BIO 208 - Microbiology - Unit 3 - Microbial Geneticspeople.cst.cmich.edu/alm1ew/208 unit 3 genetics.docx · Web viewBIO 208 Microbiology Unit 3 Patterns of Information Flow in the

1BIO 208 Microbiology Unit 3 Patterns of Information Flow in the Microbial World

This outline is intended to facilitate your preparation for lecture. This outline will NOT substitute for regular lecture attendance.

Unit 3

I. Patterns of Information Flow in the Microbial World Fig. 8.2

Within one organism (cell) From one organism to another:

o from one generation to the next (vertical transfer)o between cells of the same generation (horizontal transfer)

A. Basic genetics review:

1. Structure of nucleotides and nucleic acids

Nucleotides are

composed of 3 basic parts (label drawing on next page):


C C

C C

OCOPOPOP

O O

H H

OOO

O

O

H

O

H

O

H

3 phosphates = triphosphate

5 carbon sugar = ribose

N

C

N

C

CC

O

O

Base

Fig. 2.17 - modified


The base of a nucleotide can be one of 5 kinds:

Adenine –Guanine – Thymine – Cytosine – Uracil –

A nucleic acid is a

There are 2 kinds of nucleic acids:1. RNA – Ribonucleic acid

Sugar - Bases -

3 kinds of RNA molecules: transfer RNA (tRNA)messenger RNA (mRNA)ribosomal RNA (rRNA)

RNA molecules are generally

2. DNA – deoxyribonucleic acidSugar - Bases –

DNA molecules are generally


A nucleic acid is a polymer of nucleotides. (shown with DNA nucleotides):


H

H

H

H

Nucleotides continue to be added until a long polymer is formed:

Notice a couple things about this polymer:1.

2.

3.

4.

H3C


The sequence of the nucleotide bases in a nucleic acid has meaning. The S-P backbone is constant, the same in all DNA molecules.

**It is the sequence of the nucleotide bases that carries the information.

Base pairing -

In the example shown here:


Joining of nucleotides to make a nucleic acidFig. 8.4


The two strands of nucleic acid are complementary in base sequence and also antiparallel or of opposite orientation with respect to 5’ à 3’.

Fig. 8.3b

The 2 strands twist around each other to form a double helix


The double helix of DNA has to be organized and packed to fit inside the cell. Fig. 8.1a

In all cells, DNA is organized into chromosomes, but the size of the DNA molecule, the number, structure, and packaging of the chromosome varies among the 3 Domains:

Archaea Bacteria Eukaryahow many base pairs are in the DNA?

5 x 105 to 5 x 106 2 x 106 1 x 107 and more

how many chromosomes does cell have?

1 1 many

what is the structure of chromosome?

closed circle closed circle linear

how is chromosome packed to fit in cell?

histones, nucleosome-like

supercoiling,DNA binding proteins

histones, nucleosomes, chromatin

B. Flow of information from one generation to the next ( = vertical transfer)

1. Overview DNA Replication (repl.) (pp. 212-216)DNA replication is semiconservative – resulting ds DNA after replication is made up of 1 old strand of DNA and 1 new strand of DNA.Fig. 8.3


Fig. 8.5 Review of DNA replication - Events at the DNA Replication Fork

1. Notice the orientation of each of the strands of DNA2. Enzymes (helicases) unwind the parental double helix3. Proteins stabilize the unwound, single stranded parental DNA (otherwise it would just re-pair

and coil back up)4. DNA polymerase catalyzes the addition of new nucleotides to the new strand5. DNA polymerase can only add nucleotides to an exposed 3’OH6. The new strand of DNA is synthesized with the new strand extending in a 5’ to 3’ direction.7. But what about the other strand, how is it copied?8. The other strand has no exposed 3’OH so DNA polymerase cannot act9. But RNA polymerase does not need an exposed 3’OH in order to add nucleotides10. RNA polymerase brings in complementary RNA nucleotides to make a short section of RNA

called a “primer”11. These RNA primers have exposed 3’OH so now DNA polymerase can work.12. DNA polymerase adds nucleotides causing the new strand to grow in a 5’ to 3’ direction (as on

the other strand).13. Synthesis on this strand is discontinuous, not continuous as on the other strand.14. Discontinuous synthesis, because there are more steps, is slower.15. The synthesis on this strand will lag behind, so this strand can be called the “lagging strand”, the

other strand can be called the “leading strand”.16. Eventually, on the lagging strand, the DNA polymerase will run into the back of an RNA primer.17. The DNA polymerase removes the RNA nucleotides and replaces them with DNA nucleotides.18. Another enzyme called DNA ligase joins the fragments of the lagging strand.


In Eukarya the chromosome is linear, but in Bacteria and Archaea the chromosome is circular.

How do you replicate a circular DNA?

2. DNA replication in Bacteria Fig. 8.6

Origin of replication –

2 repl. forks form.

Bidirectional –

**Consequences –

DNA replication in Archaea -

C. Flow of information within a single cell

**DNA contains sequences of nucleotides (specifically nucleotide bases) that code for functional products – these functional products are called genes.

Gene –

Functional products may be:Structural RNAs Proteins


Pribnow sequence

DNAInitial binding site First nucleotide transcribed

Promoter

How does information stored in DNA ultimately become a functional product?

1. Transcription (transc.) (p. 216)

Transc. will require: DNA template RNA nucleotides (with the bases A, U, C, G)

DNA template sequence (of nucleotide bases)

5’-A-C-G-T-T-C-G-T-A-A-C-G-G-G-C-T-A-3’

The RNA copy of this

The enzyme RNA polymerase (RNA pol) – A large DNA binding protein whose job is to catalyze the addition of RNA nucleotides. The RNA polymerase of Archaea is more similar to that of Eukarya than to Bacteria.

2 kinds of informational DNA nucleotide sequences:Promoter –

Terminator –


Review the process of transcription Fig. 8.7

The orientation of the RNA copy (= the transcript) produced is complementary and anti-parallel to the template DNA.

The RNA transcript may be:ribosomal RNA (rRNA)transfer RNA (tRNA)messenger RNA (mRNA)

What happens next to the RNA transcript? – is the transcript modified after it is made? (called post-transcriptional modification)

Bacteria and Archaea EukaryarRNA / tRNA molecules modified modifiedmRNA not modified extensively modified


5’ 3’AUG

codon

2. Translation (transl.) (pp. 217-221)

How does the information in RNA get passed on to proteins? Translate the information carried in the mRNA molecule and use that information to build a protein (a protein is a polymer of amino acids).

Transl. will require: mRNA – genetic code tRNA - rRNA -

mRNA

Codon – 3 RNA bases in sequence, read as 3 together, a triplet

tRNA – the translator –


5’ 3’

How does translation get started? – there is a specific transl. start in the mRNA– how the cell “knows” where to start translating mRNA into a protein.

There are similarities and differences among the 3 Domains what the transl. start is

Bacteria Archaea Eukarya1 mRNA à several proteins (operon)

1 mRNA à several proteins

1 mRNA à 1 protein

Transl. start

consensus sequence consensus sequence 5’-P end of mRNA

1st aa N-formylmethionine Methionine Methionine1st a.a. – the first amino acid in the newly formed protein.

mRNA codon sequence


Where does translation take place?

Ribosomes are complex molecules composed of rRNA and proteins. Ribosomes will self-assemble on the mRNA molecule.

Bacteria and Archaea Eukarya

Subunit sizes 30S 50S

40S 60S

rRNA sizes 16S* 5S23S

18S* 5S5.8S28S

# of proteins 52 82Complete ribosome 70S 80S

Remember that S stands for “Svedberg”, which refers to how the molecule moves in a centrifugal force.* it was the DNA coding for these rRNA that Carl Woese sequenced to discover the 3 Domains of Life.


Review the process of translation - Fig. 8.9, 8.8

Summarizing where transcription and translation happen in the 3 Domains and what the consequences of where are.

Bacteria and Archaea EukaryaSite of transcription cytoplasm nucleusSite of translation cytoplasm cytoplasm


3. Gene Expression and Regulation

In Eukarya the mRNA transcript is formed in the nucleus and then leaves the nucleus, traveling to the ribosomes in the cytoplasm.

**In Bacteria and Archaea – transcription and translation both occur in the cytoplasm – this means that transcription and translation occur simultaneously.

Expression –

Eukarya regulate gene expression by regulating whether or not translation occurs (an event physically separated from transcription in the cell).

But how can Bacteria and Archaea regulate gene expression?

Regulation of gene expression in Bacteria and Archaea - happens by regulating whether or not transcription occurs. (pp. 221-226).

How can they do this?

Bacteria have 2 kinds of genes:

Constitutive – Ex. Genes for enzymes necessary to break down glucose

Inducible – Ex. Genes for enzymes for break down of lactose


**Example of regulation of inducible genes - Lactose Operon of E. coli

Operon –

1. Structure of lac operon of E. coliFig. 8.12 modified

a. 3 Structural genes - encode enzymesGene EnzymeZ -galactosidaseY Lactose permeaseA Transacetylase

b. Promoter and OperatorOperator –

c. I gene – codes for a repressor protein

RNA polymerase also involved


2. How does E. coli control expression of these genes?

a. If have glucose but no lactose – don’t want structural genes for lactose use to be expressed.

I gene is transc. & transl. into repressor protein that binds to DNA at the operator region – physically blocks the movement of the RNA polymerase so the structural genes are NOT expressed.


b. If there is no glucose but there is lactose:

I gene is transc. & transl. into repressor protein, as above. But lactose is transported into cell where it is converted into allolactose (which is called an inducer) – allolactose binds to the repressor protein. Now the repressor protein can’t bind to the operator sequence. The RNA polymerase is not blocked. The structural genes are expressed and the 3 enzymes needed to breakdown lactose are made.


D. Flow of information from one cell to another cell of the same generation

**Flow of information between cells of the same generation (called horizontal gene transfer = HGT) (pp. 233-241)

**Unlike Eukarya, which evolve principally through the modification of existing genetic information, Bacteria and Archaea have obtained a significant proportion of their genetic diversity by taking genetic material from distantly related organisms.

Importance of HGT:

• May account for 10 to 50% of all the genes in the genome of a Bacteria or Archaea.• Has occurred between diverse species and even across the boundaries of Domains (i.e.,

Bacteria have acquired genes from Eukarya). • Produces extremely dynamic genomes in which substantial amounts of DNA are introduced

into and deleted from the chromosome. • Has led to the emergence of new pathogenic microbes.

How do microbes of the same generation exchange DNA?

Overall process involves:Recombination –

Recombination always requires:Donor – Recipient –Recombinant


**3 Mechanisms of Horizontal Gene Transfer (HGT)

1. Transformation – DNA released by one bacterium (naked DNA) is taken up by a 2nd

Fig. 8.25

Ex. Streptococcus pneumoniae -

2. Conjugation – DNA transfer is mediated by a plasmid (introduced in Unit 1)

Conjugation requires direct cell to cell contact via a pilus (introduced in Unit 1)Fig. 8.27

Examples:Pseudomonas –

Clostridium tetani –

Bacillus anthracis –

Many, many antibiotic resistance


3. Transduction – bacterial DNA is transferred from donor to recipient inside a virus that specifically infects bacterial cells (a bacteriophage or phage; more about these later in this Unit)Fig. 8.28

Examples:Corynebacterium diphtheriae –

Streptococcus pyogenes –

E. coli O157:H7 -

Documents

BIO 208 - Microbiology - Unit 3 - Microbial Geneticspeople.cst.cmich.edu/alm1ew/208 unit 3 genetics.docx · Web viewBIO 208 Microbiology Unit 3 Patterns of Information Flow in the