cell biology biochemistry and cell energetics

1. carbohydrates

2. lipids

3. proteins

4. nucleic acids (DNA and RNA)

1. carbohydrates

2. lipids

3. proteins

4. nucleic acids (DNA and RNA)

macromolecules

Cn(H2nO)n

carbohydrate formula

monosaccharide

single carbohydrate

1. energy source and storage

2. structural component of cell walls and endoskeletons

3. informational molecules in cell-cell signalling

carbohydrate functions

-ose

carbohydrate suffix

lipids

naturally occurring molecules that are all \n soluble in organic solvents.

1. fatty acids

2. glycerides

3. nonglyceride lipids

4. complex lipids

four main groups of lipids

1. triglycerides

2. phospholipids

3. steroids

three most common lipids

1. primary

2. secondary

3. tertiary

4. quaternary

levels of protein structure

primary structure

sequence of amino acids from N-terminus to C-terminus, and is formed by peptide bonds between adjacent amino acids.

secondary structure

consists mainly of alpha-helices and beta-sheets, and is formed by hydrogen bonds between the backbones of amino acids. It typically involves residues that are near \n each other in the primary structure.

tertiary structure

formed by interactions within a single polypeptide chain, often between residues that are distant from each other in the primary structure.

quaternary structure

involves interactions between separate polypeptide chains, called subunits, to form a multi-protein complex

tertiary and quaternary structures

levels of protein structure that form through hydrogen bonds, salt bridges, hydrophobic interactions, and disulfide bonds between amino acid side chains to yield the \n final, three-dimensional folded form of the \n protein

hydrophobic force

important driving force behind protein folding

1. hydrophobic force

2. intramolecular hydrogen bonds

3. van der waals forces

forces favorable for protein folding

entropically unfavorable

entropic favorability of protein folding

1. it minimizes the dispersal of energy

2. it adds order to the system

reason why protein folding is entropically unfavorable

favorable cellular interactions and forces

counteracts the effects of the loss of entropy

negative delta G, spontaneous

delta G and spontaneity of protein folding

nucleic acids

polymers made by joining nucleotides together

1. pentose sugar (nucleoside)

2. one of 5 possible nitrogenous bases

nucleotide composition

the nucleotide has either a deoxyribose sugar molecule or a ribose sugar molecule

difference between nucleotides

deoxyribose

there is no oxygen at the 2' carbon position of the pentose sugar

ribose

there is an -OH group at the 2’ carbon position of the pentose sugar

1. purines

2. pyrimidines

two categories of nitrogenous bases

purines

double ring nitrogenous bases

pyrimidines

single ring nitrogenous bases

1. adenine

2. guanine

the two purines

1. cytosine

2. thymine

3. uracil

the three pyrimidines

condensation reaction

reaction that joins nucleotides together into large polymers

phosphodiester linkages

linkages that hold nucleotides together

1. mRNA

2. ncRNA

types of RNA molecules

ncRNA

non-coding RNA that has structural, functional, or catalytic roles

1. rRNA

2. tRNA

3. snRNA

4. snoRNA

5. RNAi

6. others

types of ncRNA

rRNA (ribosomal RNA)

RNA that participates in protein synthesis

tRNA (transfer RNA)

RNA that is the interface between mRNA and amino acids

snRNA (small nuclear RNA)

the RNA that forms parts of the splicesome

snoRNA (small nucleolar RNA)

RNA found in the nucleolus that is involved in the modification of rRNA

RNAi (RNA interference)

small non-coding RNA involved in regulation of expression

large RNA

RNA with roles in chromatin structure and imprinting

1. miRNA

2. siRNA

two types of RNAi

siRNA (small interfering RNA)

active RNA molecules in RNA interference

law of conservation of energy

first law of thermodynamics

energy cannot be created nor destroyed

law of conservation of energy

energy converters

function of cells

entropy of an isolated system always increases

second law of thermodynamics

entropy

the amount of disorder

cofactors or coenzymes

non-amino acid components of an enzyme that help carry out its functions

vitamins

common compounds that cofactors and coenzymes are derived from

enzyme

biological catalyst that accelerates reactions at a biologically useful time scale

catalysis

increase in reaction rate that occurs when a catalyst decreases the activation energy of a reaction

interacting with substrates to stabilize the transition state between reactant and product

way that catalysts decrease activation energy

1. lock-and-key theory

2. induced fit model

explanations for enzyme binding

lock-and-key theory

enzyme binding explanation that suggests that substrates bind readily to enzymes because their active sites are already in the correct structural conformation

induced fit model

enzyme binding explanation that suggests that as a substrate binds to an enzyme, the shape of the active site changes to accommodate the substrate

1. hydrolase

2. isomerase

3. lyase

4. oxioreductase

5. synthetase

6. transferase

classes of enzyme

hydrolase

catalyzes hydrolysis

1. lipase

2. protease

examples of hydrolases

isomerase

catalyzes the rearrangement of atoms within a molecule

phosphohexoisomerase

example of an isomerase

lyase

catalyzes the splitting of chemicals into smaller parts without the use of water

1. decarboxylase

2. aldolase

examples of lyases

oxioreductase

catalyzes the transfer of electrons or hydrogen atoms from one molecule to another

1. dehydrogenase

2. oxidase

examples of oxioreductases

synthetase

catalyzes the joining of two molecules by the formation of new bonds

1. DNA ligase

2. DNA polymerase

examples of synthetases

transferase

catalyzes the moving of a functional group from one molecule to another

1. kinase

2. transaminase

examples of transferases

Km

the concentration of substrate needed to reach 1/2Vmax

low affinity for substrate

high Km means:

Kcat

turnover number, the number of times each enzyme site converts substrate to product per unit time

V0

initial velocity for the enzyme concentration

1. competitive inhibitors

2. uncompetitive inhibitors

3. mixed inhibitors (noncompetitive inhibitors)

types of enzyme inhibitors

competitive inhibitor

inhibitor that binds an enzyme at the active site and is therefore structurally similar to the substrate

Km increases, Vmax does not change

competitive inhibitor effect on Km and Vmax

uncompetitive inhibitor

inhibitor that only binds to the enzyme-substrate complex and its binding site only forms when the substrate and enzyme have interacted

Km and Vmax both decrease

uncompetitive inhibitor effect on Km and Vmax

mixed inhibitor

inhibitor that has characteristics of both competitive and uncompetitive inhibitors

1. favors free enzyme

2. favors enzyme-substrate complex

3. favors both free enzyme and enzyme-substrate complex equally (noncompetitive inhibitor)

three types of mixed inhibitors

Km increases, Vmax decreases

effect of a mixed inhibitor that favors a free enzyme on Km and Vmax

Km decreases, Vmax decreases

effect of a mixed inhibitor that favors the enzyme substrate complex on Km and Vmax

noncompetitive inhibitor

a mixed inhibitor that binds to the enzyme and enzyme-substrate complex with equal affinity and does not affect substrate binding, but does induce conformational changes in the enzyme that inhibit its function

allosteric site

site that a noncompetitive inhibitor binds to

Km doesn’t change, Vmax decreases

noncompetitive inhibitor effect on Km and Vmax

ATP (adenosine triphosphate)

the main source of energy for cells

the P-P-P bond is broken and ATP converts into ADP

how energy is released by ATP

1. photosynthesis

2. protein synthesis

3. muscle contraction

4. any bodily activity

processes ATP is important for

1. photosynthesis

2. aerobic respiration

3. anaerobic respiration

4. fermentation

4 main pathways that produce ATP

1. glycolysis

2. kreb’s cycle

3. electron transport and chemiosmosis

subcategories of aerobic respiration

1. lactic acid fermentation

2. alcohol fermentation

subcategories of fermentation

photosynthesis

process in which light energy is transformed into chemical energy

carbon dioxide and water

photosynthesis reactants

glucose, oxygen, and water

photosynthesis products

the calvin cycle

dark reactions of photosynthesis

CO2

input for the calvin cycle

glucose and other organic compounds

output for the calvin cycle

glycolysis

first stage of cellular respiration, harvests energy from glucose by splitting it into two pyruvates

two pyruvates, two NADH, two ATP, two H2O, and two H+

products of glycolysis

cytosol

location of glycolysis