Bio Lecture Chapter 3

organic

carbon compounds

inorganic

non-carbon compounds, except CO2

versatile atom

carbon, has 4 valence electrons to form 4 stable covalent bonds

carbon

versatile atom, unparalleled in its ability to form large, complex and diverse molecules, building code for the architecture of living molecules, backbone of life

carbon

can form single, double, and triple bonds, like to form bonds with carbon

single bond

can rotate freely

double and triple bonds

can't rotate and are fixed

hydroxyl group (-OH)

alcohol, polar, dehydration

carbonyl group (C=O)

ketone aldehyde, polar

amino group (-NH2)

amine, polar, basic/positive charged

carboxyl group (-COOH)

carboxylic acid, or organic acid, polar, weak acid/negative charged

sulfhydryl group (-SH)

thiol, polar, from disulfide bond

phosphate group (OPO3^2-)

organic phosphate, polar, negative charged

methyl group (-CH3)

methylated compound, non-polar

carbon

can form new molecules either linear, branching, or rings

isomer

are compounds with the same molecular formula but different structures and properties

structural isomer

have different covalent arrangements of their atoms

Cis-trans/geometric isomer

have the same covalent bonds but differ in spatial arrangements

enantiomers/ stereoisomers/ optical isomers

are isomers that are mirror images
of each other

polymer

Very large chain-like organic molecules
Formed from many smaller unit molecules called "monomers

monomers

in the polymer chain can be identical or different

polymers

have different properties than monomers from which it was formed and can take many different shapes
-chains, lattices, helices, sheets

macromolecules

Majority of them are polymers
There are four categories of large molecules in cells:
carbohydrates (monosaccharides), lipids (glycerol), proteins (amino acid), and nucleic acids (nucleotides)

carbohydrates

Contain carbon, hydrogen, and oxygen in a 1:2:1 ratio
Empirical formula CnH2nOn (1 carbon for each water)
Monomer is simple sugar, monosaccharide
Simple sugars combined to form complex carbohydrates
Disaccharide
Polysaccharide
Attached to each other by th

carbohydrate

Used for:
main energy source (food)
structure and protection
essential part of DNA and RNA

glucose

our blood sugar and main source of energy, short term ready for use energy

fat

another energy source for long term use, stores extra sugar

monosaccharides

classified by the location of the carbonyl group (as aldose or ketose)
The number of carbons in the carbon skeleton (trio-, tetro-, pento-, hexo- and hepto-)
glucose is the most important

monosaccharide

In aqueous (watery) solutions, ____________ molecules rearrange to form ring structures
Glucose Galactose
Fructose
1?2
glycosidic bond
Dihydroxyacetone
Ribulose
?-glucose, with the C1 -OH group pointing below the plane of the ring
?-glucose, with the C1 -

glucose

monosaccharide, main fuel that cells use for energy, blood sugar
found in sport drinks

fructose

monosaccharide, found in fruits, sweetest

galactose

monosaccharide, called "milk sugar

disaccharide

double sugar, they're made by joining two monosaccharides
Involves removing a water molecule (condensation) and forming a glycosidic bond
Break down by hydrolysis (adding a molecule of water)

sucrose

(table sugar) is composed of glucose + fructose

lactose

(milk sugar) is composed of galactose + glucose

maltose

(grain sugar) is made of 2 glucose molecules

dehydration reaction

removes water and forms glycosidic bond

hydrolysis

add water to break down bonds

starch

in plants
Consists entirely of glucose monomers
Plants store starch as granules within
chloroplasts and other plastids
Potatoes and grains are major sources of starch in the human diet

glycogen

in animals
Animals store excess sugar in the form of glycogen in muscle and liver, short term energy storage
poly-glucose

cellulose

the main component
of plant cell wall
Is the most abundant organic compound on Earth
It forms cable-like fibrils in the tough cell walls
It is a major component of wood
It is also known as dietary fiber
Our body cannot digest i

lipid

Hydrophobic -"water fearing", Do Not mix with water, such as fats, oils, and waxes
Not polymer by definition, but macro-molecule

neutral lipids

triglycerides, true fats, Fatty acids + glycerol

phospholipids

major component of cell membranes

steroids

some hormones, cholesterol

lipids

Fats for long term energy storage
help to insulate the body
cushion and protect organs
Triglycerides help make bird feathers waterproof

photosynthesis

purpose is to produce glucose, stores sun energy and generates glucose

starch

plant version of poly-glucose

fatty acids

Long chains of carbon and hydrogen with a carboxyl group (COOH) at one end
The most common __________ have chains of 14 to 22 carbons
As chain length increases, fatty acids become less water-soluble and more oily

saturated fatty acids

have the maximum number of hydrogens bonded to the carbons (all single bonds between carbons), solid at room temp (butter)

unsaturated fatty acids

have at least one double bond between carbons, liquid at room temp (oil)

triglycerides/fats

Composed of 1 glycerol & 3 fatty acid chains

glycerol

forms the backbone of the fat triglyceride

ester linkage

Bond between fatty acids and glycerol formed by dehydration synthesis

trans-fat

plant oils converted commercially to saturated fats by hydrogenation

essential fatty acids

e.g. omega-3 fatty acids

phospholipid

are diglycerides in which a hydrophilic phosphate group, instead of a third fatty acid, is bonded to the glycerol.
The membranes of living cells are formed by a double layer of _____________

steroids

Four rings of carbon and hydrogen with an assortment of functional groups
Essential components of cell membranes and many hormones

cholesterol

steroid, component of plasma membranes, can't dissolve in the blood. It must be transported through your bloodstream by carriers called lipoproteins, low-density lipoprotein (LDL, bad cholesterol) vs. high-density lipoprotein (HDL, good cholesterol)

steroid hormones

sex hormones and adrenal gland cortex hormones

sex hormones

steroids, estrogen and testosterone

adrenal gland cortex hormones

steroids, corticosteroids and calcitriol for glucose and calcium metabolic regulation respectively

bile salt

Derived from steroids

phospholipid bilayer

hydrophilic head faces outside because our body is mostly made up of water

phospholipid

has 2 tails instead of 3 and has a phosphate group

protein

Are the most abundant and important organic molecules
Polymers made up of amino acids
Include enzymes, hemoglobin, non-steroid hormones, antibodies

protein functions

Support - structural proteins
Movement - contractile proteins
Transport - membrane channels, hemoglobin Communication - receptors
Regulation - transcription factors
Metabolic Regulation - enzymes
Coordination and Control - hormones
Defense - antibodies

glucose, fat, and protein (last resort)

3 types of energy source

amino acid structure

A central carbon with 4 groups bonded to it:
Glycine (GlyorG)
Alanine (AlaorA)
Valine (ValorV)
Leucine (Leuor L)
Isoleucine (IleorI)
Amino acids link together to form polypeptide
Side Group
Amino group -NH2
Carboxyl group -COOH Hydrogen -H
Side group -R

r group

ary in composition, give each amino acid different properties

amino acids

link together to form polypeptide

dehydration

when amino acids link together to form polypeptides

peptide bonds

connects 2 amino acids, covalent bonds between amino acids

polypeptide

has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus

disulfide bond

-SH groups of two Cysteine amino acids can form a disulfide bond, only between the side chains of two cysteines

primary structure

The linear sequence of amino acids along a polypeptide

secondary structure

when polypeptide chains coil or fold due to hydrogen bonds
a-helix and b-pleated sheets

tertiary structure

further folding through R groups interacting with each other
the final shape of a single polypeptide chain
The distribution and 3-D arrangement of side groups, in combination with their chemical properties, determine the overall chemical activity (functio

quaternary structure

multiple subunits
Multiple polypeptide/subunit chains, each can be encoded by different gene

colagen

single protein made up of 3 of the same polypeptide

fibrous proteins

structural sheets or strands

globular proteins

in the watery environment of a cell, most proteins become globular in their tertiary and quaternary structure

protein function

depends on shape to recognize/fit and bind to another molecule specifically

protein shape

determined by primary sequence of amino acids
Because of the reversible nature of those weak forces participating in forming the shape, within certain range, the shape is reversible
Dynamic
Flexible and inducible, allowing them to undergo
conformational c

denaturation

when protein structure loses their shape and function

primary structure

a slight change in this can affect a protein's structure and ability to function
ex. sickle cell anemia

tertiary structure

Attractions between positively and negatively charged side groups and polar or nonpolar associations also contribute to ______________

proteins

link with lipids to form lipoproteins, which form parts of cell membranes, as well as transport fats
Dynamic
Flexible and inducible, allowing them to undergo limited
Also link with carbohydrates to form glycoproteins, which function as enzymes, antibodies

proteoglycans

large polysaccharides + core protein, extracellular matrix components

proteins

link with nucleic acids to form nucleoproteins, which form structures such as chromosomes, ribosome
can fold into a higher structure

nucleic acids

Store genetic information, coding for proteins
Complex polymers constructed of nucleotide monomers

nucleotides

composed of three parts
1. A 5-carbon (pentose) simple sugar molecule (either ribose or deoxyribose) 2. 1-3 phosphate group
3. Nitrogenous base (5 types)
Adenine (A), Guanine (G), Thymine (T), Cytosine (C), Uracil (U)
Ribo- / Deoxyribo-nucleotide

DNA

nucleic acid, deoxyribonucleic acid (Deoxyribose sugar; bases A, T, G, C), gets ride of oxygen

RNA

nucleic acid, ribonucleic acid (Ribose sugar; bases A, U, G, C), extra oxygen

phosphodiester bond

Nucleotide monomers linked together by ____________
link the phosphate group on the 5? C of sugar #1 and the 3? C of the sugar #2
through hydrolysis synthesis
Sugar and phosphate groups form backbone
Nitrogenous base stick out

purine

adenine and guanine (A and G), 2 rings Pure As Gold

pyrimidine

thymine, cytosine, uracil (T, C, U)

nucleotide

is a nucleoside phosphate

DNA

Composed of two strands of nucleotide bases
Double helix structure, twisted ladder

antiparallel

DNA, the two strand run in 5'3' opposite direction from each other

chromosome

one single DNA molecule

gene

a region of DNA (segment of nucleotide sequence) that encodes functional molecules

genome

all the genetic material of an organism

hydrogen bonding

holds together the base pairing of DNA and RNA (secondary structure)

triplet

codes for a specific amino acid or tells the cell to start or stop making a protein.

RNA

single stranded, complementary pairing can also occur between two ______ molecules or between parts of the same molecule
T is replaced by uracil (U), so A - U pair
Many types
The hydroxyl group in ribose makes it less stable than DNA
Considered older than

RNA

Mediate between DNA and protein synthesis Regulate gene expression
Catalyze biological reactions

ATP

High energy compound
Direct energy provider for almost all the cellular and physiological processes, e.g. chemical reactions, molecule transportation, cell division, muscle contraction, absorption
universal energy currency (produced in all organisms)

GTP

Energy source for some processes, e.g. protein synthesis
Plays essential role in signal transduction

ATP

Energy is stored in the chemical bonds of phosphate groups
Breaking the last phosphate bond releases energy for cellular
work and produces ADP and a free phosphate

ADP

can be recycled to make more ATP, half charged

metabolism

All chemical reactions that occur in living organisms

catabolism

the breaking down of large organic molecules

anabolism

the building up of components of cells

cellular respiration

break down glucose to generate energy

enzymes

are crucial to metabolism, globular proteins, control the rate of chemical reactions by weakening bonds, thus lowering the amount of activation energy Eact needed for the reaction
Their folded conformation creates an area known as the active site

metabolic pathways

The chemical reactions of metabolism are organized into ____________
One chemical is transformed through a series of steps into another chemical, by a sequence of enzymes

metabolic turnovers

lets your body grow, change, and adapt to new conditions and activities
Your body recycles and renews all of its chemical components at intervals ranging from minutes to years

enzyme

lowers energy barrier for the chemical reaction to occur at normal body temp, have protein structure, not a reactant or product (3rd party), does not change from reaction, recycled

cofactor

An ion or molecule that binds to an enzyme before substrates can bind

coenzyme

Nonprotein organic cofactors (vitamins)