DAT- Chapter 1: Molecules and Fundamentals of Biology

matter

matter

anything that takes up space and has mass.

Element

a pure substance that has specific physical/chemical properties and can’t be broken down into a simpler substance

Atom

the smallest unit of matter that still retains the chemical properties of the element

Molecule

two or more atoms joined together

Intramolecular forces

attractive forces that act on atoms within a molecule.

Intermolecular forces

forces that exist between molecules and affect physical properties of the substance.

Monomers

single molecules that can potentially polymerize.

Polymers

substances made up of many monomers joined together in chains.

Carbohydrates contain

contain carbon, hydrogen, and oxygen atoms

Monosaccharides

are carbohydrate monomers with an empirical formula of (CH2 O)n . “n” represents the number of carbons.

isomers

same chemical formula, different arrangement of atoms

Disaccharides contain two monosaccharides joined together by a

glycosidic bond

dehydration (condensation) reaction

where a water molecule leaves and a covalent bond forms.

hydrolysis

a covalent bond is broken by the addition of water.

Sucrose

disaccharide made of glucose + fructose

Lactose

disaccharide made of galactose + glucose

Maltose

disaccharide made of glucose + glucose.

Polysaccharides contain

contain multiple monosaccharides connected by glycosidic bonds to form long polymers.

Starch

form of energy storage for plants and is an alpha (α) bonded polysaccharide.

amylose

Linear starch

amylopectin.

the branched form of starch

Glycogen

form of energy storage in animals and is an alpha (α) bonded polysaccharide. It has much more branching than starch

Cellulose

structural component in plant cell walls, and is a beta (β) bonded polysaccharide. Linear strands packed rigidly in parallel

Chitin

structural component in fungi cell walls and insect exoskeletons. It is a beta (β) bonded polysaccharide with nitrogen added to each monomer.

Proteins contain 1.—————

These atoms combine to form 2.———-,

which link together to build 3—————

1. carbon, hydrogen, oxygen, and nitrogen atoms (CHON)

2. amino acids

3. polypeptides (or proteins)

A proteome refers to

all the proteins expressed by one type of cell under one set of conditions.

Amino acids

are the monomers of proteins

Amino acid structure includes…

Amino group (NH3), Hydrogen, Carboxyl group (O-C=O), and R-group connected to a central Carbon

Polypeptides are

polymers of amino acids

Polypeptides are joined by ————

peptide bonds

polypeptides are joined by what kind of reaction?

through dehydration (condensation) reactions

The polypeptide becomes an amino acid chain that contains two end terminals on opposite sides.

what are the end terminals called?

N-terminus (amino terminus)

C-terminus (carboxyl terminus)

N-terminus (amino terminus) of a polypeptide is the side that

ends with the last amino acid’s amino group.

The C-terminus (carboxyl terminus) of a polypeptide is the side that

ends with the last amino acid’s carboxyl group.

Conjugated proteins are?

proteins that are composed of amino acids and non-protein components

2 types of Conjugated proteins are?

Metalloproteins (ex. hemoglobin)

Glycoprotein (ex. mucin)

Metalloproteins (ex. hemoglobin)

proteins that contain a metal ion cofactor.

Glycoprotein (ex. mucin)

proteins that contain a carbohydrate group.

Protein structure includes

1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Quaternary structure

1. Primary structure

sequence of amino acids connected through peptide bonds.

2. Secondary structure

intermolecular forces between the polypeptide backbone (not R-groups) due to hydrogen bonding. Forms α-helices or β-pleated sheets

3. Tertiary structure

three-dimensional structure due to interactions between R-groups. Can create hydrophobic interactions based on the R-groups. Disulfide bonds are created by covalent bonding between the R-groups of two cysteine amino acids. Hydrogen bonding and ionic bonding between R groups also hold together the tertiary structure.

4. Quaternary structure

multiple polypeptide chains come together to form one protein

Protein denaturation

the loss of protein function and higher order structures. Only the primary structure is unaffected.

Proteins will denature as a result of…

high or low temperatures, pH changes, and salt concentrations

Protein functions (there are 6)

Storage = Reserve of amino acids

Hormones = Signaling molecules that regulate physiological processes

Receptors = Proteins in cell membranes which bind to signal molecules

Structure = Provide strength and support to tissues (hair, spider silk)

Immunity = Antibodies that protect against foreign substances

Enzymes = Regulate rate of chemical reactions

Catalysts do what to reaction rates?

increase reaction rates

How do catalysts increase reaction rates?

by lowering activation energy of a reaction

The transition state is

the unstable conformation between the reactants and the products.

Catalysts reduce the energy of

the transition state.

Catalysts do NOT what?

shift a chemical reaction or affect spontaneity.

Enzymes act as biological catalysts by

binding to substrates (reactants) and converting them into products.

Active site

Where enzymes bind to substrates and is specific for the substrate that it acts upon

Most enzymes are

proteins

The specificity constant measures

how efficient an enzyme is at binding to the substrate and converting it to a product

The induced fit theory describes

how the active site molds itself and changes shape to fit the substrate when it binds. The “lock and key” model is an outdated theory of how substrates bind.

A ribozyme is

an RNA molecule that can act as an enzyme (a non-protein enzyme).

A cofactor

is a non-protein molecule that helps enzymes perform reactions

A coenzyme is

an organic cofactor (i.e. vitamins). Inorganic cofactors are usually metal ions

Holoenzymes

are enzymes that are bound to their cofactors

apoenzymes

are enzymes that are not bound to their cofactors.

Prosthetic groups

are cofactors that are tightly or covalently bonded to their enzymes.

Enzymes catalyze reactions in the following ways:

● Conformational changes that bring reactive groups closer.

● The presence of acidic or basic groups.

● Induced fit of the enzyme-substrate complex.

● Electrostatic attractions between the enzyme and substrate.

Phosphatase

Cleaves a phosphate group off of a substrate molecule

Phosphorylase

Directly adds a phosphate group to a substrate molecule by breaking bonds within a substrate molecule

Kinase

Indirectly adds a phosphate group to a substrate molecule by transferring a phosphate group from an ATP molecule. These enzymes do not break bonds to add the phosphate group.

Feedback regulation of enzymes

the end product of an enzyme-catalyzed reaction inhibits the enzyme’s activity by binding to an allosteric site.

Competitive inhibition occurs when

an inhibitor competes directly with the substrate for active site binding. Adding more substrate can increase enzyme action.

Noncompetitive inhibition occurs when

the noncompetitive inhibitor binds to an allosteric site (a location on an enzyme that is different from the active site) that modifies the active site. In noncompetitive inhibition, the rate of enzyme action cannot be increased by adding more substrate.

Vmax is

the maximum reaction velocity

Michaelis Constant (KM )

is the substrate concentration [X] at which the velocity (V) is 50% of the maximum reaction velocity (Vmax).

Saturation occurs when

all active sites are occupied, so the rate of reaction does not increase anymore despite increasing substrate concentration (causes graph plateaus).

Competitive inhibition → KM ———, while Vmax ———

Km increases

stays the same

Noncompetitive inhibition → KM ———, while Vmax ———-?

KM stays the same,

while Vmax decreases

enzyme kinetics plot

Lipids contain…

carbon, hydrogen, and oxygen atoms (CHO), like carbohydrates

Lipids have long hydrocarbon tails that make them what?

make them very hydrophobic.

Triacylglycerol (triglyceride) is a lipid molecule with a ———- backbone and ———-

a glycerol backbone (three carbons and three hydroxyl groups)

and three fatty acids (long hydrocarbon tails).

Glycerol and the three fatty acids are connected by

ester linkages

Unsaturated fatty acids

have double bonds.

Saturated fatty acids

have NO double bonds and as a result pack tightly (solid at room temperature).

What is the difference between monounsaturated fatty acids and polyunsaturated fatty acids?

one has 1 double bond while the other fatty acid have has 2 or more double bonds.

what is the difference between cis-unsaturated fatty acids and trans-unsaturated fatty acids?

Cis-unsaturated fatty acids have kinks that cause the hydrocarbon tails to bend. As a result, they do not pack tightly.

Trans-unsaturated fatty acids have straighter hydrocarbon tails, so they pack tightly.

Phospholipids are lipid molecules that have

glycerol backbone, one phosphate group, and two fatty acid tails

Phospholipids have a phosphate group that is polar, while the fatty acids are nonpolar therefore

amphipathic (both hydrophobic and hydrophilic)

Cholesterol is an amphipathic lipid molecule that is a component of the cell membranes. It is the most common precursor to

It is also the starting material for

steroid hormones (lipids with four hydrocarbon rings)

vitamin D and bile acids

What are the factors that influence membrane fluidity:

Temperature - ↑ temperatures increase fluidity while ↓ temperatures decrease it.

Cholesterol - holds membrane together at high temperatures and keeps membrane fluid at low temperatures. (acts kind of as a buffer to counteract temp)

Degrees of unsaturation - saturated fatty acids pack more tightly than unsaturated fatty acids, which have double bonds that may introduce kinks

Lipoproteins

allow the transport of lipid molecules in the bloodstream due to an outer coat of phospholipids, cholesterol, and proteins.

Low-density lipoproteins (LDLs) is also called “Bad cholesterol ”, why is this?

can cause vessel blockage and heart disease.

Low-density lipoproteins (LDLs)

have low protein density and work to deliver cholesterol to peripheral tissues.

High-density lipoproteins (HDLs)

have high protein density and take cholesterol away from peripheral tissues

High-density lipoproteins (HDLs) is also called “Good cholesterol ” because why?

they deliver cholesterol to the liver to make bile (reduces blood lipid levels).

what is used mainly as hydrophobic protective coatings? and what are there composition?

Waxes which are simple lipids with long fatty acid chains connected to monohydroxy alcohols (contain a single hydroxyl group) through ester linkages

Carotenoids

lipid derivatives containing long carbon chains with conjugated double bonds and six-membered rings at each end. They function mainly as pigments.

Sphingolipids

have a backbone with aliphatic (non-aromatic) amino alcohols and have important functions in structural support, signal transduction, and cell recognition.

Glycolipids

are lipids found in the cell membrane with a carbohydrate group attached instead of a phosphate group in phospholipids. Like phospholipids, they are amphipathic and contain a polar head and a fatty acid chain.

Nucleic acids contain what elements

carbon, hydrogen, oxygen, nitrogen, and phosphorus atoms (CHONP)

Nucleic acids contain

nucleotide monomers that build into DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) polymers

Nucleosides

contain a five-carbon sugar and a nitrogenous base.

Nucleotides

contain a five-carbon sugar, a nitrogenous base, and a phosphate group.