specific chemical properties

- some hydrophilic - can be acidic or basic

- some hydrophobic


• 20 different amino acids make up proteins

O

O–

H

H3N+ C C

O

O–

H

CH3

H3N+ C

H

C

O

O–

CH3 CH3

CH3

C C

O

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3

CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

C

O

O–

CH2

NH

H

C

O

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

Nonpolar

Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

C

O

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–


O–

OH

CH2

C C

H

H3N+

O

O–

H3N+

OH CH3

CH

C C

HO–

O

SH

CH2

C

H

H3N+ C

O

O–

H3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

O

C

C C

O

O–

NH2 O

C

CH2

CH2

C CH3N+

O

O–

O

Polar

Electrically

charged

–O O

C

CH2

C CH3N+

H

O

O–

O– O

C

CH2

C CH3N+

H

O

O–

CH2

CH2

CH2

CH2

NH3+

CH2

C CH3N+

H

O

O–

NH2

C NH2+

CH2

CH2

CH2

C CH3N+

H

O

O–

CH2

NH+

NH

CH2

C CH3N+

H

O

O–

Serine (Ser) Threonine (Thr)Cysteine

(Cys)

Tyrosine

(Tyr)Asparagine

(Asn)

Glutamine

(Gln)

Acidic Basic

Aspartic acid

(Asp)

Glutamic acid

(Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)


BUILDING A PROTEIN

process called protein synthesis

• AA bond by dehydration synthesis between

amino and carboxyl

• FORM A PEPTIDE BOND

• as build get different conformations based on

the AA sequence and the interactions of the R

groups - resulting structure will determine

function


Amino Acid Polymers

• Amino acids

– Are linked by peptide bondsOH

DESMOSOMES

DESMOSOMESDESMOSOMES

OH

CH2

C

N

H

C

H O

H OH OH

Peptide

bond

OH

OH

OH

H H

HH

H

H

H

H

H

H H

H

N

N N

N N

SHSide

chains

SH

OO

O O O

H2O

CH2 CH2

CH2 CH2CH2

C C C C C C

C CC C

Peptide

bond

Amino end

(N-terminus)

Backbone

(a)

Figure 5.18 (b) Carboxyl end

(C-terminus)


STRUCTURE OF A PROTEIN

• 1. Primary structure: sequence of amino

acids - determined by genetic information of

DNA - change in one AA can alter function


Four Levels of Protein Structure

• Primary structure

– Is the unique sequence of amino acids in a

polypeptide

Figure 5.20

–

Amino acid

subunits

+H3N

Amino

end

o

Carboxyl end

oc

GlyProThr Gly

Thr

Gly

GluSeuLysCysProLeu

Met

Val

Lys

Val

LeuAsp

AlaVal ArgGlySer

Pro

Ala

Gly

lle

SerProPheHisGluHis

Ala

Glu

ValValPheThrAla

Asn

Asp

SerGlyPro

ArgArg

TyrThr

lleAla

Ala

Leu

Leu

SerProTyrSer

TyrSerThr

Thr

Ala

ValVal

ThrAsnPro

LysGlu

Thr

Lys

SerTyrTrpLysAlaLeu

GluLle Asp


• 2. Secondary structure: alpha helix or

pleated sheets

- from interactions of Hydrogen bonds

between amino and carboxyl groups of AA

• alpha helix - H bonds every 4th AA

• pleated sheets - two regions of the chain lie

next to one another


O C helix

pleated sheet

Amino acid

subunitsNCH

C

O

C N

H

C

O H

R

C N

H

C

O H

C

R

N

HH

RC

O

R

C

H

N

H

C

O H

NC

O

R

C

H

N

H

H

C

R

C

O

C

O

C

N

HH

R

C

C

O

N

HH

C

R

C

O

N

H

R

C

H C

ON

HH

C

R

C

O

N

H

R

C

H C

O

N

HH

C

R

C

O

N H

H C R

N HO

O C N

C

RC

H O

CHR

N H

O C

RC

H

N H

O C

H C R

N H

CC

N

R

H

O C

H C R

N H

O C

RC

H

H

C

R

N

H

C

OC

N

H

R

C

H C

O

N

H

C

• Secondary structure

– Is the folding or coiling of the polypeptide into a

repeating configuration

– Includes the helix and the pleated sheet

H H

Figure 5.20


• 3. Tertiary Structure: interactions that hold the

different areas of a protein together

• hydrogen bonds

• hydrophobic region attracted to one another

• Van der Waals

• Disulfide bridges - bonds between two sulfurs

in R groups – Between 2 cysteine AA

• STRONG

• Ionic Bonds between R groups


• Tertiary structure

– Is the overall three-dimensional shape of a

polypeptide

– Results from interactions between amino acids

and R groups

CH2CH

OH

O

CHO

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3

CH3

H3C

H3C

Hydrophobic

interactions and

van der Waals

interactions

Polypeptide

backboneHyrdogen

bond

Ionic bond

CH2

Disulfide bridge


• 4. Quaternary Structure: putting other

proteins together in a cluster

EX: hemoglobin, collagen

• Shaping of the protein aided by CHAPERONE

PROTEINS (chaperonins) -direct

conformation


• Chaperonins

– Are protein molecules that assist in the proper

folding of other proteins

Hollow

cylinder

Cap

Chaperonin

(fully assembled)Steps of Chaperonin

Action:

An unfolded poly-

peptide enters the

cylinder from one end.

The cap attaches, causing

the cylinder to change shape in

such a way that it creates a

hydrophilic environment for the

folding of the polypeptide.

The cap comes

off, and the properly

folded protein is

released.

Correctly

folded

proteinPolypeptide

2

1

3

Figure 5.23


• Quaternary structure

– Is the overall protein structure that results from

the aggregation of two or more polypeptide

subunits

Polypeptide

chain

Collagen

Chains

ChainsHemoglobin

IronHeme


• The four levels of protein structure

+H3N

Amino end

Amino acid

subunits

helix


Sickle-Cell Disease: A Simple Change in Primary Structure

• Sickle-cell disease

– Results from a single amino acid substitution in

the protein hemoglobin


• Hemoglobin structure and sickle-cell disease

Fibers of abnormal

hemoglobin

deform cell into

sickle shape.

Primary

structure

Secondary

and tertiary

structures

Quaternary

structure

Function

Red blood

cell shape

Hemoglobin A

Molecules do

not associate

with one

another, each

carries oxygen.

Normal cells are

full of individual

hemoglobin

molecules, each

carrying oxygen

10 m 10 m

Primary

structure

Secondary

and tertiary

structures

Quaternary

structure

Function

Red blood

cell shape

Hemoglobin S

Molecules

interact with

one another to

crystallize into a

fiber, capacity to

carry oxygen is

greatly reduced.

subunit subunit

1 2 3 4 5 6 7 3 4 5 6 721

Normal hemoglobin Sickle-cell hemoglobin. . .. . .

Figure 5.21

Exposed

hydrophobic

region

Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu


What Determines Protein Conformation?

• Protein conformation

– Depends on the physical and chemical

conditions of the protein’s environment


Environmental Effects on Protein Structure

Denaturation - changing the protein so its no longer

effective

• pH, salt, temperature - cause protein to unravel

by breaking interlinking bonds

Denaturation

Renaturation

Denatured

proteinNormal protein

Figure 5.22


NUCLEIC ACIDS

• - direct cell function - informational polymers

• DNA – deoxyribonucleic acid

• RNA – ribonucleic acid

• Differences

• DNA -deoxyribose, two chains, adenine, thymine,

guanine, cytosine

• RNA - ribose sugar, one chain, uracil instead of

thymine

• DNA makes RNA which directs formation of proteins which

direct the chemical reactions of the cell


– Directs RNA synthesis

– Directs protein synthesis through RNA

1

2

3

Synthesis of

mRNA in the nucleus

Movement of

mRNA into cytoplasm

via nuclear pore

Synthesis

of protein

NUCLEUSCYTOPLASM

DNA

mRNA

Ribosome

Amino

acidsPolypeptide

mRNA

Figure 5.25


• Nucleic Acid Monomers: NUCLEOTIDES

1. sugar: deoxribose or ribose - difference C #2

• 2. phosphate

• 3. nitrogenous base:

• purines (bigger) : adenine and guanine

- 6 Carbon ring + 5 Carbon ring

• pyrimidines (smaller): thymine/uracil, cytosine

- 6 Carbon ring


• Each polynucleotide

– Consists of monomers called nucleotides

Nitrogenous

base

Nucleoside

O

O

O

O P CH2

5’C

3’CPhosphate

group Pentose

sugar

(b) NucleotideFigure 5.26

O


Nucleotide Monomers

• Nucleotide monomers

– Are made up of nucleosides and phosphate

groups

(c) Nucleoside componentsFigure 5.26

CH

CH

Uracil (in RNA)

U

Ribose (in RNA)

Nitrogenous bases

Pyrimidines

CN

NC

OH

NH2

CH

CHO

CN

H

CH

HNC

O

CCH3

N

HNC

C

HO

O

Cytosine

CThymine (in DNA)

T

NHC

N C

CN

C

CH

N

NH2 O

N

HC

NHH

CC

N

NH

CNH2

Adenine

A

Guanine

G

Purines

OHOCH2

H

H H

OH

H

OHOCH2

H

H H

OH

H

Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)

OHOH

CH

CH

Uracil (in RNA)

U

4’

5”

3’

OH H2’

1’

5”

4’

3’ 2’

1’


In DNA Nitrogenous bases link together by hydrogen bonds

A bonds to T

G bonds to C

- must pair purine with pyrimidine – Page 298

pur with pur to big

pyr with pyr to small

- # of correlating H bonds

Sequence of A, C, T, and G determines genetic info


N H O CH3

N

N

O

N

N

N

N H

Sugar

Sugar

Adenine (A) Thymine (T)

N

N

N

N

Sugar

O H N

H

NH

N OH

H

N

Sugar

Guanine (G) Cytosine (C)Figure 16.8

H

chapters 4 & 5 carbon and macromolecules · 5 6 h oh 4c 6ch 2 oh ch 2 oh 5c h oh c h oh h 2 c 1...

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