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Chapter 5: Structure and Function of Large Biological Molecules - Coggle…
Chapter 5: Structure and Function of Large Biological Molecules
5.3 Lipids
hydrophobic
based on molecular structure
nonpolar C-H bonds
large biological molecules
no true polymers
not big enough to be classified as macromolecules
fats
not polymers
large molecules
assembled from small molecules
by dehydration reactions
glycerol molecule joined to 3 fatty acid
making a fat
each fatty acid molecule
joined to glycerol
by dehydration reaction
result: ester linkage
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aka
triacyglycerol
and
triglyceride
glycerol is an alcohol
3 carbons bear a hydroxyl group
fatty acid
long carbon skeleton
16 or 18 carbon atoms
carbon at end is part of a carboxyl group
rest of skeleton consists of a hydrocarbon chain
C-H bonds are hydrophobic
saturated
with hydrogen
resulting in a saturated fatty acid
all carbons are single bonded
maximize the # of hydrogen atoms
attached to the carbon skeleton
most animal fats
lack doble bonds
flexibility allows it to pack together tightly
solid at room temperature
unsaturated
1 or more double bonds
between carbons in the hydrogen tail
reduces # of hydrogen atoms
attached to the carbon skeleton
every double-bonded carbon
cis
double bond
creates kink in the hydrogen chain
plant and fish fats
referred to as oils
olive oil
cod liver oil
cis
double bonds
hydrogenated vegetable oils
hydrogen was added
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liquid at room temperature
trans
fats
artificially created
during hydrogenation of oils
1 or more trans double bonds
contribute to coronary disease
function
energy storage
layer of protection
Phospholipids
major constituents of cell membranes
made up of gylcerol
joined by 2 fatty acids and a phosphate group
hydrocarbon chains are nonpolar
hydrophobic tails
rest of molecule is polar
hydrophilic head
3rd hydroxyl group of gycerol
joined to a phosphate group
negative electrical charge
additional small charged
or polar molecule
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similar to a fat molecule
form bilayers that function as biological membranes
added to water
self-assembles
into double-layered sheet (bilayer)
shields hydrophobic fatty acid tails
in cell
hydrophilic heads
outside of the bilayer
contacting with aqueous solutions
inside and outside the cell
hydrophobic tails
point toward the interior
creates a boundary
between cell and external environment
Steroids
are lipids
consist 4 fused rings
with various chemical groups attached
cholesterol
acts as a precursor
for the synthesis of other steroids
like hormones
synthesized in the liver
obtained from diet
high level
may contribute to atherosclerosis
5.4 Proteins
constructed from set of 20 amino acids
linked in unbranched polymers
bond id called
peptide bond
polypeptide is the polymer
Amino Acids (Monomers)
organic molecule
center of the amino acid
alpha carbon
partners
carboxyl group
hydrogen atom
amino group
variable group (R)
aka side chain
differs with each amino acid
may be
simple as a hydrogen atom
a carbon skeleton with many groups
basic amino acids
amino groups in side chains
generally positive in charge
acidic
basic
some speed up chemical reactions
others provide other benefits
storage
transport
defense
cellular communication
movement
structural support
most enzymes are proteins
regulate metobolism
act as catalysts
increases reaction rate
performs function many times
Polypeptides (Amino Acid Polymers)
2 amino acids
carboxyl group is adjacent to the amino group
joined by dehydration reaction
water molecule removal
resulting covalent bond: peptide bond
repeating the process yields a polypeptide
50% of cell dry mass
Structure and Function
specific activities
result from their 3-D architecture
simplest level
cell synthesizes a polypeptide
chain may fold
folding is driven and reinforced
formation of various bonds
between chain parts
depends on sequence of amino acids
roughly spherical (
globular proteins
shaped like long fibers (
fibrous proteins)
proteios
"first" or "primary"
polypeptide backbone
(R groups)
range in length
few amino acids to 1,000+
4 Levels of Structure
3 superimposed levels
secondary structure
tertiary structure
primary structure
4th level
quaternary structure
a protein has 2+ polypeptide chains
Sickle-Cell Disease
slight change in structure affects
protein's shape
protein's ability to function
inherited blood disorder
caused by substitution
1 amino acid (vafor glutamic acid
at the position of the 6th animo acid
primary structure of hemoglobin
protein that carries oxygen in red blood cells
deforms cells into sickle shape
Determining Structure
depends on
physical conditions of enviroment
chemical conditions of environment
environment
salt concentration
temperature
pH
weak chemical bonds
and interaction
may be destroyed
protein denatures
transferred from aq solution to nonpolar solvent
nonpolar solvents
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other agents
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excessive heat
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may return to functional shape
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denaturation
protein loses its shape and becomes biologically inactive
sequence of amino acids
where beta pleated sheets can exist
where disulfide bridges are located
alpha helix can form
where ionic bonds can form
Protein Folding
go through several intermediate structures
to finally become a stable shape
mature structure does not reveal the stages
misfolding causes serious problems
Alzheimer's
Parkinson's
cystic fibrosis
mad cow disease
X-ray crystallography
technique to study 3-D molecule structures
shows atom's exact position
spectroscopy
nuclear magnetic resonance (NMR)
cryo-electron microscopy
some structures are difficult to determine
a # of proteins
don't have a 3-D structure
until interacting with target protein/other molecule
20 - 30% of mammalian proteins
intrinsically disordered proteins
5.1 Macromolecules
Synthesis and Breakdown
polymers
enzymes
catalyst micromolecule
specialized macromolecules
like proteins
speed up processes
condensation reaction
monomer connects to another monomer or polymer
two molecules
bond covalently
lose a small molecule
dehydration reaction
chemical reactions
2 molecules bond covalently
lost water molecule
hydrolysis
reverse of dehydration reaction
chemical reaction that breaks bonds
by adding a water molecule
hydrogen
attaches to 1 monomer
hydroxyl group
attaches to other monomer
means breakage
hydro
water
lysis
break
digestion
organic material
food
polymers
too large for cells
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Polymer Diversity
cell
thousands of different macromolecules
varies from one type of cell to another
close relatives
small polymer variations
DNA
protein
unrelated individuals
more extensive
different species
much more extensive
polymer
polys
many
meros
part
smaller molecules
monomers
monos
single
large molecule formed by smaller molecules
carbohydrates
nucleic acid
proteins
5.2 Carbohydrates
a sugar (monosaccharide)
sacchar
sugar
end in
-ose
glucose C6H12O6
most common monosaccharide
form rings in aqueous solutions
monos
single
aldose (aldehyde sugar)
sugar
ketose (ketone sugar)
fructose (glucose isomer)
carbon skeleton
3 to 7 carbons long
glucose, fructose, other sugars
6 carbons called hexoses
trioses
3 carbon sugars
pentoses
5 carbon sugars
asymmetric carbon
carbon attached to 4 different atoms or groups of atoms
serve as raw material
for synthesis
for small organic molecules
amino acids
fatty acids
cellular respiration
cells extract energy
break down glucose
series of reactions
dimers (disaccharides)
2 monosaccharides
covalently bonded
glycosidic linkage
dehydration reaction
glyco
carbohydrate
maltose
sucrose (table sugar)
2 monomers
glucose
fructose
plants
transport carbohydrates
leaves to roots
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lactose
glucose is joined to a galactose
sugar in milk
intolerance
lack lactase
enzyme that breaks down lactose
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must be broken down into monosaccharides
user for energy by organisms
polymers (polysaccharides)
hundred to thousand monosaccharides
joined by glycosidic linkages
some serve as storage material
hydrolyzed
others serve as building material
for structures
protect the cell
protect whole organism
architecture and funtion
determined by monossacharides
and determined by glycosidic linkage positions
Storage Polysaccharides
plants
store starch
polymer of glucose monomers
as plastids
granules within cellular structures
include chloroplasts
synthesize starch
enables plants to stockpile glucose
joined by 1 - 4 linkages
animals
store glycogen
polymer of glucose
like amylopectin but more branched
stored in liver and muscle cells
release glucose when demanded
in humans
glycogen stores
depleted in a day
unless replenished by eating
concern in low-carbohydrate diets
weakness
fatigue
Structural Polysaccharides
cellulose
structural polysaccharide of plant cell walls
polymer of glucose
1-4 glycosidic linkages
straight
never branched
certain starch molecules
largely helical
function: storing glucose units
chitin
polysaccharide
used by arthropods
builds their exoskeleton
found in fungi
building material for cell walls
similar to cellulose
beta linkages
5.5 Nucleic Acids
gene
discrete unit of inheritance
consist of DNA
polymers made of monomers (nucleotides)
DNA
RNA
Roles
deoxyribonucleic acid
provides directions for its own replication
directs RNA synthesis
genetic material inherited from parents
each chromosome
contains one DNA molecule
usually carries several hundred+ genes
cell reproduces
divides
DNA molecules are copied
passed along
to one generation of cells to another
not directly involved in cell operations
ribonucleic acid
controls protein synthesis
process is called
gene expression
messenger
RNA (
m
RNA)
molecule interacts with cell's protein-synthesizing machinery
directs production of a polypeptide
folds into all or part of a protein
conveys genetic instructions
builds proteins
from nucleus to the cytoplasm
DNA -> RNA -> protein
ribosomes
sites of protein synthesis are cellular structures
in the cytoplasm in eukaryotic cells
region between the nucleus and cell's outer boundary
DNA doesn't reside in the nucleus
plasma membrane
Prokaryotic cells
lack nuclei
use mRNA to convey a message
from DNA to ribosomes and other cellular equiment
Components
macromolecules
nucleic acids
polymers
polynucleotides
many nucleotide monomers in a chain
nucleotides
building block of a nucleic acid
consists 5-carbon sugar (pentose)
covalently bonded
to a nitrogenous base and 1 - 3 phosphate group
nitrogen containing (nitrogenous) base
portion of a nucleotide
without any phosphate groups
is a
nucleoside
each nitrogenous base
has 1 or 3 rings
include nitrogen atoms
called nitrogenous
bases
because nitrogen atoms take up H^+
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add sugar
deoxyribose
sugar component of DNA nucleotides
ribose
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lacks an oxygen atom
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beginning monomer
used to build a polynucleotide
3 phosphate groups
2 are lost during polymerization process
Nucleotide Polymers
linkage of nucleotides
into polynucleotides
involves a condensation reaction
polynucleotide
adjacent nucleotides
joined by a phosphodiester linkage
contains: phosphate group
covalently links sugars of 2 nucleotides
bond results in repeating patterns
sugar-phosphate backbone
2 free ends of the polymer are different from one another
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DNA and RNA Structures
DNA molecule
2 polynucleotides
form a double helix
strands wound around an imaginary axis into a spiral shape
2 sugar-phosphate backbones
run in opposite 5' -> 3' directions
arrangement is called antiparallel
sugar-phosphate backbones are outside the helix
nitrogenous bases are paired in the interior
2 strands are hydrogen bonded
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pairings
adenine to thymine
guanine to cytosine
2 strands are
complementary
RNA molecules
single strands
complementary base pairing can occur
2 RNA molecules or 2 stretches of nucleotide
in the
same
RNA molecule
base pairing allows to take on 3-D shape for its function
transfer
RNA (
t
RNA)
brings amino acids to the ribosome
during synthesis of a polypeptide
about 80 nucleotides in length
functional shape
results from base pairing
between nucleotides
complementary stretches
of the molecule run antiparallel
pairings
adenine with uracil
thymine is NOT present
molecules vary in shape
versatile
may have preceded DNA as a genetic carrier
5.6 Genomics
bioinformatics
use of computer software
to analyze large data sets
analyzing or comparing different species genomes
proteomics
analysis of large sets of proteins
including sequences
Evolution
DNA
documents hereditary background of organisms
linear sequences determine amino acid sequences
siblings have DNA and protein similarities
"molecular genealogy"
2 closely related species
share a DNA proportion
and protein sequences
than less closely related species