Download Topic 2.1-2.4 Molecular Biology

IB BIOLOGY
Topic 2.1- 2.5
Molecular Biology
Biochemistry
• Branch of organic
chemistry that attempts
to explain chemical
characteristics and
reactions that occur in
living organisms.
• Biomolecules:
–
–
–
–
Carbohydrates
Lipids
Proteins
Nucleic Acids
Molecules to Metabolism
• Metabolism –
– Collection of chemical
reactions involving
biomolecules, that occur
during living processes
– Reactions occur in predictable
patterns
• Ex: Insulin
– Insulin is a protein hormone
that facilitates the movement
of glucose from the blood to
the inside of the cell
– Binds to hormone receptor
outside of cell glucose
channels open
– Glucose in high concentration
outside of cell glucose
continues to diffuse into cell
– Receptor molecule and
protein channel are both
coded for by DNA
Carbon-based Life
• Organic moleculecontains carbon
• Ex: CO2
• Inorganic molecule- no
carbon
• Ex: H2O
• All biomolecules are
organic
• Carbon always forms 4
covalent bonds with
other elements
• Other elements
common to organic
molecules:
– H, O, N, P
Biochemical Compounds
• Polymers of
biomolecules are
composed of
monomers.
• Pg. 54
• Fill in charts provided,
both Table 2.1 and 2.2
Metabolism Controlled by Enzymes
• Molecular movement in
an aqueous
environment causes
collisions among
molecules
• All reactions within
cells-metabolism
• Determining factors of
Reactions:
– Identity of colliding
molecules
– Orientation of colliding
molecules
– Speed of colliding
molecules
• Enzymes increase odds
of collisions reaction
Enzymes
• Enzymes are proteins
• Ex: Formation of ATP
that catalyze chemical
– ADP + Pi  ATP
reactions
– Binding a phosphate
takes energy (food,
• There are sites on the
sunlight)
enzyme that are specific
– ATP synthase increases
to the binding of a
the odds of a collision
particular reactant, or
reaction
substrate
– Facilitated the covalent
bond (adding the
phosphate)
Enzymes, cont.
• Enzymes are used in the
following:
–
–
–
–
–
–
Replication of DNA
Synthesis of RNA
Synthesis of proteins
Cellular respiration
Photosynthesis
Digestion
Catabolism and Anabolism
• Catabolic reactions:
– Break molecules down
– Break polymers to
monomers
• Hydrolysis:
– Breaking molecules
using an H2O molecule
• Anabolic reactions:
– Build molecules
– Add
monomerspolymers
• Condensation:
– Building molecules by
removing H2O molecule
https://www.youtube.com/watch?v=D
hHoz-W_3Rk
Catabolic Reaction
Anabolic Reaction
Water
• Water is solvent of life
• Living cells are in aqueous
environment
• Structure:
– Covalent bonding of H to O
– Result: partially positive
and partially negative poles
– Hydrogen bonding does
occur between hydrogens
of H2O molecules
• Ephemeral
• Polarity– Partially positive and
partially negative poles
– Affects orientation of
molecule in solution
https://www.youtube.com/watch?v=nSENolWbyYQ
Water, cont.
• Cohesive properties:
– Attracted to each other
– Hydrogen bonding
occurs
• Locked into place ice
• Liquid water lots of
movement between
molecules
• Ephemeral H Bonding:
– Why H2O forms droplets
– Why H2O has surface
tension
– Why H2O moves in a
column in plant tissues
Water, cont.
• Adhesive Properties:
– Attraction between two
unlike molecules
– Water “beads” on many
surfaces
– Adhesion keeps water
column in plants from
dropping
• Attraction of H2O to
cellulose
Water, cont.
• Thermal Properties
– High specific heat
• Can absorb or give off lots
of heat without affecting
H2O temperature
• Heat stabilizing
– High heat of vaporization
• Absorbs lots of heat as it
evaporates
– Ex: perspiration
Water, cont.
• Solvent properties:
– Like dissolves like
– Medium of biochemistry
• Animals:
– Blood
• High water content
• Solutes in blood:
–
–
–
–
Glucose
Amino acids
Fibrinogen( clotting)
Hydrogen carbonate
ions(transport of CO2)
• Plants:
– Vascular tissue:
• Xylem- carries H2O up
from roots
• Phloem- carries dissolved
sugars down from leaves
to rest of plant
Water, cont.
• Hydrophylic- H2O loving
– Polar
– Majority of
biochemically important
molecules are polar
– Polar solvent easily
dissolves polar solute
– Ex: carbohydrates
soluble due to hydroxyl
(alcohol) groups
• Hydrophobic- H2O
hating
– Non-polar
– Mainly C and H
compounds
• Ex: lipids, methane
• Proteins-differentially
polar depending on
arrangement
Table 2.4 pg 66
• Complete chart
provided
Carbohydrates and Lipids
• Monosaccharides
– Building blocks of
polysaccharides
– Most common:
• Trioses C3H6O3
• Pentoses C5H10O5
• Hexoses C6H12O6
• Condensation reactions
in monosaccharides
– Joins monomer larger
polymer
Functions of Major Polysaccharides
• Cellulose:
• Glycogen:
– Major component of plant cell
walls, gives rigidity and support to
roots, leaves, stems
– Not digestible in humans
• Dietary fiber
• Starch:
– Organic product of photosynthesis,
stored as granules in chloroplasts,
or roots (storage structure)
– Two subcomponents:
• Amylopectin
• Amylose
– 3 glucose carb is straight chained
– Excess glucose stored in liver and
muscle
– Only 24 hour supply stored
– Requires enzymes to break it down
to glucose for cellular use
• All: monomer-glucose
Fatty Acids
• All have carboxyl group
– (-COOH) at end
• All have methyl group
– CH3 at other end
• All have multiple CH2
groups in between
• Saturated Fatty Acids:
– All carbons are saturated
with hydrogen, no bends
in the chains
– Animal products;
• Butter, bacon, fat in red
meat
• Solid at room
temperature
Fatty Acids, cont.
• Monounsaturated FAs
– One double bond in
chain
• Polyunsaturated FAs
– At least 2 double bonds
– Plant based: olive oil
– Liquid at room
temperature
Fatty Acids, cont.
• Hydrogenation: cis and
trans fatty acids
– Double bonds eliminated,
totally or partially by
adding hydrogens during
processing
– Straightens out bent shape
– Naturally curved: cis FAs
– Hydrogenated: trans Fas
– Trans FAs behave like
saturated fats
• Omega-3
– Cis FA
– Fish oils
Condensation Reactions
• Formation of
triglyceride lipids:
– Fats in animal cells, oils
in plant cells
– Vary greatly
Energy Storage in Humans
• Glucose glycogen in
liver and muscle tissue
• Triglyceride
lipidsadipose tissue
– Twice the energy per
gram
– Insoluble in water
– Do not upset osmotic
balance
• Glucose stored in cells
would attract water due
to concentration
gradient difference
Chylomicrons
• Small particle made of fat
and protein
• Produced in alimentary
canal and released into
the bloodstream
• Transport fats to the liver
and other tissues
• LDL- low density
lipoproteins
• Elevation of these LDL
levels is undesirable for
health
Calculating BMI
• Uses weight and height
• Formulas:
– Metric: weight(kg) /
height(m)
– Imperial: weight(lb.) /
height(in) x height(in) x
703
Proteins
• Formation of
polypeptides:
– Cells use 20 naturally
occurring AA to make
proteins
– Polypeptide encoded by
DNA
– Genes can be expressed
differently for different
cellular proteins
• Pancreas- translates
DNA sequence that
encodes insulin
• Humans:
– 20,000-25,000 genes per
cell
– Grape plants- 30,000
– Chickens- 17,000
• All genes encode for
possible polypeptides
found in that organism
Proteins, cont.
• Synthesis of
polypeptides:
condensation reaction
– Sequence of AAs
determined by DNA, but
reactions are identical.
• Variability of
Polypeptides:
– Each has own AA
sequence and own
folding pattern
Proteins, cont.
• Levels of polypeptide and
protein structure
– (Complete Table 2.8 with
grid provided )
– Primary structure:
• Sequence of AAs
– Secondary structure:
• Repetitive shapes of either
helixes or pleated sheets
– Tertiary structure:
• A globular shape (enzymes)
– Quaternary structure:
• Two or more polypeptides
combine to make a single
functional protein
(hemoglobin)
Proteins, cont.
• Proteins vs. polypeptides:
– Proteins are organic
substances consisting of
covalently bonded amino
acids, ready to carry out
function
– Polypeptides are single AA
chains with its own
primary structure that may
or may not be able to serve
a biochemical function
without further
modification
• Genome:
– Unique DNA sequence of
one individual
• Proteome:
– Unique set of proteins for
each individual
Denaturing Proteins
• Intramolecular bonds
that determine protein
shape can be altered by
temperature and pH.
– Alteration of unique 3-D
shape renders them
useless in biochemical
reactions
– Can be reversible if most
covalent bonds remain
when temperature and
pH return to normal