BIO 151

Units 2-4

What does the # of protons determine?

Determines identity of the atom (Atomic #)

What does the # of electrons determine

Determines the bonding behavior of the atom and its charge.

What does the # of neutrons

Determines the mass or isotope of an atom

CHNOPS

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur.

Atomic mass (Neutrons)

Add the amount of Protons and Neutrons together

Isotopes

Atoms with same # of protons, but different amount of neutrons = different atomic mass

The # of Electrons

determines how atoms will bond with other atoms

Orbitals

Outside the nucleus of an atom, can hold 2 electrons

Orbital Shells

1st shell has only 1 orbital = 2 electrons

2nd shell has 4 orbitals = 8 electrons

2nd shell etc. can each fit 8 electrons

Distance found between the nucleus determines which electron shell an electron is found in

Outermost Shell

# of electrons in the Valence Shell determines the reactivity of the atom

Chemical Bonds

Attractive forces holding atoms together to form a molecule.

Ionic Bond

Electron ‘stealing’, the transferring of electrons from one atom to another

Formed between a metal and non-metal

Covalent Bond

Electron ‘sharing’, Two atoms share a pair of valence electrons

Formed between two non-metals

Hydrogen Bond

Doesn’t alter the amount of valence electrons

Attraction between two polar molecules

_____ are weak individually, but strong collectively

Non-polar Covalent Bond

If two atoms are from the same element, they share the electrons equally

Charge is evenly distributed, more or less neutral, mostly C & H

Polar Covalent Bond

Two different atoms share electrons, one will attract more strongly

Partial + / - charge, often includes F, O, and or N

Electronegativity (EN)

How strong an atom pulls electrons towards itself

Stronger atom will have a slight - charge while the weaker will have a slight + charge

Two atoms are similar in EN, their bond is PRACTICALLY non-polar

Two atoms have a huge difference in EN, their bond is polar

‘Like Dissolves Like’

Polar substances dissolve well in polar solvents (HYDROPHILIC)

Non-Polar substances dissolve in non-polar solvents (HYDROPHOBIC)

POLAR molecules dissolve in water

Water Properties

Extensive H-Bonding among water molecules creates a number of unique properties

• Ice floats

• High specific heat and heat of vaporization

• Cohesion/Surface Tension

• Excellent Solvent

Ice Floats

Liquid water molecules move, but in a solid state, H-bonds lock the molecules into a rigid lattice structure

• Molecules are more spread apart in ___ than in water

• Lower density means it floats

• __ insulates the water from cold air above

High Heat of Vaporization

Takes a large amount of energy to change states from liquid to gas

H-Bonds must be broken

Evaporation has a cooling effect on the environment

High Specific Heat

Takes a lot of energy to warm up water

H-Bonds must be broken to increase molecular movement

Helps keep temp. constant

Cohesion/Surface Tension

Surface of water is difficult to puncture bc the molecules are tightly bonded

Carbon

Forms 4 covalent bonds

4 electrons in the valence shell (outermost)

PCLN / Macromolecules

• Proteins

• Carbohydrates

• Lipids

• Nucleic Acids

All polymers : repeating smaller molecules (monomers)

Functional Groups

Small groups of atoms found in biological molecules

Different groupings of atoms within molecules that have their own characteristic properties

Hydroxyl

Polar, H-bond with water help dissolve molecules

Aldehyde

Important in building molecules and energy releasing reactions

Keto

Body burns fat for energy, instead of carbohydrates

Carboxyl

Acidic, Ionizes in living tissues to form, Some carboxylic acids are important in energy releasing reactions

Amino

Found in all amino acids which are building blocks of proteins

Phosphate

Acidic, crucial role in ATP, nucleic acids (DNA,RNA), and cell membrane components (phospholipids)

Sulfhydryl

By giving up a H, two -SH groups react to form a disulfide bridge, thus stabilizing the protein structure

hydrolysis

a chemical reaction where a water molecule breaks up a chemical bond

Breaks bonds between monomers

Release energy

Function of a macromolecule

Ranges from structural support, genetic information, transporting molecules, storing energy, etc.

Condensation Reactions

Link monomers together (covalent bonds)

Energy input

Proteins

Hormones

Antibodies

Membrane receptors

Gene regulatory problems

Structural proteins

Enzymes

Amino Acids

Building blocks of proteins

20 different A A’s

A protein consists of one or more linear chains of amino acids

Polypeptide

Many bonds between amino acids is called peptide bonds

First Protein Structure

Primary function is the sequence of amino acids in the chain

Secondary Structure

Folding of the polypeptide chain from H-bonding between amino acids

Alpha Helix and Beta Pleated sheet

Alpha Helix

A coil with R-groups

Beta Pleated

Two parts of a polypeptide chain are aligned and held by H-Bonds

Tertiary Structure

3-D Folding of the protein chain due to interactions between R-groups,

R-group

is a variable side chain attached to a carbon atom in a molecule

Quaternary Structure

Only found in proteins that consist of multiple polypeptide chains or subunits

Functional Relevance

The function of a given protein is determined by its final shape and exposed R-groups on the surface

Conditions affecting Protein Structure

Increase in temp.

Changes in pH

change in solvent polarity

Chaperones

Special proteins called ___ provide a suitable environment for new (or denatured) proteins to fold into correct shape

Incorrect folding

Spongiform encephalopathies (A group of rare, fatal neurodegenerative diseases that affect both humans and animals) are diseases caused by abnormal folding of proteins

Abnormally folded prions trigger normal prions to change their shape as well

Incorrect folding diseases

BSE/Mad cow diseases

Creutzfeld-Jacob disease; Kuru

Scrapie

Carbohydrates

Primarily a source of energy for cells

Used as raw materials to build molecules, such as fats

Monomers

Atoms or small molecules that bond together to form more complex structures such as polymers (Sugars, Amino Acid, Fatty acids, etc.)

Monosaccharides

6-carbon are called hexoses (Fructose, Mannose, and Galactose)

5-carbon are called pentoses (Ribose and Deoxyribose RNA/DNA)

Disaccharides

To make a bigger molecule, monosaccharides are linked together via condensation reaction

Two ________ are covalently linked, the result is a ________

Sucrose = glucose + fructose

Polysaccharides

Consists of hundreds-thousands of monosaccharides linked together

Purpose : energy storage and structural material

Not always linear but can be branched

Starch

Energy storage in plants

Consists of glucose monomers

Moderately branched

Can form aggregates called ___ grains in seeds

Cellulose

Cell wall component of plants

The most abundant of macromolecules

Glycogen

Energy storage in animals

Highly branched, making the glucose monomers ready for fast breakdown

‘Special’ Carbohydrates

Substituting an amine group for a hydroxyl on glucose makes glucosamine

Saturated Fatty Acid

Has no double bonds in its chain

These molecules pack tightly together

Unsaturated Fatty Acids

At least one double bond in the carbon chain

Phospholipids

molecules that make up cell membranes and perform many important biological functions

Phospholipids Form Cell Membranes

In water, phospholipids heads contact water while the tail is kept away

Makes phospholipid bilayer structure of the cell membrane

Pigments & Vitamins

Carotenoids are the _____ that gives carrots, tomatoes, pumpkins, etc. their color

Also in green leaves with chlorophyll

Steroids

Multiple carbon rings linked together

Cholesterol is a cell membrane component

___ hormones are synthesized from cholesterol

Waxes

Hydrophobic and malleable at room temp

Secreted by glands in the skin of birds and mammals to coat hair or feathers

Coating on plant leaves

Nucleic Acids

Polymers specialized for the storage and transmission of genetic information

DNA

Encodes hereditary info and passes it from generation to generation

RNA

A molecule that carries genetic info and performs many functions in a cell

Usually single stranded and much shorter than _NA

Can sometimes base-pairs with itself

The Monomers

Nucleotides are linked via phosphodiester bonds to form huge polymers acids

Phosphodiester bonds

Covalent bonds that connect to phosphate groups and sugar molecules in the nucleic acids

Nucleotides of DNA

Adenine

Guanine

Cytosine

Thymine

Nucleotides of RNA

Adenine

Guanine

Cytosine

Uracil

Base Pairing

Two antiparallel strands of DNA are held together linked by H-bonds

A is always with T

C is always with G

DNA Structure

A ladder with sugar and phosphate as the sides

Double Helix

DNA replication

Purpose is to pass on genetic information to the new cell (offspring)

Transcription

Process of making RNA copy of DNA to make a protein based on the info of the gene

ATP

Energy carrier for chemical reactions

GTP

Energy source in protein synthesis

cAMP

Transmission of information within cells

Cell Membrane

Composed of phospholipid bilayer

The Membrane has a Hydrophobic Interior

The Polar phospholipid heads stick out on either side

Membrane Components

Lipids

Proteins

Carbohydrates

Lipids (cell membrane)

Provide a semi-permeable barrier

Proteins (cell membrane)

Transports ___ to help move substances across the membrane

Carbohydrates (cell membrane)

Attached to proteins and lipids

Glycolipids and Glycoproteins

Cell Membrane is a Semi-Permeable Barrier

Due to NON-polar interior, it is permeable to only some molecules

Polar molecules cannot diffuse across

Membrane Composition Varies

Different cells or organelles may have different lipid compositions

Saturated vs. Unsaturated Fatty Acids

Membrane fluidity is affected by

Lipid Composition and Temp.

Two Types of Membrane Proteins

Peripheral membrane proteins and Integral Membrane Proteins

Peripheral Membrane Proteins

No hydrophobic region

Not embedded in the membrane

Integral Membrane Proteins

At least partially embedded in the membrane

Contain both hydrophilic and hydrophobic parts

Cell-Cell Recognition

Involves plasma membrane

Essential to the formation of maintenance of tissues within an organism

How does Cell-Cell recognition work and Adhesion?

Cells recognize and bind to each other via membrane proteins or carbohydrates attached to membrane proteins or lipids

Cell junctions

Places where cells are attached to each other