Transcript Ch 3 The Molecules of Cells

The Molecules of Cells
Chapter 3
Overview
• Introduction to Organic
Compounds
• Categories of Reactions
• Molecules of Life
–
–
–
–
Carbohydrates
Lipids
Proteins
Nucleotides
What Are Organic Compounds?
Unique to living systems
Contain C & at least one H atom
Each has a functional group:
– Specific atoms/groups of atoms covalently
bonded to C
– Have specific physical & chemical properties
Why Carbon?
Versatile bonding
Can covalently bond with up to 4 atoms
Forms stable bonds
Helps form backbone for other elements to bond
with
How Do Cells Build Organic
Compounds?
Monomer:
Individual subunit of larger molecules needed to
maintain cell structure & function
e.g. amino acids
Polymer:
Combination of 3 to millions of subunits
e.g. proteins
Hydrocarbons
H covalently bonded to C
e.g. gasoline, other fossil fuels
All 2 million+ are non-polar
Some of Earth’s most important energy sources
(electric & heat energy)
Functional Groups
Specific atoms or groups of atoms covalently
bonded to carbon atoms in organic
compounds
More reactive than hydrocarbon groups
Can affect how structurally similar molecules
work
e.g. estrogens & testosterone
(different positions of functional groups determines
sexual traits)
Types of Functional Groups
Hydroxyl
– Alcohols, sugars,
amino acids
– Water-soluble
—OH
Methyl
– Fatty acid chains
– Insoluble in water
H
C
H
H
Types of Functional Groups continued
Carbonyl
–
–
–
–
Sugars, amino acids, nucleotides
Water-soluble
Aldehyde if at end of carbon backbone
Ketone if within carbon backbone
C
H
O
—CHO
(aldehyde)
C
O
CO
(ketone)
Types of Functional Groups continued
Carboxyl
–
–
–
–
Amino acids, fatty acids
Water-soluble
Highly polar
Acts as acid by giving up H+
C
OH
O
—COOH
(non-ionized)
C
O-
O
—COO(ionized)
Types of Functional Groups continued
Amino
– Amino acids, some nucleotide bases
– Water-soluble
– Acts as weak base by accepting H+
N
H
H
—NH2
(non-ionized)
H
N
H+
H
—NH3+
(ionized)
Types of Functional Groups continued
Phosphate
– Nucleotides (e.g. ATP), DNA, RNA, some
proteins, phospholipids
– Water-soluble
– Acidic
O-
O
P
O
O-
—
P
Types of Functional Groups continued
Sulfhydryl
– Cysteine (an amino acid)
– Helps stabilize protein structure via disulfide
bridges
—SH
—S—S—
(disulfide bridge)
Categories of Reactions
(1) Functional Group Transfer
a.k.a. exchange reaction
AB + CD → AD + BC
1 molecule gives up group to another
Making & breaking of bonds
e.g. ATP gives phosphate group to glucose in
cellular respiration
(2) Electron Transfer
a.k.a. redox reaction
One molecule loses e-s
Another gains them
e.g. cellular respiration, where glucose is oxidized
(loses e-s) to CO2 & O is reduced (gains e-s) to
H 2O
(3) Rearrangement
Internal bonds reform to turn one organic
compound into another
= structural isomer of original
(same molecular formula,
different order of bonding)
(4) Condensation
a.k.a. synthesis reaction
A + B → AB
2 molecules covalently bond to form a larger
molecule
(1 water molecule produced for each joining)
Making of bonds (= anabolic)
e.g. Na & Cl forming NaCl, amino acids forming a
protein
(5) Cleavage
a.k.a. decomposition reaction
AB → A + B
Molecule is split into 2 smaller ones
Breaking of bonds (= catabolic)
e.g. glycogen being broken down into glucose,
carbs being broken down into simpler sugars
e.g. hydrolysis
Cleavage reaction
Molecule split by enzyme action
OH & H from H2O attached to exposed sites
e.g. hydrolysis of
sucrose into glucose
& fructose
Factors Influencing Reaction Rates
For reactions to occur, atoms & molecules must
collide with enough force to overcome repulsion
between e-s
Temperature
– ↑ temp, ↑ rxn rate
– ↑ kinetic energy, ↑ collisions
Concentration of reactants
– ↑ concentration, ↑ frequency of collisions
Particle size
– Smaller move faster so collide more
frequently
Catalyst
– Substance that speeds up chemical rxns
– Does not become chemically changed or part
of product
Molecules of Life
• Carbohydrates
• Lipids
• Proteins
• Nucleotides
(1) Carbohydrates
Sugars & starches
Make up 1-20% of cell mass
Contain C, H, O
Important source of energy
Also serve some structural purpose
e.g. ribose & deoxyribose in RNA &
DNA
Classified by size & solubility
(a) Monosaccharides
“1 sugar”
Building blocks of other carbs
Most water-soluble sugars
2 or more –OH groups bonded to C
backbone
1 aldehyde or ketone (carbonyl) group
—CHO
CO
Most have a 5-C or 6-C ring
Monosaccharide Structure
glucose
fructose
ribose
galactose
deoxyribose
(b) Disaccharides
Double sugar
Consist of 2 monosaccharides
Must be broken down to be absorbed
(c) Oligosaccharides
“Few” or short-chain sugars
Includes disaccharides
Often found as side-chains on
lipids & proteins
(d) Polysaccharides
“Many sugars”
Chains of glucose
Least water-soluble of carbs
More complex = less soluble
Good energy storage product
Must be broken down to be absorbed
Polysaccharide Structure: Starch
Spiral structure
OH groups stick out from coils
Storage carbohydrate of plants
Polysaccharide Structure: Glycogen
Filamentous (branched) chains
Storage carbohydrate of animal tissues
Equivalent to starch in plants
Stored in muscle & liver cells
Polysaccharide Structure: Cellulose
Every other sugar is “upside-down”
Sheets form by H-bonding between chains
Structural carbohydrate of plants
Makes up cell walls
Polysaccharide Structure: Chitin
Modified polysaccharide
Nitrogen groups attached to glucoses
Strengthens cuticle of arthropods & cell walls of
fungi
=structural carbohydrate of animals & fungi
Simple Carbohydrates
a.k.a. simple sugars
Monosaccharides & disaccharides
Taste sweet
Few essential nutrients & high in calories
e.g. candy, milk products, fruit
Complex Carbohydrates
a.k.a. starches & fibres
Oligosaccharides & polysaccharides
Taste pleasant but not sweet
e.g. whole grains, legumes, starchy vegetables
(potatoes, etc.)
Fibre
= cellulose
↑ fibre in diet = ↓ risk of cancer, diabetes,
hypertension, etc.
Processing plant foods decreases the amount
of fibre & vitamins
In excess, carbs can lead to:
• Increased blood sugar
• Excess sugar being stored as fat
• Increased risk of heart disease, etc.
Diet rich in whole grains, fruits, & vegetables may
reduce risk of heart disease & some cancers
(2) Lipids
Fats & oils
Contain C, H, O
Less O than carbs
Some also have P
Non-polar
Insoluble in water
(a) Fatty Acids
Carboxyl group attached to backbone of up to 36
atoms
Each C is covalently bonded to 1-3 H atoms
(i) Saturated fatty acids
C backbones completely filled with attached H
atoms
Single covalent bonds only
Animal fats:
Usually solid at room temperature
Associated with heart disease,
clogged arteries, etc. = bad fats
e.g. palmitic acid, stearic acid
(ii) Unsaturated fatty acids
Not all Cs have H attached
≥1 double covalent bond
Causes kinks in tails
Plant fats:
Usually liquid at room temperature
Mono- vs. polyunsaturated fats
Mono-unsaturated
e.g. oleic acid
– Only 1 double bond
– Thought to lower cholesterol
Polyunsaturated
e.g. linoleic acid
– More than 1 double bond
Partial hydrogenation of vegetable oils
Artificial saturation
Turns liquid oils into solids (e.g. margarine)
Oil is heated; H2 gas & nickel catalyst added
Breaks C double bonds & attaches H
Partial hydrogenation & trans-fatty acids
Partial hydrogenation = bad!
Fat is now saturated
Trans-fats created by heat (e.g. deep frying) &
hydrogenation
Double bonds fold in unnatural direction
Enzymes that process fat are unable to process transfatty acids in a normal way
Domino effect:
Because trying to process trans-fatty acids, don’t
process essential fatty acids properly
Essential fatty acids
Body can manufacture some
(palmitic acid, oleic acid, etc.)
Others must be ingested via foods
(omega-3 & omega-6 fatty acids)
(b) Neutral Fats
3 fatty acid tails attached to
glycerol backbone
= triglycerides
Large & found throughout entire
body
“Body fat” used for insulation,
protection, energy production
Yield > double the energy of complex
carbs
e.g. butter, lard, veg. oils
(c) Phospholipids
Glycerol backbone with
phosphorus group & 2
fatty acid tails
– Tails are non-polar
– Head is polar
Make up double-layered cell
membranes
Help regulate what crosses
boundary of cell
(d) Waxes
Long-chained fatty acids bonded
to long-chain alcohols or
carbon rings
Repel water
Protect
Lubricate
Add pliability to hair, skin, etc.
(e) Sterols
Backbone of 4 C-rings
Differ in functional groups
In all eukaryotic cell membranes
Steroids are essential for human life
(homeostasis, vitamin D, sex & metabolic hormones)
Cholesterol
Found only in animal foods
Made in liver
Can’t dissolve in blood
Is carried to & from cells by lipoproteins
(LDL & HDL)
Note: cholesterol itself is not bad
LDL (low-density lipoprotein)
Carries cholesterol through blood to body
cells
Can form fatty deposits (plaques) in artery
walls
– Eventually blocks blood flow
– Leads to heart attack, stroke, etc.
HDL (high-density lipoprotein)
Carries cholesterol through blood to liver
(will eventually be processed & excreted)
High levels appear to protect against heart
attack
(may remove excess cholesterol from plaques,
which slows build-up)
(3) Proteins
Make up 10-30% of cell mass
Contain C, H, O, N & sometimes S & P
Form basic structural material & aid in cell function
Long chains of amino acids (from 50 to 10,000+)
joined by peptide bonds
Sequence of amino acid chain dictates which
protein is made
(a) Amino Acids
Amino group (NH3+), carboxyl group (COO-),
H atom, & R group
Can act as bases or acids
R
20 amino acids
– Identical except for R group
– Chemically unique
Types of R-groups: Acidic
In neutral solutions, R-group can lose proton to
become negatively-charged
If interaction with basic R-group, forms salt bridge:
helps stabilize a protein
Types of R-groups: Basic
In neutral solutions, R-group can gain proton to
become positively-charged
If interaction with acidic R-group, forms salt bridge:
helps stabilize a protein
Types of R-group: Aromatic
R-group is an aromatic (benzene) ring
Generally hydrophobic & non-reactive
Types of R-group: Sulfur
R-group contains S
Helps stabilize globular protein structure
Types of R-group:
Uncharged Hydrophilic
R-groups can form H-bonds
Types of R-group:
Inactive Hydrophobic
R-groups do not form H-bonds
Rarely reactive
Usually buried deep within a protein
Types of R-groups: Special
R-group & amino group are directly connected
Usually located at the turn of a polypeptide chain in
3D protein structure
Essential & non-essential amino acids
Non-essential:
– Can be synthesized from other substances in the body
Essential:
– Can not be synthesized in the body
– Must come from food
– If not adequate intake, can’t make proteins
• Unable to sustain body structurally & functionally
= illness & eventually death
9 essential amino acids
Histidine
Isoleucine
Leucine
Lysine
Methionine
(cysteine partially meets needs because has S)
Phenylalanine
(tyrosine partially meets needs)
Threonine
Tryptophan
Valine
Most animal sources:
“Complete protein”: all of essential aas
Vegetables:
Missing or low in certain aas
If combine different vegetables, can get all
essential aas
Lysine & tryptophan hard to get from plants so
vegetarians need to ensure adequate intake
From Amino Acids to Proteins
Amino acids form proteins by dehydration reactions
Peptide bonds form between amino acids
2 amino acids bonded together
= dipeptide
Many amino acids linked
= polypeptide
Types of Proteins
Structural = hair, tendons, ligaments
Contractile = muscles
Defensive = antibodies
Signal
Transport = e.g. hemoglobin
Storage
Plus many more!
(b) Levels of Protein Structure
1° structure
Linear polypeptide chain
(unique sequence of amino acids)
Determined by inherited genetic info
2 ° structure
Proteins tend to twist or bend
H-bonds form between NH &
CO groups
α-helix (coiled)
or
β-pleated sheet
Tertiary structure
Proteins continue to fold
upon themselves
Quaternary structure
Two or more
polypeptide chains
bonding & folding
together
(c) Other Types of Protein Structure
Glycoprotein:
Oligosaccharide + polypeptide
Lipoprotein:
Lipid + protein
Both types important in cellular processes
The Importance of Structure
Protein structure determines biological
function
3D structure allows recognition & binding
with specific molecular
targets”
(d) Fibrous Proteins
Mostly 2° structure; some have
quaternary structure
Insoluble in water
Structural functions:
chief building materials of body
e.g. collagen, elastin, keratin
Globular Proteins
Tertiary or quaternary structure
Water-soluble
Chemically active
Used in all biological processes
e.g. antibodies, enzymes, proteinbased hormones
(e) Enzymes
Biological catalysts that keep metabolic &
biochemical reactions happening
Decrease the amount of activation energy
required for chemical rxn to proceed
May be pure protein or may have cofactor (e.g.
vitamin, metal ion)
Chemically specific
– Named for type of reaction they catalyze
– Usually end in “ase”
Some must be activated before use
Others are inactivated directly after use
All have an active site:
Allows binding of substrate so that rxns can
proceed
Why Is Protein Structure Important?
Structure dictates function
Proteins can only function if configured
in specific way
Denaturation of Proteins
Breaking of H-bonds that results in shape change
Caused by temperature, pH, foreign substances, etc.
Can’t perform physiological functions
Active site is destroyed when bonds are broken
e.g. high fevers
• Denature proteins in body
• Proteins can no longer function
• Can result in serious damage/death
Denaturation is usually irreversible
e.g. albumin in cooked egg can’t regain
original shape
one
way
Note: not all changes are bad—can sometimes
result in variation in traits
(4) Nucleotides
Contain C, H, O, N, P:
N base, sugar, & phosphate
5 N bases:
adenine, thymine, guanine, cytosine, uracil
Important in energy production, metabolism, cell
signalling
Nitrogen-Containing Bases
Purines (double-ringed)
Adenine
Guanine
Pyrimidines (single-ringed)
Thymine
Cytosine
Uracil
(a) DNA
Genetic material contained in cell nucleus
(replicates itself before cell division so info in
cells is identical)
Contains deoxyribose sugar
Each species has unique base sequences
somewhere in their DNA molecules
The History of DNA
Pre-1920s scientists knew that:
– Genes are responsible for variation in traits
among individuals of a species
– Genes are located within chromosomes
– Chromosomes are made of DNA & proteins
BUT most researchers thought genes were made
of proteins that held heritable traits
– Diverse traits from diverse molecules?
Frederick Griffith (1928):
– Tried to develop vaccine against Streptococcus
pneumoniae
– Did not succeed BUT managed to transfer genetic
material from one bacterial strain to another
Oswald Avery (1940s):
– DNA-digesting enzymes (NOT protein-digesting)
prevented bacterial cells from becoming pathogenic
Thus, genes are made of DNA
Still …
How does DNA store genetic info?
The answer lies in the structure of DNA
DNA Structure
Polymer of nucleotides:
– Phosphate
– Deoxyribose sugar
– Nitrogen-containing base
(A, C, G, T)
All nucleotides are identical
except for base
What does DNA actually look
like?
Clues in Chargaff’s ratios:
In any species
#A = #T
#G = #C
Differs between species
e.g. humans 30% A/T & 20% G/C
E.coli 26% A/T & 24% G/C
Also clues in X-ray shadows:
X-ray diffraction of DNA crystals
No direct picture of DNA structure but
could tell:
(a) long & thin
(b) helical
(c) repeating subunits
Watson & Crick Model
DNA resembles ladder
Bases on each strand pair to
make rungs
G pairs with C
A pairs with T
Explains Chargaff’s ratios
Also …
Ladder is twisted = double
helix
Explains x-ray shadows
Watson & Crick Model
DNA is a double helix of
nucleotides
Sugar-phosphate backbone
Nucleotides held together
at N bases by H bonds
How does DNA store genetic info?
Sequence of bases in DNA codes for genetic info
Different sequences = different information
(b) RNA
Carries out protein synthesis
Similar to DNA except:
– Single strand of nucleotides
– Ribose instead of deoxyribose
– Uracil replaces thymine
(c) ATP
Stores & releases chemical energy for all life
processes
Adenosine, ribose, 3 phosphate groups
Enzymes transfer terminal PO4- group from ATP to
other compounds so can use energy released from
bonds breaking
Brief Overview of How ATP Works
ADENOSINE
P
P
P
Energy via glucose
P
ADENOSINE
P
P
+
So essentially:
ATP
ADP
+
P
+
energy
energy