Chapter 1: Biochemistry and the organization of cells

biomolecules, energy

all living things use the same ___ and ___

simple (CH4, CO2, NH3etc), atoms

with the originmolecules and cells must have risen from ___ molecules and likewise those from ___

Amino acids

building blocks of proteins, contain carboxyl (CHOO-) and amino (-NH3+), hydrogen, and a variable R group

Carbohydrates

-compounds made up of C, H, and O

-general formula (CH2O)n, where n is at least 3

monosaccharides

-simplest form of sugar for example glucose

-make up larger polymers and are used for energy, storage, and structural components

nucleotides

-basic unit of hereditary materials DNA and RNA, composed of 5 carbon sugar, nitrogen containing ring and 1 or more phosphate groups

-can have 1 or 2 phosphate groups, 3 makes ATP

Lipids

poorly soluble in water, has long chains of hydrophobic hydrocarbons

abiotic (nonliving),

Ex) Friedrich Wohler and his experiment with ammonium cyanate into Urea

It has been shown that important biomolecules can be produced

under ____ conditions from simple compounds postulated to have been present in the atmosphere of the early Earth.

Alkenes

double bonds

Alcohols

hydroxyl group( —OH)

Ethers

Ether group (—OR)

Thiols

sulfhydryl group (—SH)

Aldehydes

carbonyl group

Ketones

carbonyl group

carboxylic acid

carbonyl group

esthers

Ester groups

Amides

Amide group

Phosphoric acid Ester

Phosphoric esther group

Phosphoric acid anhydrides

phosphoric anhydride group

H, He, Li

The first three elements on Earth

-theorized to be the start of the universe

-universe was once condensed to a very small space but then exploded causing expansion and heat

What’s the big bang

4 to 5 billion yrs

how old is earth

monomers

small molecules that can bond to others to form polymers

proteins

macromolecules formed by polymerization of amino acids

nucleic acids

macromolecules formed by polymerization of nucleotides Ex) DNA and RNA

catalytic activity

enzymes increase rates of chemical reactions compared to uncatalyzed reactions

nucleotide, amino, protein, informational

____ sequence determines ___ acid sequence which determines ___ function and catalytic speed. Biological macromolecules are _____

genetic code

information for the structure and function of all living things

carboxyl, amino, H2O

Amino acids build proteins by connecting the ___ group of one amino acid with the ____ group of the next amino acid. With elimination of ___

1st, 4th, H2O

Polysaccharides are built by linking the __ carbon of one sugar with the ___ carbon of the next sugar. With elimination of __

3’-OH, 5’-OH, H2O

n nucleic acids the ___ of the ribose ring of one nucleotide forms a bond to the __ of the ribose ring of a neighboring nucleotide. With elimination of __

-believed that RNA was once capable of coding its own replication and perform catalytic activity like modern day proteins. Eventually, the system evolved to the point of being able to encode the synthesis of more effective catalysts, namely proteins.

How is RNA associated with the origin of life

Prokaryotes

-bacteria and cyanobacteria (single-celled)

-no membrane enclosed organelles

-no nucleus, only nuclear region

-energy yielding reactions on plasma membrane

-ribosomes free in cytosol

-photosynthesis in chromatophores (an extension of plasma membrane) no chloroplasts

Eukaryotes

-single and multicellular

-nucleus with a membrane separating it from the rest of the cell

-membrane enclosed organelles

-energy yielding reactions in the mitochondria

-ribosomes on the endoplasmic reticulum

-uses chloroplasts

similarities in eukaryotes and prokaryotes

-plasma membrane separating the whole cell from the rest of the outside world

-uses ribosomes

-plasma membrane is a double bilayer with lipid molecules

-cell wall (bacteria and plants)

nucleus

-location of main genome, site of most DNA and RNA

-surrounded by a nuclear double membrane

-contains nucleolus (Rich in RNA)

-contains chromatin (aggregation of DNA and protein)

-contains chromosomes (condensed chromatin, coiled due to protein before replication)

mitochondrion

-site of energy yielding oxidation reactions

-has its own DNA

-double membrane

—>outer smooth

—>inner= folds called cristae

—> matrix: space within inner membrane

endoplasmic reticulum

-continuous membrane throughout the cell

-rough has ribosomes smooth does not

chloroplasts

-site of photosynthesis in green plants and algae

-has its own DNA

-contain grana: membranous bodies stacked within chloroplasts

-double membrane

Golgi apparatus

series of flattened membranes involved in secretion of proteins from cells in reactions that line sugars to other cellular components

Lysosome

membrane enclosed sacs containing hydrolytic enzymes

peroxisomes

sacs containing enzymes involved in metabolism of hydrogen peroxide

cell membrane

separates the cell contents from the outside world

cell wall

Rigid exterior later of plant walls made up of cellulose

vacuoles

cavities within the cytoplasm of a cell typically enclosed by a single membrane that may serve secretor, excretory, or storage features

cytosol

-portion of cell that lies outside the nucleus and other membrane enclosed organelles

-contain cytoskeleton: lattice of fine strands consisting mostly of proteins that hold structure in place and provide pathways for materials like a highway

monera (prokaryotes), protista (single cell eukaryotes), animals, plants, fungi

Five kingdom classification

Bacteria, archea, eukaryotes

3 Domains

reduction

gain of electrons

oxidation

loss of electrons

thermodynamics

study of transfer of energy

free energy (G)

diagnostic for the spontaneity of a reaction at a constant temp

spontaneous

reaction without outside intervention

delta G<0

free energy of a system decreases in a spontaneous (energy releasing process)

delta G>O

nonspontaneous process, energy is supplied

delta G =0

equilibrium

delta S(universe)>0

in any spontaneous process

deltaG= deltaH -TdeltaS

Gibbs free energy formula