BIO 311C - SATA - EXAM 1

Why study cellular and molecular biology?

The connecting basis of all life is at the cellular and molecular level. DNA, RNA, proteins and the cellular mechanisms behind each of these form the fundamental basis of life. Many biological phenomena are better understood at the biochemical and molecular level.

What are the 8 emergent properties of life?

Reproduction

Growth and Development

Order and Structure

Metabolism

Respiration

Response to environmental stimuli

Adaptation and evolution

Autonomous movement

What is a model system?

Because there are millions of living organisms, and we cannot study each one individually, so we use these selected organisms to study the mechanisms of life. It is a representative organism or cell type used for experiments. They are easy to grow, manipulate, and study.

What are some common examples of model systems among prokaryotes?

- E. coli

- Salmonella

What are some common examples of model systems among eukaryotes - plants?

• Arabidopsis

• Corn

• Rice

What are some common examples of model systems among eukaryotes - fungi?

• Yeast

What are some common examples of model systems among eukaryotes - animals?

• Fruit fly

• Nematode

• Mouse

• Zebra fish

• HeLa cells (human cell lines)

In vivo

Experiments used to study physiology, ecology of organisms under living conditions.

Ex: rats, rabbits, plant tissue culture, etc.

Can be holistic or reductionist

In vitro

Experiments performed under non-living AKA abiotic condition

Ex: in a test tube with known quantities of chemical, enzymes added, particular temperature, pH, etc.

Strictly reductionist

What is the biological hierarchy?

Atoms →Molecules→Macromolecules→Parts of cells→Cells→Tissues→Organs→Organ systems→Organisms→Population→Community→Ecosystem→Biome→Biosphere

Name the 3 domains and 4 kingdoms.

1) Bacteria

2) Archaea

3 Eukarya

- Protista

- Fungi

- Plantae

- Animalia

mass number

# protons + # neutrons

molecular weight

sum of the weight of all atoms in a molecule

expressed in Daltons (Da)

valence

Refers to an atom's bonding capacity and is determined by how many unpaired valence electrons there are out of 8.

Covalent bonds

Occur when two atoms share a pair of electrons, stronger IMF

Polar Covalent bonds

Unequal sharing of electrons

Ex: H2O, NH3

Non-polar Covalent bonds

Equal sharing of electrons

Ionic bonds

Occurs when the electronegativity of one atom is greater than that of the adjoining atom, the one with higher electronegativity pulls electrons to its valence shell from its neighboring atom, thereby becoming an anion. The atom it took the electron from becomes a cation. The ionic bonding occurs because of the attraction between the positive and negative charges.

H - bonds

Hydrogen covalently attached to one electronegative atom is attracted to another electronegative atom.

Van der Waals interactions

Takes place when molecules interact; there are pockets of constantly changing positive and negative charges. This takes place due to the changing distribution of electron clouds and results in weak forces of attraction.

Hydrophilic interactions

Polar, charged molecules

Soluble

Hydrophobic interactions

Non-polar

lipid- soluble

Excluded from aqueous solutions bc of hydrogen bonding among polar molecules

Biological example of Covalent bonds

Carbohydrates - glycosidic bonds

Lipids - ester bonds

Proteins - peptide bonds

DNA/RNA - phosphodiester bonds

Biological example of Ionic bonds

NaCl

Biological example of H-bonds

H2O, NH3

DNA

RNA

Proteins

Biological example of Van der Waals interactions

Lipids in biological membranes

Cellulose in plant walls

Biological example of Hydrophilic/Hydrophobic interactions

Phospholipids in biological membranes have a hydrophilic region outside the membrane bilayer, hydrophobic region within

Amino acids with hydrophobic side chains are in the interior of the protein while those with hydrophilic side chains can be in the interior or the exterior

What is the relation between the properties of water and H-bonding? How do they help support life on earth?

Water molecules have two partial positive and two partial negative charges, allowing for 4 counts of hydrogen bonding, and thus water molecules can bond with up to four other water molecules. The H-bonding is strong in water and is the main reason for its unique properties.

Properties of Water

cohesiveness

adhesiveness

high specific heat

high heat of vaporization

freezing and expansion

versatile solvency

medium for biochemical reactions

ingredient of many biochemical reactions

cohesiveness

due to the constant forming and breaking of H-bonds in liquid water, H2O molecules stick together

- important for water uptake ( transport from roots ) and imbibition ( water absorption by seeds )

adhesiveness

water can adhere to surfaces

- important for the attachment of water ( adsorption ), which leads to absorption

high specific heat

1 cal/g/C°

Water can absorb and release heat to stabilize the temperature in the surrounding area, making it habitable.

high heat of vaporization

it takes lots of energy to evaporate water, which is important in evaporative cooling in animals and plants in hot weather.

freezing and expansion

as water freezes, it expands, becoming less dense; the resulting ice floats on the top of the water, keeping water below warmer, and thus providing a favorable environment for aquatic organisms during freezing cold conditions

versatile solvent

water is an excellent solvent for all polar and charged molecules because of its polarity

minerals and nutrients dissolved in water are available for easy uptake and transport by plants and animals.

medium for biochemical reactions

living cells contain up to 95% water so many biochemical reactions in a cell occur under aqueous conditions

ingredient of many biochemical reactions

many biochemical reactions need water as a reactant

Ex: photosynthesis, hydrolysis

How to prepare solutions of different molar concentrations when given a molecular weight, percent weight, volume solution, etc.

MW (g/mol) X M (mol/L) x L = g

From stock solution to a diluted solution

C1V1 = C2V2

C1 - concentration of stock solution

V1 - volume of stock solution

pH

pH > 7 base

pH = 7 neutral

pH < 7 acid

Kw

water constant = 10^-14

As pH increases

[H+] decreases

[OH-] increases

becomes more basic

A solution with a pH of 4 has ____ x more [H+] that one with a pH of 6

100

pK

when acid and base have a ratio of 1:1

mid point of buffering range

buffer

weak acid/base/both substance that minimizes pHchange by donating or accepting protons

example of acid

stomach acid

example of weak base

blood

example of strong base

bleach

Organic molecules

carbon

hydrogen

nitrogen

oxygen

phosphorus

sulfur

structural isomer

same molecular formula but different structures

geometric isomer

form due to inflexibility of double bonds between carbons

cis - same types of functional groups on the same side

trans - same types of functional groups away from each otehr

optical isomer

also called enantiomers

mirror images

Functional groups

hydroxyl

hydroxyl

hydroxyl

confers polarity to a molecule, making it more soluble in water

hydroxyl

almost all carbs, proteins, nucleic acids have these

hydroxyl

molecules with these groups are called alcohols

carbonyl

if the carbonyl is at the end of an organic molecule it is

an aldehyde (glucose)

if the carbonyl is in the middle of an organic molecule it is

a ketone (fructose)

carbonyl

slightly polar

carbonyl

present in simple sugars, some proteins and nucleotides

carboxyl

carboxyl

an acidic group that ionizes to form -COO- and H+ to increase [H+] of a solution

carboxyl

acetic acid, formic acid, citric acid, malic acid

ionized by this group to become

acetate, formate, citrate, malate

carboxyl

present in all amino acids and proteins

amino group

amino group

can act as a base by accepting protons

(-NH2 + H+ = -NH3+)

amino group

found in all amino acids, proteins, and some specific nucleotides

sulfhydryl

sulfhydryl

two of these groups within a protein can combine to make a disulfide bridge to stabilize a protein structure

sulfhydryl

found in active sites involved in the catalysis of enzymes

phosphate

phosphate

highly polar

phosphate

important in energy compounds such as ATP

phosphate

present in DNA, RNA, and all nucleotides

phosphate

found in phospholipids

phosphate

acidic and reactive group

methyl

methyl

non-polar functional group

methyl

affect the solubility of a compound in aqueous or organic solutions

methyl

strong influence on the bioactivity of the molecule involved

methylation

adding a methyl group to a DNA molecule can make it non-functional

methylation

this makes somedrugs and pesticides more permeable through cell membranes

methyl

found in alcohols, fatty acids, some amino acids, and nucleotides

Four major groups of biological molecules

carbohydrates

lipids

proteins

nucleic acids

condensation synthesis

combines two monomers and releases a water molecule by removing an -H and -OH group

synthesizes polymers

hydrolysis

breaks down polymers into monomers by adding an -H and -OH group by splitting a water molecule

hydrolysis

important for catabolic processes

Carbohydrate monomers

monosaccharides

Simple sugars are made up of

C, H, and O

In carbs, C:H:O

1:2:1

Carbon skeleton size variation

3 to 7 carbons

Within a carbon skeleton

an -OH group is attached to each C, except for one which is double-bonded to an O (carbonyl-CO)

In aqueous solutions, sugars with _ to _ carbons form a ring structure

5, 7

Monosaccharide (sugar) function

provides a major source of energy for cells

energy stored in sugars is harvested by cells through respiration

carbon skeletons are used for making other molecules

Disaccharide

formed by enzymes which combine two monosaccharides through glycosidic linkages

maltose

glucose + glucose

lactose

glucose + galactose

sucrose

glucose + fructose