Unit 1 biochemistry Test (Part 2)

matter

anything that takes up space and has mass

elements

a substance that cannot be broken down into other substances by chemical reaction

92

how many elements occur on nature

compound

a substance consisting of two or more elements is a fixed ration

Essential elements

elements essential to survive and reproduce

CHOPN

CHOPN

make up 96% of living matter

Atomic #, # of protons

# above element

Atomic mass #, proton + neutrons average over all isotopes

# below element

elements in same vertical column (group)

have same # of valence

elements in same horizontal row (period)

have same # of electron shell

1st, 2nd, 3rd Shells can hold

2,8,18 electrons

bohr model

model with a electron shell

Lewis dot model

model with a dot of valence electrons

Octet rule

Elements wants to get all 8 electron to be stable so they gain, lose, share their valence shell electron. (like noble gases)

Electronegativity

The ability of an atom to attract electrons to itself

increase - left to right of period

decrease - top to bottom of group

covalent bond

two or more atom share electrons (nonmetals)

polar covalent bond

Electron is unequally shared

Ionic bonds

attraction between oppositely charged atoms (Ion)

hydrogen bond

the partially positive hydrogen atom is one polar covalent molecule will be attracted to an electronegative (-) atom in another polar covalent molecule

Intermolecular bond (hydrogen bond in water)

bond formed between molecules (exist among particles)

Intramolecular bond (covalent bond in water)

bond formed exhibited inside a particle

8 properties of water

polarity, cohesion, adhesion, capillary action, high specific heat, evaporative cooling, floating ice/ density, universal solvent (also surface tension)

polarity

unequal sharing of the electrons make water a polar molecule

Cohesion

Attraction of molecules for other molecules of the same kind

responsible for surface tension

living system of cohesion

Increase Hydrogen bond makes a surface tension

- Leaf floating: plants often time rest in surface of water and allowing them to have more access to sunlight for process of light photosynthesis

Ice float: Water's cohesive properties allows for unique hydrogen bond intercalations in water's solid state. And this makes water as a solid less dense than water as a liquid.

- Aquatic organism able to live in water in freezing climates because the water will freeze on the surface leaving liquid water underneath for those organism

High heat capacity: water's cohesive property allows it to absorb a lot of thermal energy before changing chemical states resisting sudden changes in temperature

- Many aquatic organism like the fish will depend upon this property of water, so that they can maintain appropriate temperature regulations of their bodies

Adhesion

The clinging if one molecule to a different molecule

living system of adhesion

Water's adhesive property gives water a high solvency ability in liquid state

- Organism must obtain key nutrients from their environment. Considering that living things are made up of 70% water. Dissolved materials in the water allow for easy access by cells

living system of cohesion and adhesion

Capillary action is a result of both the adhesive and cohesive properties of water

- Plants can access water from the soil through this capillary action ability into their roots (xylem of leaf)

Evaporative cooling

Water has a high heat of vaporization (meaning it takes a lot of energy to convert liquid to gas)

importance of evaporative cooling

moderates Earth's climate

Stabilizes temp in lakes and ponds

Prevents terrestrial organisms from overheating (sweat)

Prevents leaves from overheating

solution

Homogenous mix of 2+ substances

solvent

Dissolving agent in a solution

solute

Substance that is dissolved

“like dissolves like”

Water will form hydrogen bonds with the sugar or protein to dissolve it

pH

depends on the hydrogen ion concentration in that solution

high concentration low pH

low concentration high pH

pH levels

pH 7 being neutral, pH less than 7 being acidic, and pH greater than 7 being basic

organic compounds

compounds that contain carbon and hydrogen

organic chemistry

the study of compounds with covalently bonded carbon

H, O, N

carbon most commonly forms bonds with

Hydrocarbons

Compounds composed of only carbon and hydrogen

skeleton

carbon chains form the ______ of most organic molecules

functional groups

Chemical groups attached to the carbon skeleton that participate in chemical reactions

Molecular diversity

variations in carbon skeletons allows for

Macromolecule

carbon can form large molecules known as

4 macromolecules

Carbonate

Protein

Nucletic acid

lipids

polymers

Chain like macromolecules of similar or identical repeating unit that are covalently bonded together

monomers

the repeating units that makes up polymers

dehydration reaction

bonds two monomers with the loss of H2O

monomer + monomer = polymer +H2O

hydrolysis reaction

breaks the bonds in a polymer by adding H2O

Polymer +H2O = monomer + monomer

Carbohydrates

C,H,O

carbonyl group and hydroxyl group

what functional group does carbohydrate have?

monosaccharides

simple sugar

monomer of carbohydrates

*most common is Glucose - form a ring in aqueous solutions

Alpha Glucose

 (OH bottom) makes starch (covalent bond \ o/) Branch

Beta Glucose

 (OH top) makes cellulose (covalent bond / o\) linear

Diaccharides

two monosaccharides joined together by covalent bonds

*most common Sucrose = Glucose + fructose

Polysaccharides

polymer of carbonates

many sugar joined via dehydration reaction

storage polysaccharides

Plants - STARTCH: allows plants to store excess glucose

animals - GLYCOGEN: stored in liver and muscle cells

structural polysaccharides

Cellulose: tough substance that forms plant cell walls

Chitin: forms exoskeleton of arthropods.

Proteins

C,H,O,N,S

molecule consisting of poly peptides folded into a 3D shape

shape determine the function

protein order

Amino acid small → peptide → polypeptide → protein large

Amino Acids

monomer of protein

structure of amino acid

R (variable side chain) CH3 hydrophobic, H - polar

amino group — C — carboxyl group

N terminus H C- terminus

(Base) (Acid)

Polypeptides

polymer of protein

many amino acid liked by peptide bonds

*unique sequence of polypeptide = Gene

Function of protein

Antibody: help protect the body from disease

Enzyme: Carry out chemical reactions or assist in creating new molecules

Messenger: Transmit signals (ex. hormones)

Structural: Provide structure and support

Transport/storage: Bind to and carry small atoms and molecules through the body

Level of protein structure

Primary, Secondary, tertiary, Quaternary

Primary protein structure

Linear chain of Amino Acids

• determined via Gene

Secondary protein structure

Coils and folds due to HYDROGEN BONDING within the polypeptide backbone

Beta Pleated sheet - hydrogen bonds between polypeptide chains lying side by side

Alpha - hydrogen bonding between every 4th amino acid

Tertiary protein structure

3D folding due to interactions between the side chains of the Amino Acids

- Reinforced by hydrophobic interactions and disulfide bridges of the side chains

Quaternary protein structure

Association of two or more polypeptides

• Found in only some proteins

Nucleic acid

Polymers made of Nucleotide monomers - DNA, RNA

Function of nucleic acid

Store, transmit, and express hereditary information

components of nucleic acids

nucleotide(monomers) → polynucleotides → nucleic acid (polymers: DNA, RNA)

3 parts of nucleic acid

Nitrogenous base

Five carbon Sugar (pentose)

Phosphate groups (in polynucleotides each monomer only has one phosphate group

Nitrogenous base (nucleic acid)

Pyrimidines and purines

Pyrimidines

One ring with 6 atoms

- Cytosine; C

- Thymine; only found in DNA

- Uracil; only found in RNA

Purines

One ring with 6 atoms bonded to one ring with 5 atoms

- Adenine

- Guanine

A, T

has 2 hydrogen bond

C, G

has 3 hydrogen bond

Five carbon Sugar

A sugar is bonded to the base

- In DNA the sugar is deoxyribose (H)

- In RNA the sugar is ribose (OH)

Phosphate Group

Functional group in Nucleic Acid

Polynucleotides

Phosphate groups like adjacent nucleotide

- Phosphodiester linkage

- Directionality (5' phosphate end to 3' hydroxyl end)

The sequence of bases along the DNA or mRNA is unique for each Gene

- Dictates AA sequence

○ Dictates the primary structure of a protein

(Dictated 3D structure of a protein)

DNA

Consist of TWO polynucleotides (Deoxyribose)

- Forms a double helix

○ Strand are antiparallel

• Held together by hydrogen bonds between bases

  Cytosine binds to guanine

  Adenine binds to thymine

antiparallel

5’ to 3’ + 3’ to 5’

RNA

single helix

Ribose

Adenine binds to Uracil

Lipids

Class of molecules that do not include true polymers

- Generally small in size

○ Often not considered to be a macromolecule

Lipids are nonpolar-hydrophobic

Types of lipids

Fats, Phospholipids, Steroids

Fat

composed of Glycerol and Fatty Acid (monomer of lipids)

Glycerol

classified as an alcohol (hydroxyl group)

Fatty Acids

long carbon chains (carboxyl group at one end)

3 fatty acids join to a glycerol via Ester linkage

Saturated and unsaturated

hydroxyl groups, carboxyl group

Functional groups of lipid

Saturated fatty acid

NO double bonds between carbons in the carbon chain = more hydrogen (think: saturated with hydrogen)

Unsaturated fatty acid

Contains one or more double bonds

Phospholipids

major component of cell membranes

- Two fatty acids attached to a glycerol and a phosphate

Assemble as a bilayer in H2O

- Tails are hydrophobic

- Head is hydrophilic

Steroids

Lipids that have four fused rings

- Unique groups attached to the ring determine the type of steroid

Ex. testosterone

Hydroxyl group

—OH

Carbonyl Group

\

C = O

/

Carboxyl group

—COOH

Amino Group

—NH2

Sulfhydrl group

—SH

Methyl Group

H

|

— C — H

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H