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78 Cards in this Set

  • Front
  • Back
The three key processes of macromolecular synthesis
1) DNA replication

2) transcription

3) translation
synthesis of RNA from a DNA template
synthesis of proteins using messenger RNA as a template
The three types of RNA
1) Messenger RNA (mRNA)

2) Transfer RNA (tRNA)

3) Ribosomal RNA (rRNA)
Role of mRNA
used to encode polypeptides (proteins)
Role of tRNA and rRNA
paly part in protein synthesis but do not themselves encode genetic information for making proteins
Three characteristics of Prokaryotic Genetics
1) circular DNA

2) no membrane separating the chromosome and cytoplasm

3) vast majority have no introns
Three characteristics of Eukaryotic Genetics
1) linear DNA

2) chromosomes inside nucleus and ribosomes in the cytoplasm

3) all have introns between exons
Borrelia burgdorferi
rare instance of prokaryotes with linear DNA
Eukaryotic Coding/Non-coding regions
most eukaryotic genes have both coding regions(exons) and noncoding regions (introns)
Primary Transcript
both introns and exons transcribed into this

an unprocessed RNA molecule that is the direct product of transcription
Three characteristics of DNA structure
1) DNA is a double-stranded molecule

2) forms a helical configuration

3) measured in terms of numbers of base pairs
Nucleotide pairs (with number of hydrogen bonds)
Adenine (A) pair with Thymines (T) [2 hydrogen bonds]

Guanines (G) pair with Cytosines (C) [3 hydrogen bonds]
How do the complementary strands of DNA run in respect to one another?
They run in an "antiparallel" fashion, where the sense strand (5' to 3') runs antiparallel to the antisense strand (3' to 5')
What is meant by DNA being a right handed molecule?
This means that it is twisted in a right to left direction
Kilobases (kb)
The way DNA size is measured(1kb= 1000 bases)
Megabases (mb)
The way DNA size is measured in respect to genome sizes (1 mb= 1 million bases)
Inverted Repeats
Short repeated sequences in DNA molecules
Stem-loop structures
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
breaks apart hydrogen bonds

when two strands of a DNA molecule are separated by heat
when denatured strands are cooled

double stranded DNA molecule will reform
invovles putting together two DNA strands from different sources

annealing can be used to do this
very long DNA molecule can be packaged into the cell because it is further twisted

can occur in a positive or negative direction
Negatively supercoiled
Most DNA is supercoiled this way

twisted in the oppposite direction from the right handed double helix
DNA gyrase
produces negative supercoiling in bacteria and Archae

belongs to group of enzymes caled "topoisomerases"

classified as topoisomerase II
a group of enzymes

DNA gyrase classified as type II of this
Three facts about viruses
1) Consist of either RNA or DNA

2) control their own replication

3) viral chromosome may be linear or circular
Three facts about plasmids
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
Three facts about organellar genomes
1) Examples are chloroplasts and mitochondria

2) DNA is separate from nuclear DNA

3) DNA replicated independently of nuclear DNA
Transposable Elements
Molecules of DNA

can move from one site on a chromosome to another

paly an important role in genetic variation
DNA Polymerase
Catalyzes the addition of nucleotides to the 3'-OH group
short (<15 bases) single stranded pieces of RNA

primer strand synthesized by "primase"

has an available free 3' OH
Bidirectional replication in circular chromosomes
1) replication is bidirectional from the point of origin of replication

2) two replication forks on chromosome replicating in opposite directions
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
Restriction Enzymes/Endonucleases (Three facts)
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
How do prokaryotes protect their own DNA
they do so by modifying through methylation
specific bases within the recognition sequence have methyl groups attached to them
How does the Restriction Enzyme Digest work?
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
What is nucleic acid hybridization and the southern blot used for and how do they work?
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
What does DNA sequencing require? (5)
1) DNA template

2) Primer

3) Deoxy nucleotides

4) Dideoxy nucleotides

5) A polymerase enzyme
What method is preferred for DNA sequencing and what does this method entail?
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
Difference between normal deoxynucleotide and dideoxy analog
dideoxy analog is missing an OH at the 3' end
Automated Sequencing
based on sanger dideoxy method

fluorescent labeled primers or nucleotides are used
Synthetic DNA
automated procedure used to synthesize short oligonucleotides (<100 bp)

can be used as primers or probes (may contain a label)
Polymerase Chain Reaction
amplifys DNA

multiplies DNA sequence by a billioni fold

DNA template is dantured by heat (requires Taq polymerase, a thero-stable enzyme)
Uses for the polymerase chain reaction (3)
1) DNA sequencing

2) Cloning

3) DNA footprinting
Transcription Terminators (3)
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
Specific Protein factors
other termination factors require this

example is a Rho protein
Rho protein
binds directly to RNA

causes both the RNA polymerase and newly synthesized RNA strand to be released from the DNA
Rho dependent termination site
site where newly synthesized RNA is released from teh DNA
RNA Longevity
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
Polycistronic mRNA
genes encoding related proteins are clustered together in prokaryotes

mRNA encoding a group of "cotranscribed" genes
Genes that are transcribed from a single promoter consitute this
triplet of bases that encode a specific amino acid

64 possible codons (4 bases taken three at a time 4^3)
Whats so special about the 3rd base position in the codon?
1) changing this may not always change the amino acid

2) irregular base pairing may be tolerated at the 3rd base position
Start codon
AUG (begins the reading frame)

establishes the open reading frame
Stop codons (3)
UAA, UAG, UGA (transcription terminates)
organisms where nonsense codons encode amino acids (3)
Paramecium (Eukarya)

Mycoplasm (Bacteria)

Some animal mitochondria
What is meant by the term "codon usage bias"?
for multiple encoded amino acids, not all codons will be used equally
Transfer RNA
contain an anit-codon portion that base pairs with teh codon portion of the mRNA
aminoacyl-tRNA synthetases
enzyme that helps tRNAs bind a specific amino acid
Structure of tRNAs (4 facts)
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
How many different types of tRNAs are in bacteria cells and mammalian cells respectively?
60 in bacteria

100-110 in mammalian cells
one of the variable regions

consists of three nucleotides found on teh anti-codon loop
acceptor end
where the amino acid is attached
Site of protein synthesis

consist of two sub units meausured in Svedberg units

consist of ribosomal RNA and ribosomal proteins
How long are prokaryotic subunits
30S and 50S subunits
composition of 30S subunit
consists of 16S rRNA and ~21 proteins
composition of 50S subunit
consists of 5S and 23S rRNA and ~34 proteins
how do antibiotics inhibit protein synthesis
do so by inhibiting the activity of bacterial ribosomes
the four steps of protein synthesis
1) Initiation

2) Elongation

3) Termination

4) Release
Initiation in protein synthesis
involves Shine Delgarno sequence on the mRNA (3-9 bp long)
Shine Delgarno Sequence
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"
3 Key sites on the ribosome
1) Acceptor Site

2) Peptide Site

3) Exit Site
Acceptor Site
where the charged amino acid first arrives
Peptide Site
where the growing polypeptide chain is held
Exit Site
where the tRNA is released from the ribosome
several ribosomes can simultaneously translate a single mRNA

increases the speed of translation