Download Nucleic Acid Notes

Chapter 5.
Macromolecules
Macromolecules
• Smaller organic molecules join together to form larger molecules
• macromolecules
• 4 major classes of macromolecules:
•
•
•
•
carbohydrates
lipids
proteins
nucleic acids
Polymers
• Long molecules built by linking chain of repeating smaller units
• polymers
• monomers = repeated small units
• covalent bonds
How to build a polymer
• Condensation reaction
• dehydration synthesis
• joins monomers by “taking” H2O out
• 1 monomer provides OH
• the other monomer provides H
• together these
form H2O
• requires energy
& enzymes
How to break down a polymer
•Hydrolysis
• use H O to break apart monomers
2
• reverse of condensation reaction
• H2O is split into H and OH
• H & OH group attach where the covalent bond used to be
• ex: digestion is
hydrolysis
Nucleic Acid Notes
AP Biology
NUCLEOTIDES AND NUCLEIC ACIDS
•
INFORMATION FLOW IN CELLS
= “Central Dogma of Molecular
Biology”
• DNA→ RNA→ PROTEINS
FUNCTION
• DNA- genetic code contains
info that programs cell
activities
• RNA-carries message from DNA
to cell; protein synthesis
BASIC STRUCTURE
• NUCLEOSIDE = nitrogenous base + sugar
NUCLEOTIDE = nitrogenous base + sugar +
phosphate group
PURINES = 2 rings; Adenine (A), Guanine (G)
• PYRIMIDINES = 1 ring; Cytosine (C), Thymine (T),
Uracil (U)
Nitrogen Bases
Nitrogen bases
A purine
always bonds
with a
pyrimidine.
NUCLEOTIDES
O
• Can have one, two, or
three phosphate groups
(mono, di, triphosphates)
• High energy bond between
phosphate groups is
important energy
transport
-O
O
O
-P~O-P~O-P-OO-
O-
O-
Nucleotides are….
• Named for nitrogen base and number of phosphate
groups
• EX: adenosine triphosphate (ATP)
cytosine diphosphate (CDP) guanosine
monophosphate (GMP)
IMPORTANT NUCLEOTIDES
• ADENOSINE TRIPHOSPHATE (ATP) = main energy currency in ALL
living things (GTP & UTP also used)
• CYCLIC AMP (cAMP)- “Second messenger”
Important in cell signaling and response to hormones
• COENZYMES- Many coenzymes are nucleotides or their
derivatives (vitamins)
EX: Flavin adenine dinucleotide (FAD) & nicotinamide adenine dinucleotide
(NAD) used in cellular respiration
nicotinamide adenine dinucleotide phosphate (NADP)
used in photosynthesis
NUCLEIC ACIDS (DNA & RNA)
•DEHYDRATION SYNTHESIS forms polymers of
nucleotide building blocks
•PHOSPHATES and SUGARS form backbone
Bonds in DNA
• To distinguish sugar and nitrogen base
carbon atoms when numbered, sugar
atoms have a prime ( ‘ )
Phosphate group attached to 5’ carbon
on one sugar and the 3’ carbon of next
sugar
• PHOSPHATE LINKAGE between carbon
3’ of one sugar and carbon 5’ of the
next
3’
5’
RIBONUCLEIC ACID (RNA)
•Single stranded
•Sugar = ribose
•Nitrogenous bases =
A, U, G, C
•Can fold up in 3D
shape
NUCLEOTIDE SUBUNITS:
SUGAR = Ribose (RNA) OR Deoxyribose (DNA)
NITROGEN BASES:
DNA
RNA
Adenine
Adenine
Guanine
Guanine
Cytosine
Cytosine
Thymine
Uracil
DEOXYRIBONUCLEIC ACID (DNA)
• Double stranded
• Sugar = deoxyribose
• Nitrogenous bases =
A, T, G, C
• Strands run in opposite
directions (ANTIPARALLEL)
• Backbone = sugars and
phosphates
DNA Structure
•Rungs of ladder = nitrogenous bases
•Hydrogen bonds between nitrogenous bases
hold sides of ladder together
•Purine always bonds to a Pyrimidine
• CHARGAFF’S RULE: A = T; G = C
•The double strand twists around its axis like a
spiral staircase, forming a DOUBLE HELIX
Evolutionary significance
•DNA and protein sequences can be used as
tape measures of evolution
•linear sequences of nucleotides in DNA
molecules are passed from parents to
offspring
•more distantly related species have chains
that are less similar
PROTEINS- “Cellular toolbox”
• Make up 50% or more of dray mass of most
cells
• Humans have tens of thousands of different
proteins
• Typical protein = 200-300 amino acids; biggest
known = 34,000
• We know the amino acid sequences of >
875,000 proteins/3D shapes of about 7,000
• Scientists use X-ray cystallography to
determine protein conformation
• A protein’s function = determined by its
conformation
EXAMPLES OF VARIETY OF
PROTEINS/FUNCTIONS:
• Structural: hair, fingernails, bird feathers (keratin); spider silk;
cellular cytoskeleton (tubulin & actin); connective tissue
(collagen)
• Storage: egg white (ovalbumin); milk protein (Casein); plant seeds
• Transport: Transport iron in blood (hemoglobin);
• Hormonal: Regulate blood sugar (insulin)
• Membrane proteins (receptors, membrane transport, antigens)
• Movement: Muscle contraction (actin and myosin); Flagella
(tubulin & dynein); Motor proteins move vesicles/chromosomes
• Defense: Antibodies fight germs
• Metabolism: Enzymes act as catalysts in chemical reactions
• Toxins (botulism, diphtheria)
AMINO ACIDS
Central (α carbon) with CARBOXYL, AMINO, H,
and R groups attached
20 common amino acids used by living things;
•lys-arg-his-asp-glu-ala-val-leu-ile-pro-phemet-trp-gly-cys-ser-thr-tyr-asn-gln
Essential AA’s
“VEGGIE” ALERT !
9 “essential” amino acids
can’t be synthesized by humans;
must come from diet especially
Lysine and tryptophan
(in low amounts in most plant proteins)
Strict vegetarians need to make sure that their diet contains
sufficient amounts of these
In cells, protein structure changes depending
on pH
Bonds in Proteins
• POLYPEPTIDE = polymer of amino acid subunits
connected in a specific sequence
An enzyme joins the carboxyl of one amino acid and the
amino group of another via DEHYDRATION SYNTHESIS
condensation reaction to form a PEPTIDE BOND
Peptide bonds are rigid, planar structures
• The -NH bond and the -C=O bond, point away from each
other so these groups can hydrogen bond to other parts
of chain
LEVELS OF PROTEIN ORGANIZATION/3STRUCTURE
• Primary Structure =unique sequence of amino
acids; determined by DNA code; unique for each
protein
• Secondary Structure: Determined by amino acid
sequence;
• HYDROGEN BONDS (between the oxygen of C=O
and the hydrogen of
N-H of peptide bonds) stabilize structure & form
pattern
• Α HELIX- polypeptide chain
winds clockwise like a spiral
staircase
EX: KERATIN, the main protein component of
hair, nails, horns
• Β PLEATED SHEET- chains joined
together like the logs in a raft
EX: SILK
Tertiary Structure: Hydrogen
bonding, ionic interactions,
hydrophobic interactions, and
disulfide bridges between R
groups stabilize 3 D shape
hy dr op hy lli c
+
S
S
S
Tertiary Structure
io nic
hy dr op hob ic
hy dr og en
di su lfid e
Quaternary Structure: protein made up of more
than one amino acid chain
• EX: COLLAGEN
3 polypeptide chains
twisted in super coil
EX:HEMOGLOBIN
4 polypeptide chains
What Do You Call It?
• two or more amino acids bonded together = PEPTIDE
• chain of many amino acids = POLYPEPTIDE
• complete folded 3D structure = PROTEIN
Final overall protein shapes
- FIBROUS. - long fiber shape EX: actin or collagen
- GLOBULAR - overall spherical structure EX: hemoglobin
MUTATIONS CAN CHANGE PROTEIN SHAPE
• Since shape is determined by amino acid sequence;
changing sequence changes 3D shape
• EX: Sickle cell anemia mutation changes one amino acid in the
sequence (glu → ala)
Abnormal hemoglobin
molecules
crystallize;
cause blood cells to
become sickle shaped
FACTORS AFFECTING CONFORMATION
Folding occurs as protein is synthesized, but physical/chemical
environment plays a role
DENATURATION: = unraveling/ loss of native confirmation
• makes proteins biologically inactive
~ Reason high fevers can be fatal
• • does NOT break peptide bonds
• so primary structure remains intact
• may regain its normal structure if conditions change
• sometimes = irreversible (ie. cooking an egg)
Denaturing CAUSED BY
• changes in pH (alters electrostatic interactions
between charged amino acids)
• changes in salt concentration (does the same)
• changes in temperature (higher temperatures
reduce the strength of hydrogen bonds)
• presence of reducing agents (break S-S bonds
between cysteines)
Other Kinds of Proteins• Simple proteins contain only amino acids
Conjugated proteins contain other kinds of molecules
Ex: glycoproteins contain carbohydrates, nucleoproteins contain
nucleic acids, lipoproteins contain lipids