Microbiology Nucleic Acids

What does RNA structure contain?

• nitrogenous bases

  • A, G, C, U

• pentose sugar (ribose)

• usually consists of single strand

  • can coil back on itself

What are the three types of RNA?

rRNA, tRNA, mRNA

How do the different types of RNA differ?

In function, site of synthesis in eukaryotic cells, and structure

Genome

All genetic material of an organism

Plasmids

Small circular “minichromosomes” that carry benefical genes not needed for normal function

Fertility Factors

Allow transfer of genes between cells

Resistance Factors

Resistance to antibiotics or heavy metals

Bacteriocin factors

For bacteriocin toxins to kill other bacteria

Virulence factors

Provide functions involved in pathogenesis

How many chromosomes and protein coding genes do human cells have?

46 chromosomes containing 20,000 protein coding genes

What does a bacterial chromosome contain?

• single DNA molecule

• No histones

• haploid

  • no dominance/recessivness

  • located in nucleoid

What 5 things can happen to genetic information?

1. it can be copied

2. it can be expressed

3. it can be changed

4. it can be repaired if damaged

5. it can be recomined/exchanged

What is Prokaryotic DNA?

A closed circular supercoiled molecule associated with basic proteins

Why is supercoiling important?

• Allows DNA to fit in the cell

• Helps control access

What is topoisomerase?

Molecules responsible for supercoiling and relaxing DNA

i.e. Gyrase

What does Eukaryotic DNA contain?

• linear molecules

• associated with histones

• coiled into repeating units called nucleosomes

What does the central dogma state?

Genetic information flows from DNA→RNA→protein, this flow is unidirectional and irreversible

What is Transcription?

Conversion of DNA encoded information to RNA

What is Translation?

Conversion of information from mRNA to protin

Genetic code

Nucleotide sequence in DNA dictates the end product synthesis

What does semiconservative mean?

One strand from parental DNA is always conserved in the new DNA

Describe semiconservative DNA replication

1. DNA double helix denatures (strand separates)

2. Each strand serves as the template for the synthesis of new 2nd strand

3. DNA polymerase adds complementary nucleotides

What is the pattern of DNA synthesis in prokaryotes?

• bidirectional from a single origin of replication

Replicon

Portion of the genome that contains an origin and is replicated as a unit

What is the pattern of DNA synthesis is eukaryotes?

• bidirectional

• multiple origins of replication

• some small circular genomes (i.e. viruses and plasmids)

• replicate by rolling-circle mechanism

Helicase

Unzipping the DNA helix

Primase

Synthesizing an RNA primer

DNA polymerase III

Adding bases to the new DNA chain; proofreading the chain for mistakes

DNA polymerase I

Removing primer, closing gaps, repairing mistakes

Gyrase

Supercoiling

Ligase

Final binding of nicks in DNA during synthesis and repair

What does DnaA do?

Initiation of replication, binds to Ori

What does DnaB do?

Helicase, breaks hydrogen bonds

What does DnaC do?

Helicase loader, DnaC and DnaA help DnaB to stay on the template DNA

What do SSB proteins do?

Bind single-stranded DNA after strands are separated

What does Ribonuclease H do?

Removes primer

What does Tus do?

Termination of replication

What does Topoisomerase IV do?

Separation of chromosome upon completion of DNA replication

What is the genetic code?

The manner in which genetic instructions for polypeptide synthesis are stored within genome

What is collinearity?

Sequence of base pairs in DNA corresponds to the amino acid sequence of polypeptide encoded

What is a codon?

• Genetic code word

• Specifies an amino acid

• meaning deciphered by Marshall Nirenberg, Khorana (1960)

What is code degreneracy?

Up to six different codons can code for a single amino acid

What are sense codons?

The 61 codons that specify amino acids

What are stop (nonsense) codons?

• The three codons used as translation termination signals (UGA, UAG, UAA)

• do not encode amino acids

What is cistron?

Gene that encodes a polypeptide

What is a reading frame?

Organization of codons such that they can be read to give rise to a gene product

What is gene structure?

• linear sequence of nucleotides with a fixed start and end point

• encodes a polypeptide, a tRNA, or an rRNA

Where does transcription start?

At promoter DNA (TATA box)

Where does transcription end?

At terminator DNA (stop)

What is the enzyme responsible for the production of the RNA molecule?

RNA polymerase

How is RNA different from DNA?

• RNA has a sugar ribose, DNA has a sugar deoxyribose

• RNA contains uracil (U), DNA has thymine (T)

• RNA molecule is single-stranded, DNA is double stranded

How does RNA polymerase function?

• Breaks nucleotides at the H-bond between bases

• Moves along one of the DNA strands and links RNA nucleotides together

• No “lagging strand” as only one DNA strand is transcribed

What is the Sine Dalgerno Sequence?

Ribosomal binding site in the prokaryotic mRNA about 8 bases upstream of start codon

What is the Pribnow Box (in bacteria)?

TATAAT

When is RNA processing needed?

In a Eukaryotic cell, not needed in prokaryotic cell

What is RNA processing?

• Maturation of pre-RNA molecules

• Cap (7-methylguanosine) and tail (poly A 150-250 adenylated) added

• Introns spliced out by spicesome and exons come together

Where does RNA processing occur?

Nucleus

What happens when RNA processing is finished?

A mature RNA molecule leaves the nucleus to the cytoplasm

What does mRNA do?

Carries the message for a specific protein

What is mRNA made up of?

500-1000 nucleotides, and codons

What does tRNA do?

Picks up amino acid in cytoplasm and transports it to mRNA

What is tRNA made up of?

75-80 nucleotides long

What does tRNA contain?

Contains anticodons that are complementary to mRNA codons

What is rRNA made up of?

100-3000 nucleotides

What does rRNA do?

Associates with proteins to form ribosomes

What is snRNA?

Small nuclear RNA, with proteins forms complexes that are used in RNA processing in eukaryotes (not prokaryotes)

What is miRNA?

Micro RNA, functions as post-transcriptional regulator that binds to mRNA, silencing it

What is siRNA?

Small interfering RNA, interferes with gene expression by binding to mRNA transcripts facilitating their degradation