1.

1 structure of water and hydrogen bonding

-the subcomponents of biological molecules determine the properties of
that molecule
-water is composed of 2 main elements, oxygen and hydrogen, in a 1:2
respectively
-covalent bond is a term used to describe the bond type in which atoms
share electrons
-oxygen is more electronegative compared to
hydrogen, resulting in an unequal sharing of
electrons between oxygen and hydrogen
-covalent bonding can result in polarity when
there are differences in atomic electronegatives,
a water molecule has polarity.

-a hydrogen bond is a weak bond interaction between the negative and

positive regions of two separate molecules
-water can form hydrogen bonds with other water molecules or with other
charged molecules
-when two of the SAME molecules form hydrogen bonds with each other
this is called cohesion.
-when two
DIFFERENT
molecules form
hydrogen
bonds with
each other this is
called
adhesion.
living systems depend upon properties of water
-the hydrogen bonds between water molecules can result in surface
tension
-cohesion, adhesion, and surface tension allow for water to demonstrate
additional chemical behaviors known as emergent properties
-life depends upon water’s properties
-surface tension is a result of increased hydrogen bonding forces between
water molecules at the surface. (leaf floating on water, droplet on penny)
-water’s adhesive property gives water a high solvency ability in its liquid
state (salt in water)
-water’s cohesive property allows for unique hydrogen bond interaction to
occur when water is in a solid state, making ice less dense than liquid
water (ice floating)
-water’s cohesive property allows it to absorb a lot of thermal energy
before changing chemical states, resisting sudden changes in
temperature (fish in water)
-capillary action is a result of both the adhesive and cohesive properties
of water (adding a thin tube to a liquid)

1.1 take aways:

-water contains 1 oxygen atom covalently bonded to 2 hydrogen atoms
-oxygen has a higher electronegativity compared to hydrogen resulting in
a water molecule having polarity
-polarity allows molecules to form hydrogen bonds when oppositely
charged regions of two molecules interact
-the term cohesion refers to molecules of the same type forming hydrogen
bonds with one another and adhesion refers to different types of
molecules forming hydrogen bonds with one another
-living systems depend upon water’s properties, like surface tension

1.2 elements of life

-living systems require a constant input of energy
-the law of conservation of energy states that energy cannot be created or
destroyed only transformed
-living systems follow the laws of energy
-living systems need a constant input of energy to grow, reproduce, and
maintain organization
-living systems mainly use the energy stored in chemical bonds (working
out)
-living systems require an exchange of matter
-atoms and molecules from the environment are necessary to build new
molecules
-carbon is used to build biological molecules such as carbohydrates,
nucleic acids, and lipids
-nitrogen is used to build proteins and nucleic acids
-phosphorus is
used to build
nucleic acids and
certain lipids

-carbon is used to build macromolecules

-carbon can bond to other carbon atoms creating carbon skeletons to
which other atoms attach
-carbon skeletons allows for the creation of very large and complex
molecules
-carbon containing molecules can be used to store energy
-carbon containing molecules can be used to form basic cell structures

1.2 take aways:

-living systems need a constant input of energy to grow, reproduce, and
maintain organization
-atoms and molecules from the environment are necessary to build new
molecules
-carbon is used to build all macromolecules, store energy and form cells
-nitrogen is used to build proteins and nucleic acids
-phosphorus is used to build nucleic acids and certain lipids

1.3 introduction to macromolecules

-monomers have important properties
-monomers are chemical subunits used to create polymers
-polymer is a macromolecule made of many monomers
-a covalent bond is formed between two interacting monomers
-monomers have specific chemical properties that allow them to interact
with one another
-polymers are specific to the monomers they consist of

-dehydration synthesis reactions form covalent bonds

-dehydration synthesis reactions are used to create macromolecules
-the subcomponents of a water molecule (H and OH) are removed from
interacting monomers and a covalent bond forms between them
-the H and OH join together to form a molecule of water, water is a by
product of this reaction

-hydroysis reactions cleave covalent bonds

-polymers are hydrolyzed (broken down) into monomers during a
hydrolysis reaction
-covalent bonds between the monomers are cleaved (broken) during a
hydrolysis reaction
-a water molecule is hydrolyzed into subcomponents (H and OH) and each
subcomponent is added to a different monomer
-a dehydration synthesis creates carbohydrates
-carbohydrate monomers have hydroxides (OH) and hydrogen atoms (H)
attached
-one monomer will lose an entire hydroxide while the other monomer will
only lose the hydrogen from a hydroxide
-a covalent bond will form where the hydroxide and hydrogen atom were
removed
-the hydroxide (OH) and hydrogen (H) join forming a water molecule (H2O)

-a dehydration synthesis creates proteins

-protein monomers are called amino acids
-each amino acid has an amino group (NH2) terminus and a carboxyl
group (COOH) terminus
-a hydroxide (OH) is lost from the carboxyl group of one amino acid and a
hydrogen atom (H) is lost from the amino group of another amino acid
-a covalent bond will form between the monomers in the location where
the hydroxide and hydrogen atom were removed
-the hydroxide (OH) and the hydrogen atom (H) will join forming a water
molecule
-proteins can undergo hydrolysis reaction
-covalent bonds between amino acids can be cleaved (broken)
-a water molecule is hydrolyzed and each subcomponent of water (H and
OH) will be bonded to different amino acids
-the result is separate amino acid monomers

1.3 take aways:

-all monomers contain carbon and are used to build biological
macromolecules
-covalent bonds are used to connect monomers together
-dehydration synthesis reactions are used to create biological
macromolecules and water is an additional product
-hydrolysis reactions use water to break down biological macromolecules

1.4 carbohydrates
-monosaccharides (simple sugars) are the monomers for polysaccharides
(complex carbohydrates)
-monosaccharide monomers are connected by covalent bonds to form
polymers

-the structure of a polymers (branched or linear) determines its function

-glycogen: main storage form of glucose in animals and provide quick
energy when needed
-cellulose: structural component in plant cell walls, providing rigidity and
strength
-starch (amylopectin): major component of starch in plants which a
branched structure for rapid glucose release
-starch (amylose): major component of starch in plants which store energy
in long, unbranched chains of glucose

1.4 take aways:

-monosaccharides are the building blocks of polysaccharides (complex
carbs)
-covalent bonds link monomers to form complex carbohydrate polymers
-polysaccharides can be linear or branched in structure
1.5 Lipids
-Lipids are typically nonpolar, hydrophobic molecules whose structure
and function are derived from the way their subcomponents are

assembled.

-some lipids (triglycerides and phospholipids) contain fatty acids

-what role do bonds play in lipids?

-first image is saturated, second is unsaturated.

-double bonds in unsaturated fatty acids results in a kink in the carbon
chain. The more double bonds in the fatty acid tail, the more unsaturated
a lipid becomes.
-the more unsaturated = more liquid
Types of lipids

-fats provide energy storage and support cell function. In some cases they
can also provide insulation to help keep mammals warm.
-steroids are hormones that support physiological functions including
growth and development, energy, metabolism, and homeostasis
-a common steroid found in cell membranes is cholesterol, which is
essential to structural stability to animal cell membranes.
-phospholipids group together to form the lipid bilayer in plasma and cell
membranes.

1.5 take aways:

-lipids are nonpolar, hydrophobic molecules with structures that
determine their functions
-fatty acids can be saturated (single bonds) or unsaturated (one or more
double bonds, creating kinks)
-the more double bonds a fatty acid has, the more unsaturated it
becomes, making lipids more liquid at room temperature.
-lipids serve vital roles as energy storage, insulation, and cell membrane
structure.
-examples of lipids include fats, steroids (like cholesterol and hormones),
and phospholipids, which form cell membranes.
1.6 nucleic acids
-similarities between DNA and RNA:
-both are assembled from nucleotide subunits which are composed of a …
-5 carbon sugar
-phosphate group
-nitrogenous base
-each nucleotide monomer is connected by covalent bonds forming the
sugar-phosphate backbone
-each linear strand of nucleotides has a 5’ end and a 3’ end
-the nitrogenous bases are perpendicular to the sugar-phosphate
backbone

-differences between DNA and RNa

-DNA contains deoxyribose and RNA contains ribose
-DNA contains thymine and RNA contains uracil
-DNA is usually double stranded; RNA is usually single stranded
-the two DNA strands in double stranded DNA are antiparallel

1.6 take aways:

-both DNA and RNA from nucleotide subunits connected by covalent
bonds to form linear molecules with 5’ and 3’ ends. Each nucleotide is
composed of a sugar, phosphate group, and nitrogenous base.
-differences include the type of sugar, one of the nitrogenous bases (RNA
contains uracil whereas DNA contains thymine), and number of strands.
DNA has two nucleotide strands that are antiparallel.

-directionality of the subcomponents influences structure of nucleic acid

polymers
-the linear sequence of all nucleic acids is characterized by a 3’ hydroxyl
and a 5’ phosphate of the sugar in the nucleotide
-DNA is a nucleic acid polymer containing two strands, each strand in an
antiparallel 5’-3’ direction
-adenine – thymine base pairs are held together by 2 hydrogen bonds and
Guanine – cytosine base pairs are held together by 3 hydrogen bonds
-hydrogen bonds between base pairs in a DNA molecule stabilize the
molecule’s structure

-the linear sequence of nucleotides encodes biological information

-any change to the sequence of the nucleotides may lead to a change in
the encoded information
-during the synthesis of nucleic acid polymers, nucleotides can only be
added to the 3’ end
-covalent bonds are used to connect free nucleotides to the strand

1.6 takeaways:
-the linear sequence of all nucleic acids is defined by the 3’ hydroxyl and 5’
phosphate of the sugar in the nucleotide
-DNA is structured as an antiparallel double helix with two strands running
in opposite 5’-3’ directions. This allows for the two strands of DNA to be
held together by hydrogen bonds between the base pairs. A–T held
together by 2 hydrogen bonds; G–C held together by 3 hydrogen bonds
-during DNA and RNA synthesis, nucleotides can only be covalently added
to the 3’ end of a growing nucleotide strand
-changes in the linear sequences of the nucleotide bases may lead to
differences in the encoded biological information or the structural
stability of the molecule

1.7 proteins
-directionality of the subcomponents influences structure of proteins
-proteins comprise linear chains of amino acids that have directionality
with an amino terminus and a carboxyl terminus
-amino acids are connected by the formation of covalent bonds at the
carboxyl terminus of the growing peptide chain

-4 elements of protein structure:

1.7 take aways
-amino acids have directionality with an amino terminus (NH2) and a
carboxyl terminus (COOH) on the other. Amino acids are added to the
carboxyl terminus of a growing peptide chain by the formation of covalent
bonds
-there are 4 elements of protein structure: primary, secondary (alpha
helices and beta sheets), tertiary, and quaternary. Levels of structure
beyond the primary linear sequence of amino acids arise through local
folding and other chemical interactions among amino acids. The resulting
3D shape gives rise to the protein’s specific function.
-a change in an amino acid subunit at the primary level of structure may
lead to a change in the structure and function of the protein at
subsequent levels.

-amino acids are composed of a central carbon atom with a hydrogen

atom, a carboxyl group, an amine group, and a variable R group
covalently bonded to it.

-proteins comprise linear chains of amino acids connected by the

formation of covalent (peptide) bonds that form between a carboxyl group
(-COOH) of one amino acid and an amine group (-NH2) of the next amino
acid, resulting in a growing peptide chain

-the specific sequence of amino acids in proteins will determine its overall
shape
-primary structure

-secondary structure
-hydrogen bonding between the atoms of the polypeptide backbone of
the amino acid side chain

-terriary structure
-the three dimensional shape of the tertiary structure of a protein results
from the hydrogen bonds, hydrophobic interactions, ionic interactions, or
disulfide bridges.

-Quaternary structure
-the quaternary structure arises from interactions between multiple
polypeptides
1.7 take aways:
-proteins are made of linear chains of amino acids connected by covalent
(peptide) bonds
-each amino acid has a central carbon, a hydrogen atom, a carboxyl
group, an amine group, and a variable R group that affects its properties
-the sequence of amino acids determines a protein;s primary structure
and overall shape
-secondary structures, such as alpha-helices and beta-pleated sheets,
form through hydrogen bonding
-tertiary structure results from various interactions, including hydrogen
bonds, hydrophobic interactions, ionic interactions, and disulfide bridges
-quaternary structure forms when multiple polypeptides interact, and all
four levels of structure determine a protein’s function.