microreview2txt.txt

chemical substanes as source of energy

light as a source of energy

CO2 as a source of carbon

organic compounds as source of carbon

organic compounds as soruce of electrons

inorganic compounds as source of electrons

bacteria play critical role, such as nitrogen fixation

conversion of N2 from the air into NH3

storage molecule for chemical enegry in all cells

degradation

biosynthesis

catabolism

ATP is hydrolyzed to ADP + Pi + energy

where endergonic reactions that would not occur in living cells can be effectively promoted by coupling them into ATP hydrolysis

loss of electrons

gain of electrons

oxidation-reduction / electrons are transferred from one substace that becomes oxidized to another substance that becomes reduced.

two electrons and two hydrogen ions are transferred simultaneously

proteins that are imbedded in membranes that transfer electrons and hydrogen ions in such a way that a pH gradient is generated accross the membrane

proton motive force - it drives the synthesis of ATP catalyzed by the enzyme ATP synthase when hydrogen ions pass through the enzyme.

biological catalysts; most are proteins but some are catalytic RNAs (ribozymes)

enzyme's site where the substrate binds

compounds that compete for the binding of substrate to the enzyme

(distinct from the active site) where a noncompetitive inhibitor (or activator) can bind thereby affecting the activity of the enzyme

the final product of the pathway acts as a noncompetitive inhibitor of the first enzyme in the pathway.

some anabolic pathways (byosynthetic)

lower activation energy needed for catalysis

pH, temperature, and the concentration of substrate

the cleavage of glucose into two 3-carbon compounds

it converts acetyl-CoA into 2 CO2

2ATP / glucose

2GTP = 2 ATP

it converts NADH and FADH2 into ATP

38 ATP/ glucose; actual yield = 30-32 ATP/ glucose

serios of redox reactions in which an inorganic substance is the final electron acceptor. example: oxygen is this substance in aerobic respiration

series of redox reactions in which an organic substance is the final electron acceptor. example: a small organic acid or alcohol.

bakers' and bewers' yeast (S. cerevisiae)

2ATP/glucose

lipids and proteins

so that the same or similar pathways can be used for production of energy or production of carbon chains for biosynthesis

carbon fixation (CO2 added to carbohydrate) powered by ATP produced form the absorption of light by chlorophylls organized into photosystems.

cyclic electron flow and does not produce oxygen

noncyclic electron flow and produces oxygen

in chloroplasts in eukaryotes and in the plasma membranes of prokaryotes

monomers are polymerized into polymers. for example: amino acids into proteins. nucleotides into nucleic acids. monosaccharides into polysaccharides.

genetic material in all cells and many viruses

Griffith's transformation experiment

cell division

within a generation

it is a molecule consisting of two strands - polymers of nucleotides attached by phophodiested bonds. each strand has 5' to 3' polarity

it is antiparallel wit respect to the polarity of the two strands

4 bases (ACGT); form base pairs (AT and GC); two strands are complementary with respect to base pairing

it is where sequence-specific DNA binding proteins bind

separation of the two strands of parental DNA and copying as templates resulting in the synthesis of two new strands of daugter DNA

DNA polymerase; other important enzymes: primase and DNA ligase

in the synthesis of proteins

DNA synthesis is discontinuous

DNA synthesis is continuous

it has only one origin of DNA replication

many origins of DNA replications

(both DNA and RNA) proceed in the 5' to 3' direction

repeated DNAs on both ends of eukaryotic chromosomes

by the action of telomerase (enzyme that copies RNA in making DNA)

synthesis of RNA complementary to the template strand of DNA in the gene

enzyme that catalyzes the polymerization of ribonucleotides into RNA

a sequence of DNA called the promoter

E.Coli has one that syntesizes mRNA, rRNA and tRNA; eukaryotes have separate RNA polymerases for each of them

they are clustered together and transcribed into plycistronic mRNAs that are translated into several proteins

they are transcirbed individually into monocistronic RNAs that are translated into one protein

eukaryotic genes coding sequences

eukaryotic genes noncoding sequences that separate exons

heterogeneous nuclar RNA (jmRNA) - must be spliced (by sliceosomes) to remove introns

complex of small nuclear RNAs and proteins; they perform splicing

genetic code

3 nucleotides in mRNA encode one amino acid i nthe protein product of the gene

20

61

more than one codon per amino acid

AUG

UAA, UAG, UGA

an anticodon that matches the sequence in the codon.

by aminoacyl-tRNA synthetases (requires ATP)

23S rRNA

28S rRNA

they catalyze the formation of peptide bonds between amino acids

70S bacteria

80S eukaryotes

protein initiation factors (IFs), elongation factors (EFs) and GTP

stop codons and mediate termination of protein synthesis

specific proteins that some proteins require to fold. (protein folding may occur spontaneously)

at the level of transcription by proteins biding to specific sequences of DNA

at the level of translation, especially in eukaryotes. mRNA splicing can also be regulated

always expressed

function in catabolism; not expressed but can be turned on

function in anabolism; expressed but can be turned off

by a repressor that binds to an operator. (like the trp operon)

transcription is blocked

when lactose (inducer) is present and binds to the repressor and causes it to change shape so that it can't bind to DNA

by a repressor that binds to an operator. (like the lac operon)

it binds to the repressor and activates itso that it bind to the operator sequence of DNA

inhibition of transcription

stimulation of transcription

both: negative by the repressor and positive by the CAP- cAMP

adenlyl cyclase converts ATP into cyclic AMP (cAMP) + PPi. then, cAMPbiind to the catabolite activator protein (CAP) to form a functional complex that binds to DNA and stimulates the binding of RNA polymerase to its promoter

small nuclar RNAs (siRNAs) bind to m RNAs and cause them to be degraded by a nuclease (dicer)

DNA sequence recombination

change in the sequence of nucleotides in DNA.

by chemicals (mutagens) or electromagnetic radiation (UV or x-rays)

changes in one base pair in the DNA

change a codon into a codon for another amino acid

change a codon for an amino acid into a stop codon

chagne a codon for an amino acid into another codon for the same amino acid

when DNA absorbs UV light?

repair enzymes: excision repair and mismatch repair

any DNA sequence

newly replicated DNA only

they remove damaged DNA segments, polymerization of nucleotides to fill in the gap, and DNA ligation

chemicals that cause cancer; mutagens in the Ames test that measures the frequency of reversion of a his- mutation to the wild type, his+.

nutritional mutant

between related DNA sequeces

at specific sites

small circular DNAs with their own origin of DNA replication. they replicate independently of baterial chromosomal DNA

plasmid that is requried for conjugation; the F factor itself is transferred; it can integrate into the bacterial chromosomal resulting in a Hfr (high frequency of recombination) cell.

F+

F-

an F- cell; chromosomal genes are transferred

mobile sequence of DNA; they harbor genes for drug resistance

uptake and integration of DNA. (occurs in high frequencies in bacteria)

uptake and incorporation of DNA mediated by a virus

encapsidation of a piece of bacterial DNA into a virus particle

DNA from two sources that is spliced together

cut DNA at specific sequences (palindromes); many have been isolated from different microbes.

sequence of DNA that can be used for the formation of recombinant DNA

production of DNA inserts

prodcution of the proein product of that gene

gene for resistance to an antibiotic; used to ensure that transformed bacteria contain the recombiant DNA desired

series of cloned DNAs (genomic, cDNA)

separated by size by agarose gel electrophoresis

comibnes the separation of DNA by size with the detection of specific DNA sequences by hybridization (allowing mixed duplexes to form between a test DNA or probe and the DNA being studied)

way to aplify DNA

it uses oligonucleotide primers and Taq DNA polymerase (thermostable) in a thermocycler to produce many copies of DNA in a test tube

it uses dideoxynucleotides as chain terminators

by polycrylamide gel electrophoresis

public database where tens of billions of nucleotides of DNA sequences are available

consist of all genes in an organism

many genes can be analyzed simultaneously

the proteome

by a two-dimensional gel electrophoresis