Biochem

matter

anything that takes up space and has mass

element

Pure substance, cannot be broken down into simpler substances

compound

A substance formed when two or more DIFFERENT elements chemically combine in fixed ratios. (Molecules can be same element)

essential elects vs trace elements

essential:organisms need in large amounts, C, H, O, N

Trace: need small amount, Iron, zinc

Reading an element on PT

Atomic #= protons

Protons=electrons in neutral atom

Atomic mass-protons=neutrons

Ions

anion: gain e-

Cation: lose e-

Isotope

change # of neutrons

Groups

Vertical columns

Elements with similar chemical properties, valence electrons

Period

Horizontal row, # of electron shells

Electronegativity

A measure of an atoms ability to attract and hold electrons in a chemical bond

Increases leftover to right across PT and decreases down a group

Bonds

Non polar covalent: nonmetals, electrons shared equally, 0-0.4 EN

Polar covalent: nonmetals, shared unequally (one atom is more electroneg), 0.5-2 EN

Ionic:btw ions, one atom donate e- to another atom, metal+ nonmetal, >2 EN

Hydrogen bond: attraction btw H with + charge part of a molecule (with nitrogen, oxygen, or fluorine (f)) is attached to a negative region of another another molecule

Elements found most in life

CHNOPS

Carbon: Maine structure and chains, H: make water→support life, N: for protein and DNA, O: cellular respiration, P: store cell energy + build DNA frame, S: build amino acids

Bond strength in water

nonpolar covalent→ polar covalent→ionic→hydrogen

Water charges

partial negative on oxygen

Partial positive on hydrogen

(Oxygen has higher EN so pulls more e- so it has net -)

Where is pos and neg charge on water

partial positive charge on hydrogen atom and partial neg charge on oxygen atom Due to the difference in electronegativity

The hydrogen electrons are pulled toward oxygen

Cohesion

the attraction btw water molecules due to hydrogen bonds. Stick together, cause surface tension (no h20 above so the molecules on the surface have a higher attraction and form a stronger layer)

Adhesion

attraction btw water molecules and other charged molecules

Cohesion and adhesion in plants

Help weather transport from roots to leaves through the xylem in processes called transpiration

Capillary action

Ability to climb narrow spaces and defy gravity. Adhesion helps water stick to the side and climb up, cohesion pulls the water molecules below up.

High specific heat

Water can absorb or release large amounts of heat with only a slight change in its own temp. Important for homeostasis in organisms

Evaporation cooling

when water evaporates it takes heat away from the surface, cooling the organism (sweating, transpiration in plants)

Density

Ice is less dense than liquid water, due to hydrogen bonds forming crystalline structure in ice (molecules further apart)

Causes ice to float on water, insulate water below for habitat for aquatic creatures

Universal solvent

water can dissolve many substances

Ionic compounds and polar molecules

Essential for transporting nutrients gases etc

Solvent

Substance that dissolves other substances

Solute

what is dissolved

Solution

homogenous mixture

Organic compounds

carbon atoms bonded to hydrogen, oxygen, nitrogen

Found in living things

Carbs, lipids, proteins, and nucleic acids

Inorganic compounds

Do not primarily consist of carbon hydrogen bonds

Minerals, salt, water

Found in non-living stuff but also vital to life

Carbons tetravalency

Carbon has 4 valence electrons, can form 4 covalent bonds

Carbon catenation

carbon can bond with other carbon atoms to form long chains and rings

Essential for complex organic molecules

Hydrocarbon chains

length of hydrocarbon chain affects shape of the molecule

Foundation for complex molecules and major complements of lipids and fuels

Monomer and polymer

basic molecular units

Polymer-large molecules of retreating monomers

Macromolecules are formed through

Dehydration synthesis

Dehydration synthesis

2 molecules covalent bonds, lose a water molecule To make larger polymer

One looses an OH, the other looses an H

Hydrolysis

water is added to break the bonds between monomers

Polymer→monomer

Carbs

Organic molecules

C,H,O in 1:2:1 ratio

Monosaccharides are monomer

Simplistic formula: (H2O)n→ if n is 6 C6H12O6

Glycosidic linkage btw monomers

Monosaccarides

monomer of carb

Glucose, fructose, galactose

Immediate energy

Isomers: same chem formula but different structures

Disaccharides

2 sugars, mostly immediate energy

Sucrose (glucose+fructose) table sugar

Lactose(glucose + galactose), milk/dairy

Maltose (glucose + glucose)

Oligosaccharide

3-10 sugars

Polysaccharide

long chains

Starch: store energy in plants, roots and seeds, spirals of glucose so doesn’t pack tightly and is easier to pick apart

Glycogen: energy storage in animals, muscles and liver, shape of branching Y

Cellulose: structure in plant cell walls, straight line tightly packed

Chitin: structure in exoskeleton of arthropods and cell wall of fungi, straight lines

Redox reaction

e- is added to an element/molecule which becomes more (-) and changes, its charge is reduced

Oxidation reaction

e- is stolen/taken, molecule/atom that e- is stolen from gets a more (+) charge

Proteins

made of amino acids linked by peptide bonds

Essential and nonessential amino acids

essential: cannot by synthesized by body must be obtained through diet- 9 of them

Non: can be made by body- 11 of them

20 total

Amino acid structure

Amino group, carboxyl gorup, hydrogen atom, and r group (side chain) to central carbon atom

Side chain determine the properties of amino acids

Amino group atoms

NH2

Carboxyl group atoms

COOH

Non polar

hydrophobic

Found in interior of proteins

Polar

hydrophilic found on exterior of proteins

Amino acid

amino group, R group/side chain, carboxyl group, central carbon

Each amino acid has its own unique side chain, can be (+),(-),polar, non polar

Peptide bonds

formed by dehydration rxt btw the amino group of one amino acid and carboxyl group of another

Polypeptide

long chain of amino acids (>10)

Proteins are made of one or more polypeptides

Protein structure

Primary: sequence of amino acids in polypeptide chain

Secondary: local folding into alpha-helices and beta-sheets due to hydrogen bond interactions

Tertiary: overall 3D shape of polypeptide, determined by R groups→sulfer attracted to sulfer, +/- ,hydrophobic/physdrophilic rats with water

Quaternary: arrangement of multiple polypeptide chains into a functional protein

Functions of protein

antibody: defense against pathogens

Enzyme: catalysts for biochemical reactions

Messenger: horses and signaling molecules

Structural: provide support and shape

Transport: carry substances (hemoglobin)

Protein denaturing

Structure falls apart due to an input of too much energy→mechanical force, heat, radiation, acids/bases, freezes

Change conformation (shape), loose structure-loose function

Nucleic acids

Macromolecules that stores and transmits genetic info. DNA and RNA

Monomers are nucleotides

DNA

Stores genetic info, double-stranded helix

RNA

transmits genetic info and helps in protein synthesis

Single stranded

Parts of a nucleotide

sugar, phosphate group, nitrogenous base (adenine A, thymine T, cytosine C, guanine G

uracil U replaces thymine in RNA

Pyrimidines: single ring base (C,T,U)

Purines: double-ring bases (A,G)

Phosphodiester linkages

bonds between the phosphate group of one nucleotide and the sugar of another

Directionality of nucleic acids

5’ to 3’ important for replication and transcription

Lipids

hydrophobic (Expect phospholipids)

Energy storage,membrane structure, signaling

Have a glycerol (three carbon alcohol) and fatty acid (long hydrocarbon chain with carboxyl group)

Fats, oils,waxes, membrane building blocks, seroids

Fat

triglycerides

One glycerol and three fatty acids (carboxyl group and hydrocarbon chain) linked by ester bonds

>2x better than carbs/protein (4 ca/g) for storing energy fats(9 cal/g)

Insulation, cushion organs

Cals

energy required to heat 1 g h2O by 1 degree celcius

Saturated fats

no double bonds, saturated with H, straight line pack together more tightly, solid at room temp, found in animal products, butter and coconut oil, avocado, nuts

Unsaturated fats

one or more double bonds, liquid at room temp, olive oil, avocado, nuts, etc

Cis unseat

Hs repeal and cause FA to repel, so don’t pack tightly, liquid at room temp, from plants

Trans fats

created by hydrogenating oils, found in processed and fried food, rate bad cholesterol and lower good cholesterol increase heart disease risk

Hs on opposite sides so dont repel, made by humans

Phospholipids

structure: glycerol, two fatty acids, and phosphate group

Form cell membranes

Amphipathic

Hydrophilic head

Hydrophilic tails

steriods

(lipid)

Structure: four fused carbon rings

Functions include hormones like testosterone and cholesterol, diffuse through cell membrane, bind to DNA and regulate gene expression