what is a genome?

the sum total of genetic material of an organism, the most exists in the form of chromosomes, some may appear in non-chromosomal forms

what are the non-chromosomal forms of a genome?

plasmid and organelles

what is a plasmid?

tiny extra pieces of DNA

non-chromosomal genome in organelles?

mitochondria and chloroplasts have their own DNA

what is a chromosome?

a distinct cellular structure composed of a neatly packaged DNA molecule

what is a eukaryotic chromosome?

located in the nucleus; they vary in number from a few to hundreds; they can occur in pairs (diploid) or singles (haploid); they have a linear appearance

what is a bacterial chromosome?

usually single, circular (double-stranded) chromosome, although many bacteria have multiple, circular chromosomes and some have linear chromosomes

what is a gene?

basic informational packets in which a chromosome is subdivided containing the necessary code for a particular cell function

what are the three categories of genes?

structural genes that code for proteins

genes that code for the RNA machinery used in protein production

regulatory genes that control gene expression

what is a geneotype?

the sum of all types of genes constituting an organism's distinctive genetic makeup

what is a phenotype?

the expression of the genotype that creates certain structures or functions (traits)

structure of DNA

phosphate, deoxyribose sugar, nitrogenous base

nitrogenous bases

purines (A,G) and pyrimidines (T,C)

adenine always pairs with

thymine

guanine always pairs with

cytosine

DNA arrangement

antiparallel

one side of the helix runs in the opposite direction of the other (5'-3' and 3'-5')

what are the steps of DNA replication?

semiconservative replication

each daughter molecule is identical to the parent in composition

neither is completely new

the template strand is an original parental DNA strand

helicase

unzipping the DNA helix

primase

synthesizing an RNA primer

DNA polymerase 3

adding bases to the new DNA chain and proofreading the chain for mistakes

functions once the DNA helix strands are unwound and separated

synthesizes a daughter strand of DNA using the parental strand as a template

can only add nucleotides to an existing chain 5'-3' direction

DNA polymerase 1

removing primer, closing gaps, and repairing mismatches

ligase

final binding of nicks in DNA during synthesis and repair

topoisomerase 1

making single-stranded DNA breaks to relieve supercoiling at origin

topoisomerase 2 and 4

making double-stranded DNA breaks to remove supercoiling ahead of origin and separate replicated daughter DNA molecules

replication fork

the place in the helix where the strands are unwound and replication is taking place

each circular DNA molecule will have two replication forks

primer

a length of RNA that is inserted initially during replication before being replaced by DNA

how does the synthesis of the leading strand differ from the synthesis of the lagging strand?

leading strand: new DNA synthesized continuously in a 5' to 3' direction

lagging strand: new strand must be synthesized in short segments (5' to 3'), later sealed together to form a strand in 3' to 5' direction

Okazaki fragments

short segments of DNA synthesized in a 5' to 3' direction which are then sealed together to form the 3' to 5' strand

the central dogma

transcription: DNA is used to synthesize RNA

translation: RNA used to produce proteins

why is the central dogma incomplete?

a wide variety of RNAs are used to regulate gene function

many genetic malfunctions that cause human disease are found in regulatory RNA, not in genes for proteins

the DNA that codes for these crucial RNA molecules was once called "junk" DNA

connection between DNA and an organism's traits

a protein's primary structure determines its characteristic shape and function

proteins ultimately determine phenotype

DNA mainly a blueprint that tells the cell which kinds of proteins to make and how to make them

participants in transcription and translation

mRNA

tRNA

rRNA

ribosomes

several types of enzymes

many raw materials

mRNA

transports the DNA master code to the ribosome

synthesized in a process similar to synthesis of the leading strand during DNA replication

tRNA

brings amino acids to ribosome during translation

rRNA

forms the major part of a ribosome and participates in protein synthesis

3-dimensional shapes that create the two subunits of the ribosome

miRNA

regulation of gene expression and coiling of chromatin

primer

primes DNA

ribozymes and spliceosomes

remove introns from other RNAs in eukaryotes

codon

a series of triplet bases that hold the message of the transcribed mRNA

anticodon

found at the bottom loop of the cloverleaf

designates the specificity of the tRNA and complements the mRNA codon

redudancy

certain amino acids are represented by multiple codons

allows for the insertion of correct amino acids even when mistakes occur in the DNA sequence

wobble

only the first two nucleotides are required to encode the correct amino acid

the third nucleotide does not change its sense

permits some variation or mutation without altering the message

start codon

the first 3 RNA nucleotides that signal the beginning of the message

AUG

stop codons

nonsense codons - one of three codons that has no corresponding tRNA and causes translation to be terminated

UAA, UAG, UGA

introns

intervening sequences of bases that do not code for protein

excised into lariats by spliceosome

exons

coding regions

promoter sequence

recognized by RNA polymerase

operator

acts as an on/off switch for transcription

regulator

composed of the gene that codes for the repressor, a protein capable of repressing the operon

A site

A site accepts incoming tRNA molecules carrying amino acids

P site

P site holds the tRNA attached to the growing polypeptide chain until the next amino acid is added

operons

coordinated set of genes regulated as a single unit

found only in bacteria and archaea

can be inducible or repressible, determined by how transcription is affected by the environment surrounding the cell

transcription factors

insert into the grooves of the DNA molecule and enhance the transcription of specific genes

regulate gene expression in response to environmental stimuli

DNA "knot"

cytosines bind to other cytosines forming a "knot" in the helix of DNA

blocks the promoter region of genes in order to stop transcription

drugs that inhibit protein synthesis

rifamycins

actinomycin D

drugs that interfere with the ribosome

erythromycin

spectinomycin

recombination

an event in which one bacterium donates DNA to another bacterium

recombinant

any organism that contains and expresses genes that originated in another organism

horizontal gene transfer

any transfer of DNA that results in organisms acquiring new genes that did not come directly from parent organisms

conjugation

direct

donor cell with pilus

fertility plasmid in donor, both donor and recipient alive, bridge forms between cells to transfer DNA

transformation

indirect

free donor DNA (fragment), live; competent recipient cell

the acceptance by a bacterial cell of small fragments of soluble DNA from the surrounding environment

transduction

indirect

toxins; enzymes for sugar fermentation; drug resistance

conjugation F factor

resistance (R) plasmids or factors

carry genes for resisting antibiotics or other drugs

commonly shared among bacteria through conjugation

can confer multiple resistance to antibiotics

R factors can also carry genetic codes for resistance to heavy metals or for synthesizing virulence factors

competent

cells that are capable of accepting genetic material through transformation

generalized transduction

random fragments of disintegrating host DNA are taken up by a phage during assembly

any gene from the bacterium can be transmitted

specialized transduction

a highly specific part of the host genome is incorporated into the virus when the prophage DNA separates from the chromosome (carrying host genes with it)

transposable elements

jumping genes shift from one part of the genome to another

from one chromosomal site to another, from a chromosome to a plasmid, and from a plasmid to a chromosome

insertion elements

the smallest TEs consist only of two tandem repeats

retroptransposon

a type of TE that can transcribe DNA into RNA and then back into DNA for insertion in a new location

general effects of TEs

scramble genetic language

can be beneficial or adverse, depending on: where the insertion occurs in a chromosome, what kind of genes are relocated, the type of cell involved

effects of TEs in bacteria

changes in colony morphology, pigmentation, and antigenic characteristics

replacement of damaged DNA

transfer of drug resistance between bacteria

pathogenicity islands

contain multiple genes that are coordinated to create a new trait in bacterium, making it pathogenic

mutation

any change to the nucleotide sequence in the genome

the driving force of evolution

in microorganisms, mutations become evident in altered gene expression, such as altered pigment production or development of resistance to a drug

wild type mutation

a microorganism that exhibits a natural, non-mutated characteristic

the trait present in the highest numbers in a population

mutant strain

an organism that bears a mutation

spontaneous mutation

a random change in the DNA arising from errors in replication that occur randomly

induced mutations

result from exposure to known physical or chemical agents that damage DNA (known as mutagens)

nitrous acid, bisulfite

chemical agent

remove an amino group from some bases

ethidium bromide

chemical agent

inserts between the paired bases

acridine dyes

chemical agent

cause frameshift due to insertion between base pairs

nitrogen base analogs

chemical agent

compete with natural bases for sites of replicating DNA

ionizing (gamma rays, X rays)

radiation agent

form free radicals that cause single or double breaks in DNA

ultraviolet

radiation agent

causes cross-links between adjacent pyrimidines

point mutation

small mutation that affects only a single base on a gene

involve addition, deletion, or substitution of single bases

lethal mutation

mutation that leads to cell dysfunction or death

neutral mutation

produce neither adverse nor helpful changes

missense mutation

any change in the code that leads to the placement of different amino acids

nonsense mutation

changes in normal codon into a stop codon

silent mutation

alters a base but does not change the amino acid

the redudancy by a change in the third base of the codon

back mutation

occurs when a gene that has undergone mutation reverses to its original base composition

frameshift mutation

occurs when one or more bases are inserted into or deleted from a newly synthesized DNA strand

alters the reading frame of mRNA

nearly always results in a nonfunctional protein

photoactivation

light repair of damage caused by ultraviolet radiation

requires visible light and a light-sensitive enzyme called DNA photolyase, which can detect and attach to the damaged areas

mismatch repair

a repair system can locate mismatched bases that were missed during proofreading

the base must be replaced soon after the mismatch is made, or the repair enzymes will not recognize it

excision repair

mutations are excised by a series of enzymes that remove the incorrect bases and add the correct ones

the ames test

used to rapidly detect chemicals with carcinogenic potential

uses bacteria (salmonella typhimurim) rather than experimental animals

histone + colonies arising from spontaneous back-mutation on control plate

histone + colonies in presence of chemical on test plate