Lecture 2 Flashcards
(39 cards)
1
Q
Types of Chemical Bonds
A
- van der Waals interactions – dipole moment dependent, very weak
- Hydrogen bond – polar molecules, due to electronegative atom being bound to nonelectronegative atom, very weak
- Ionic bond – electrostatic interaction between oppositely charged molecules or functional
groups, relatively weak - Hydrophobic interactions – non-polar molecules or regions of molecules interact to prevent
association with aqueous environments - Covalent bond – formed by sharing of electrons to complete valence shell, very strong;
single, double, or triple
2
Q
The Versatility of the Carbon Atom
A
- Carbon-carbon covalent bonds essential for life
- Carbon atoms can form 4 chemical bonds
- Provides versatility essential for life
- Can link to a carbon or other type of atom
- Carbon bonds - excellent for backbones of large molecules
- Strong enough to hold molecule together
- Not too strong to prevent cell from breaking
3
Q
Making Carbon Atoms “Spicy” Addition
of Functional Groups
A
- Carbon-carbon bonds - non-polar
- Makes them chemically and biologically “boring”
- Hydrophobic
- Chemically non-reactive
- Addition of functional groups makes them more
reactive
4
Q
Hydroxyl group
A
Hydroxyl group (alcohol) - addition of -OH to carbon,
very polar, affects solubility and reactivity
5
Q
Carbonyl group
A
Oxygen double bonded to carbon
Two types, adehyde and keytone, both are polar
6
Q
Aldehyde carbonyl group
A
carbon double bonded to
oxygen and bonded to at least 1 hydrogen
7
Q
Keytone carbonyl group
A
- carbon double bonded to
oxygen and two other carbon atoms
8
Q
Carboxyl group
A
carbon double
bonded to oxygen and single bonded
a hydroxyl group, very polar and
weakly acidic, due to high
electronegativity of oxygen atom;
proteins, fatty acids.
9
Q
Amino group
A
carbon bonded to
nitrogen that is bound to 2 hydrogens,
polar, weakly basic, due to high
electronegativity of nitrogen atom;
proteins, nucleotides.
10
Q
Methyl group
A
carbon bonded to at least 3
hydrogens, non-polar, extremely
hydrophobic; fatty acids, proteins
11
Q
Phosphate ester group -
A
phosphorus single
bonded to 2 hydroxyls, double bonded to
one oxygen, and single bonded to a second
oxygen. Single bonded oxygen attaches
group to carbon chain, very polar, weakly
acidic; nucleotides and lipids
12
Q
Sulfhydryl group
A
carbon bound to a sulfur
atom that is bound to a hydrogen atom.
Important in protein structure.
13
Q
Ester
A
carbon bound to a carboxylic acid group,
lipids, attachment of amino acids to nucleotides
14
Q
Thioester
A
carboxylic acid group attached to a
sulfur; energy metabolism – biosynthesis of fatty acids
15
Q
Ether
A
oxygen joining two carbons, sphingolipids
and lipids of Archea
16
Q
Acid Anhydride
A
carboxylic acid bound to
phosphate; energy metabolism
17
Q
Phosphoanhydride
A
two phosphates joined
together; high energy bond of ATP
18
Q
Assembly of Biological Macromolecules
A
- Majority of biological molecules carbon based – organic
- Pure carbon/hydrogen molecules hydrophobic
- Hydrophobicity limits usefulness in aqueous environments
- All biological processes require water
- Addition of functional groups increases solubility in water
- Dramatically increases versatility of carbon based molecules in biological systems
- Carbon based molecules comprise four major classes of biologically relevant macromolecules
19
Q
Many Different Types of Polymers in Biological Systems
A
- Carbohydrates
- Lipids
- Proteins
- Nucleic Acids
20
Q
Carbohydrates
A
- Monosaccharide - simple sugar, usually
3 to 7 carbon atoms - 5 and 6 carbon sugars can be
circular molecules - Hydroxyl group bound to each
carbon except 1 - One carbon is bound to a carbonyl
group - 5 carbon sugars – important
structural role in nucleic acids - 6 Carbon sugars commonly used as
energy source
21
Q
Complex Carbohydrates
A
- Long chains of carbohydrates – covalently attached by
glycosidic bond - Three types of glycosidic bonds
- a-1,4 – 1carbon from one sugar covalently attached to 4
carbon of adjacent sugar, hydroxyl group on anomeric carbon
beneath the plane of the ring - a-1,6 – 1 carbon from one sugar attached to 6 carbon on
adjacent sugar, hydroxyl group on anomeric carbon beneath the
plane of the ring - b-1,4 – 1 carbon from one sugar attached to 4 carbon of
adjacent sugar, hydroxyl group on anomeric carbon above the
plane of the ring
22
Q
Starch and glycogen
A
- Starch and glycogen – energy storage for plants and
animals, respectively - Both have long chains of sugars joined by a-1,4
linkage - Glycogen often branched, branch point formed by a-1,6 linkage
- Cellulose – no branching
- Sugars joined exclusively by b-1,4 linkage
- Useful for structural role, most animals do not have the enzyme
required to break
23
Q
Simple Lipids - Triglycerides
A
- Extremely hydrophobic compounds
- Two components - glycerol and a fatty acid
- Glycerol is an alcohol
- Fatty acid - long hydrocarbon chain attached to a carboxyl group
- Fatty acid is attached to glycerol via a covalent bond between the carboxyl group of the fatty acid and a
hydroxyl group on the glycerol - Fatty acids can be saturated or unsaturated
- Saturated fatty acids have no carbon-carbon
double bonds - Unsaturated fatty acids have at least 1 carboncarbon double bond
24
Q
Phospholipids
A
- Phospholipids critical to life – also
called complex lipids - Main component of cellular
membranes - Consist of lipid bound to
phosphate group - Phosphate attached to one of the
-OH groups of glycerol in the lipid - May have additional functional
groups bound to phosphate
25
Nucleic Acids
* Transmit genetic information, allows production of protein
* Two kinds
* Deoxyribonucleic Acid (DNA)
* Responsible for transfer of genetic information
* Harbors coding information for all proteins
* Ribonucleic Acid (RNA)
* Transcribes genetic information
* Allows cellular machinery to make proteins
* Both are composed of nucleotides
26
Nucleotides
* All have 3 components
* Phosphate
* 5 carbon sugar (ribose
or deoxyribose)
* Nitrogenous base
* Two classes of
Nitrogenous bases
* Purines (Adenine and
Guanine)
* Pyrimidines (cytosine,
thymine, and uracil)
27
Joining of Nucleic Acids
* Nucleotides assembled into DNA or RNA via
phosphodiester linkage
* 5’ phosphate from one covalently bound to 3’
hydroxyl of ribose (or deoxyribose) of next nucleotide
* Order in which deoxynucleotides are added
determines genetic information carried
28
DNA vs. RNA
* DNA – bearer of genetic information
* Only represents information
* Cannot do anything
* RNA essential for realizing potential of DNA, converts into molecules that can perform
cellular “work”
* Three types of RNA required
* mRNA – transcripts
* tRNA – delivery of amino acids to the ribosome
* rRNA – catalytic component of ribosome
29
Proteins
* Proteins - the machines that run the cell
* Enzymes are proteins
* Catalyze most biological reactions
* Reactions essential for life of cell
* Proteins have building blocks
* Amino acids - monomers of proteins, all have same basic structure
* Joined together via peptide bonds
30
Structure of Amino Acids
* 20 different amino acids
* Basic structure for all the same
* Only variable is side chain
* 3 classes of side chains - polar,
charged, hydrophobic
* All 20 amino acid side chains
are distinct - confer different
properties/reactivity
* Allows for extreme diversity in
structure/function of proteins
31
Types of Isomers
Structural Isomers - different covalent arrangement
of atoms
Geometric Isomers - identical in arrangement of
covalent bonds, different spatial orientation of
groups
Enantiomers - mirror images of each other, cannot
be superimposed, gives molecules “handedness”,
all amino acids have enantiomers
32
Protein Structure
* Four levels of Protein Structure
* Primary
* Secondary
* Tertiary
* Quaternary
33
Primary Level of Polypeptide Structure
* Amino acids - linked together by peptide bonds
* Several amino acids joined together make a polypeptide
* The order in which the amino acids are joined together is
the PRIMARY LEVEL OF PROTEIN STRUCTURE.
34
Secondary Level of Protein Structure
* Polypeptide chains can fold into 2 conformations -a-helix, bpleated sheet
* a-helix - coiled structure, like a
slinky or a corkscrew
* Structure formed and
maintained by hydrogen
bonding
* Bonds between amine and
carboxyl groups of amino acids
in successive turns of coil
35
Secondary Level of Protein Structure cont
* Polypeptide chains can fold into 2 conformations - a-helix, b-pleated sheet
* b-pleated sheet - flat structure , due to
polypeptide chain folding back towards itself,
draw on board
* Structure also formed and maintained by
hydrogen bonding
* Bonds between amine and carboxyl groups of
amino acids of different regions of chain folded
back on its self
36
Tertiary Level of Protein Structure
* Overall shape of protein molecule
* Forms when secondary structures interact
with each other
* Tertiary structure occurs when:
* Two or more a-helices interact
* Two or more b-pleated sheets interact
* Any number of a combination of both ahelices and b-pleated sheets interact
37
Tertiary Level of Protein Structure cont
* Held together by a number of
interactions
* Ionic bonds
* Hydrogen bonds
* Disulfide bridges
* Hydrophobic interactions
38
Quaternary Level of Protein Structure
* Occurs when two or more different
polypeptides interact
* Same types of interactions that
stabilize tertiary interactions also
stabilize quaternary interactions
* Ionic bonds
* Hydrogen bonds
* Disulfide bridges
* Hydrophobic interactions
39
Protein Denaturation
* Loss of protein activity, may be permanent or transient
* Due to loss of secondary, tertiary,
and/or quaternary structure
* May be induced by chemicals –
chaotropic agents (urea)
* May be induced by physical means –
heat or desiccation
* Some proteins renature (refold)
spontaneously, need only relieve cause
of denaturation
* Others require assistance – chaperones
