Brock Biology Of Microorganisms Chapter 7

Front 1

The three key processes of macromolecular synthesis

Back 1

1) DNA replication

2) transcription

3) translation

Front 2

Transcription

Back 2

synthesis of RNA from a DNA template

Front 3

Translation

Back 3

synthesis of proteins using messenger RNA as a template

Front 4

The three types of RNA

Back 4

1) Messenger RNA (mRNA)

2) Transfer RNA (tRNA)

3) Ribosomal RNA (rRNA)

Front 5

Role of mRNA

Back 5

used to encode polypeptides (proteins)

Front 6

Role of tRNA and rRNA

Back 6

paly part in protein synthesis but do not themselves encode genetic information for making proteins

Front 7

Three characteristics of Prokaryotic Genetics

Back 7

1) circular DNA

2) no membrane separating the chromosome and cytoplasm

3) vast majority have no introns

Front 8

Three characteristics of Eukaryotic Genetics

Back 8

1) linear DNA

2) chromosomes inside nucleus and ribosomes in the cytoplasm

3) all have introns between exons

Front 9

Borrelia burgdorferi

Back 9

rare instance of prokaryotes with linear DNA

Front 10

Eukaryotic Coding/Non-coding regions

Back 10

most eukaryotic genes have both coding regions(exons) and noncoding regions (introns)

Front 11

Primary Transcript

Back 11

both introns and exons transcribed into this

an unprocessed RNA molecule that is the direct product of transcription

Front 12

Three characteristics of DNA structure

Back 12

1) DNA is a double-stranded molecule

2) forms a helical configuration

3) measured in terms of numbers of base pairs

Front 13

Nucleotide pairs (with number of hydrogen bonds)

Back 13

Adenine (A) pair with Thymines (T) [2 hydrogen bonds]

Guanines (G) pair with Cytosines (C) [3 hydrogen bonds]

Front 14

How do the complementary strands of DNA run in respect to one another?

Back 14

They run in an "antiparallel" fashion, where the sense strand (5' to 3') runs antiparallel to the antisense strand (3' to 5')

Front 15

What is meant by DNA being a right handed molecule?

Back 15

This means that it is twisted in a right to left direction

Front 16

Kilobases (kb)

Back 16

The way DNA size is measured(1kb= 1000 bases)

Front 17

Megabases (mb)

Back 17

The way DNA size is measured in respect to genome sizes (1 mb= 1 million bases)

Front 18

Inverted Repeats

Back 18

Short repeated sequences in DNA molecules

Front 19

Stem-loop structures

Back 19

result from formation of inverted repeats

more common in RNA molecules than in DNA

creat a type of secondary structure that can be critical to the function

Front 20

Melting/Denaturation

Back 20

breaks apart hydrogen bonds

when two strands of a DNA molecule are separated by heat

Front 21

Annealing

Back 21

when denatured strands are cooled

double stranded DNA molecule will reform

Front 22

Hybridization

Back 22

invovles putting together two DNA strands from different sources

annealing can be used to do this

Front 23

Supercoiling

Back 23

very long DNA molecule can be packaged into the cell because it is further twisted

can occur in a positive or negative direction

Front 24

Negatively supercoiled

Back 24

Most DNA is supercoiled this way

twisted in the oppposite direction from the right handed double helix

Front 25

DNA gyrase

Back 25

produces negative supercoiling in bacteria and Archae

belongs to group of enzymes caled "topoisomerases"

classified as topoisomerase II

Front 26

Topoisomerase

Back 26

a group of enzymes

DNA gyrase classified as type II of this

Front 27

Three facts about viruses

Back 27

1) Consist of either RNA or DNA

2) control their own replication

3) viral chromosome may be linear or circular

Front 28

Three facts about plasmids

Back 28

1) replicate separately from chromosomes

2) Double Stranded DNA that is usually circular but can be linear

3) Do not cause dammage and do not have extracellular forms

Front 29

Three facts about organellar genomes

Back 29

1) Examples are chloroplasts and mitochondria

2) DNA is separate from nuclear DNA

3) DNA replicated independently of nuclear DNA

Front 30

Transposable Elements

Back 30

Molecules of DNA

can move from one site on a chromosome to another

paly an important role in genetic variation

Front 31

DNA Polymerase

Back 31

Catalyzes the addition of nucleotides to the 3'-OH group

Front 32

Primer

Back 32

short (<15 bases) single stranded pieces of RNA

primer strand synthesized by "primase"

has an available free 3' OH

Front 33

Bidirectional replication in circular chromosomes

Back 33

1) replication is bidirectional from the point of origin of replication

2) two replication forks on chromosome replicating in opposite directions

Front 34

Exonucleases

Back 34

DNA Polymerase I and III

have a proofreading function

they can remove mismatched bases and replace them with the correct bases

mutation rate 10^-8 to 10^-11 errors per base insertion

Front 35

Restriction Enzymes/Endonucleases (Three facts)

Back 35

1) Found in both Archae and Bacteria (rarely found in Eukaryotes)

2) recognize specific DNA sequences and cut the DNA at those sites

3) Essential for in vitro DNA manipulation

4) in prokaryotes protect them from invading foreign DNA

Front 36

How do prokaryotes protect their own DNA

Back 36

they do so by modifying through methylation

Front 37

methylation

Back 37

specific bases within the recognition sequence have methyl groups attached to them

Front 38

How does the Restriction Enzyme Digest work?

Back 38

DNA frament can undergo this

Restriction enzyme will cut DNA at each site it recognizes

eletrophoresis gel contains digested fragments and yields a restriction map

Front 39

What is nucleic acid hybridization and the southern blot used for and how do they work?

Back 39

used to check for the presence of DNA sequence in a DNA sampe

Double stranded DNA fragments from a gel are transferred to a membrane and denatured

Single stranded denatured DNA fragments are annealed to complementary strands probe containing a label or are probed using a labeled single stranded oligonucleotide

Front 40

What does DNA sequencing require? (5)

Back 40

1) DNA template

2) Primer

3) Deoxy nucleotides

4) Dideoxy nucleotides

5) A polymerase enzyme

Front 41

What method is preferred for DNA sequencing and what does this method entail?

Back 41

The sanger method is used

DNA is sequenced by making a copy of a single stranded DNA template strand

polymerase adds nucleotides

dideoxy analog acts as the specific chain termination reagent

Front 42

Difference between normal deoxynucleotide and dideoxy analog

Back 42

dideoxy analog is missing an OH at the 3' end

Front 43

Automated Sequencing

Back 43

based on sanger dideoxy method

fluorescent labeled primers or nucleotides are used

Front 44

Synthetic DNA

Back 44

automated procedure used to synthesize short oligonucleotides (<100 bp)

can be used as primers or probes (may contain a label)

Front 45

Polymerase Chain Reaction

Back 45

amplifys DNA

multiplies DNA sequence by a billioni fold

DNA template is dantured by heat (requires Taq polymerase, a thero-stable enzyme)

Front 46

Uses for the polymerase chain reaction (3)

Back 46

1) DNA sequencing

2) Cloning

3) DNA footprinting

Front 47

Transcription Terminators (3)

Back 47

1) Intrinsic terminators that involve sequence patterns only

2) inverted repeats that lead to stem loop formation

3) GC rich followed by AT rich sequences

Front 48

Specific Protein factors

Back 48

other termination factors require this

example is a Rho protein

Front 49

Rho protein

Back 49

binds directly to RNA

causes both the RNA polymerase and newly synthesized RNA strand to be released from the DNA

Front 50

Rho dependent termination site

Back 50

site where newly synthesized RNA is released from teh DNA

Front 51

RNA Longevity

Back 51

1) in prokaryotes, mRNA's have short "half lives" (usually only minutes)

2) rRNAs and t RNAs are more stable because of their highly folded structures

3) RNAs are degraded by cellular ribonucleases

Front 52

Polycistronic mRNA

Back 52

genes encoding related proteins are clustered together in prokaryotes

mRNA encoding a group of "cotranscribed" genes

Front 53

Operon

Back 53

Genes that are transcribed from a single promoter consitute this

Front 54

Codon

Back 54

triplet of bases that encode a specific amino acid

64 possible codons (4 bases taken three at a time 4^3)

Front 55

Whats so special about the 3rd base position in the codon?

Back 55

1) changing this may not always change the amino acid

2) irregular base pairing may be tolerated at the 3rd base position

Front 56

Start codon

Back 56

AUG (begins the reading frame)

establishes the open reading frame

Front 57

Stop codons (3)

Back 57

UAA, UAG, UGA (transcription terminates)

Front 58

organisms where nonsense codons encode amino acids (3)

Back 58

Paramecium (Eukarya)

Mycoplasm (Bacteria)

Some animal mitochondria

Front 59

What is meant by the term "codon usage bias"?

Back 59

for multiple encoded amino acids, not all codons will be used equally

Front 60

Transfer RNA

Back 60

contain an anit-codon portion that base pairs with teh codon portion of the mRNA

Front 61

aminoacyl-tRNA synthetases

Back 61

enzyme that helps tRNAs bind a specific amino acid

Front 62

Structure of tRNAs (4 facts)

Back 62

1) short single stranded molecules with extensive secondary structure

2) have lengths of 73-93 nucleotides

3) have conserved and variable regions

4) have cloverleaf structure

Front 63

How many different types of tRNAs are in bacteria cells and mammalian cells respectively?

Back 63

60 in bacteria

100-110 in mammalian cells

Front 64

Anti-Codon

Back 64

one of the variable regions

consists of three nucleotides found on teh anti-codon loop

Front 65

acceptor end

Back 65

where the amino acid is attached

Front 66

Ribosomes

Back 66

Site of protein synthesis

consist of two sub units meausured in Svedberg units

consist of ribosomal RNA and ribosomal proteins

Front 67

How long are prokaryotic subunits

Back 67

30S and 50S subunits

Front 68

composition of 30S subunit

Back 68

consists of 16S rRNA and ~21 proteins

Front 69

composition of 50S subunit

Back 69

consists of 5S and 23S rRNA and ~34 proteins

Front 70

how do antibiotics inhibit protein synthesis

Back 70

do so by inhibiting the activity of bacterial ribosomes

Front 71

the four steps of protein synthesis

Back 71

1) Initiation

2) Elongation

3) Termination

4) Release

Front 72

Initiation in protein synthesis

Back 72

involves Shine Delgarno sequence on the mRNA (3-9 bp long)

Front 73

Shine Delgarno Sequence

Back 73

located at the 5' end of mRNA

binds by complementary base paring to regions in the 3' end of the 16S RNA portion of the ribosome

sets up teh correct "reading frame"

Front 74

3 Key sites on the ribosome

Back 74

1) Acceptor Site

2) Peptide Site

3) Exit Site

Front 75

Acceptor Site

Back 75

where the charged amino acid first arrives

Front 76

Peptide Site

Back 76

where the growing polypeptide chain is held

Front 77

Exit Site

Back 77

where the tRNA is released from the ribosome

Front 78

Polysome

Back 78

several ribosomes can simultaneously translate a single mRNA

increases the speed of translation