Micro Chapter 8 Lecture

the study of genes: what they are, how they are replicated, how they carry information, and how they're expressed.

a length of DNA that encodes the instructions for making RNA

deoxyribonucleotides that are linked together

a DNA structure that carries hereditary information (a gene)

the entire genetic complement of an organism

it is made up of chromosomes and plasmids

a nitrogenous base, deoxyribose, and a phosphate group

genotype- an organisms genetic makeup 

phenotype- the physical or physiological expression

• small pieces of DNA that replicate independently because they carry their own information
• - they aren't essential for normal microbial growth, replication, or reproduction
• -they do provide survival advantages

• 1. Fertility (F) factors: conjugation pili
• 2. Resisitance (R) factors: beta lactamase
• 3. Bacteriocin factors: E. coli colicins 
• 4. Virulence plasmids: ex. salmonella modulates immune system to keep it from being killed

*HUMANS DO NOT HAVE PLASMIDS but other Eukaryotes can

• prokaryotes
• complexity: simple
• genome includes: chromosomal DNA and plasmids
• chromosomes: few, usually unicellular and haploid (one copy)
• location of chromosomes: nucleoid region
• DNA organization: histone-like proteins

• eukaryotes
• complexity: complex
• genome includes: chromosomal dna, dna in mitochondria/chloroplasts, and plasmids
• chromosomes: many, nuclear chromosomes are linear and diploid (2 copies)
• location of chromosomes: nucleus
• DNA organization: histones

organizational proteins

euchromatin- loose, allow the gene to be expressed

heterochromatin- tight, do not allow the gene to be expressed

replication- genetic information vertically transferred between generations of cells 

recombination- genetic information transferred between cells of the same generation 

expression- genetic info in the cell produce proteins needed for cell function

• -sugar phosphate backbone (phosphodiester bonds)
• -strands are held together by the hydrogen bonds between the base pairs (AT, GC)
• -the double helix is due to the nucleoproteins
• -strands are anti-parallel and complementary to each other

• purines- AT
• pyrimidines-GC

nucleotides have a 3' and a 5' end. the 3' end must be available with the hydroxyl (-OH) group present to add new nucleotides. 

if the 3' hydroxyl isn't present, the chain stops.

5' to 3' because it starts at the 5' phosphate of one nucleotide to the 3' hydroxyl of the next nucleotide (they are linked together by phosphodiester bonds)

at the origin of replication. 

-the DNA strand's hydrogen bonds are broken by helicase at the replication fork. SSBs (single-stranded binding proteins) help keep the stands separated until they're copied. 

• -leading strand: DNA polymerase adds complementary bases 5' to 3'
• -lagging strand: RNA primase lays down RNA primer in short segments. DNA polymerase III lays new DNA behind it in okazaki fragments. DNA polymerase I then replaces the RNA fragments with DNA and ligase links the okazaki fragments together.

*dna replication is bi-directional (replication bubble)

-each new "daughter" helix of DNA contains an original strand of DNA and a new strand of DNA. 

• -this helps DNA have high fidelity because complements to the original strands are being replicated. 
• -DNA polymerase acts as a proof-reader

players: dNTPs (ATGC), origin, helicase, SSBs, RNA primase, DNA polymerase III and I, Okazaki fragments, and ligase

• -DNA
• -DNA

-dna methylation is when a methyl group (CH₃) is added to an adenine or cytosine

-it plays a role in many processes:

-making an RNA copy of DNA 

-making a protein from RNA transcription (protein synthesis)

DNA is transcripted into RNA 

RNA is translated into proteins (polypeptides)

• RNA primer
• mRNA
• tRNA 
• rRNA

• initiation- when RNA polymerase binds to the promoter, the DNA strand begins to unwind
• (prokaryotes use signma factors, eukaryotes use transcription factors)

elongation- RNA synthesizes a new strand by adding free complementary nucleotides (AUGC) to the template DNA strand. After the DNA has been transcribed, it rewinds

termination- when the mRNA reaches a termination sequence, the strand is let go. We have a completed strand of mRNA

you start with DNA

players involved are: RNA polymerase, promoter, rNTP (nucleotides), and termination sequence

you end with mRNA

• -RNA polymerase doesn't need a primer or helicase
• -Uracil is used in place of thymine
• -rNTPs are used instead of dNTPs
• -RNA polymerase isn't as good at proof reading as dna polymerase. it has a low fidelity=more mutations

*this is why HIV and influenza is constantly mutating and changing

• -in eukaryotes, transcription occurs in the nucleus (mainly), the mitochondria, and chloroplasts 
• -it uses 3 types of polymerases with transcription factors (instead of polymerase and sigma factors) 
• -mRNA is transcribed in the nucleus, before translation. in eukaryotes it is not simultaneous (in prokaryotes transcription and translation happens at the same time in the cytoplasm)

• eukaryotes
• transcription-nucleus, mito and chloroplasts
• translation- cytoplasm

• prokaryotes
• transcription- cytoplasm
• translation- cytoplasm

for eukaryotes the region of DNA/RNA genes that code for proteins contains extrons (protein coding) and introns (non coding). So, the mRNA has to be processed before it leaves the nucleus and is transcribed. 

• alternative splicing- new combinations of exons
• spliceosomes run across the mRNA strand, removing the introns creating just a full strand of RNA with coding exons to be read by the ribosome

it is used for EVERYTHING, even viruses

• start: AUG (methionine) 
• stop: UAA or UAG (tyrosine)

• start: don't write "start", write methionine
• stop: don't write stop, leave empty (or should we write serine)? 

• *this completed code is the strand of protein 
• *the 3rd letter is the wobble position

• mRNA- gives the instructions to make the protein
• tRNA- amino acid carrier 
• ribosomes- amino acid barriers, protein factories 
• amino acids- protein parts; monomers
• GTP- energy 

• you start with mRNA nucleotides that give instruction 
• you end with proteins/amino acids

initiation- the ribosome attaches to the mRNA and the tRNA helps it read and look for a start codon

elongation- as the codons are read, peptide bonds join them together to make a protein/amino acid. each peptide costs 1 GTP. this is why translation is considered high energy. 

termination- when the ribosome and tRNA read the stop codon, the termination factors remove the peptide from the mRNA strand and ribosome

protein synthesis requires a lot of energy. 75% of genes are making proteins all the time for cellular life processes. 

the other 25% is regulated and made only when the cell needs it to conserve energy

• pre-transcriptional control
• translational control

it is when the cell controls gene expression by regulating the amount of mRNA from a specific gene/enzyme is made 

repression- it responds when there is too much final product in the pathway, and it works to turn the gene off 

induction- when there is too little of the gene, the inducible enzymes are turned on and more genes are expressed

• operons
• quorum sensing
• epigenetic control (DNA methylation)
• recruitment of transcriptional factors

heavily methylated genes are turned of

when there is a change in the density of the population, bacteria can tell each other when to stop and start synthesizing to increase their chances of survival

-the functional unit of genes (mainly prokaryotes)

-1 operator (regulates like a stop like), 1 promoter, and structural genes

*the combination of the 3 is the Lac operon

-inducible: genes are turned off until they are needed and turned on 

-repressible: genes are turned on until they are not longer needed and turned off

one of the genes that gets transcribed then translated is tryptophan. when it is made in excess, it binds to the repressor protein. then the repressor protein binds to the operator, which blocks RNA polymerase from synthesizing tryptophan.

instead of regulating how much of an mRNA is made, it regulates how often the mRNA is made into a protein (it affects how readily ribosomes are to read the mRNA)

it allows fine control and can protect proteins from making viruses

siRNA (silence) binds to the mRNA that carries gene that it doesn't want to be expressed. the antisenseRNA (RISC) breaks down the mRNA complex and no protein is made because the ribosomes aren't able to respond to it

• ribosome recruiting to mRNA 
• controlling mRNA stability
• riboswitches
• eukaryotes can control RNA processing and nuclear export

a permanent change in the nucleotide sequence. it can be spontaneous and is usually harmful

• somatic- they happen in body cells and are not heritable 
• ex. cancer

germ line mutation- they happen in reproductive cells (egg or sperm/from mom or dad) and are heritable

point mutation- a change in the nucleotide base at a specific location in gene, leads to codon change, leads to mRNA change, leads to change in amino acid, therefore a change in the protein

Frameshift mutation- there is an addition (insertion) or subtraction (deletion) of a nucleotide base from a gene sequence. the gene's reading frame is altered. (1 codon=3 nucleotides)

silent mutations- they change the nucleotide sequence, but do not change the amino acid sequence (missense mutation=aa change)Â

-there could be no effect if the new protein works like the original (silent mutation) 

-there could be a good effect if the new protein works better than the original (rare) 

-the new protein could work worse than the original, or not work at all. (most common)

spontaneous- these happen in the absence of DNA altering agents. they happen during replication due to base pairing mistakes 

induced- happen when DNA-altering agents are involved=mutagens

ultraviolet (UV) lights- causes thyamines to be inserted, so base pairing is prevented  during replication. this leads to gaps in the DNA. transcription is stopped, and no protein is made

x-rays, gamma rays- generates free radicals that are highly energetic. they cause DNA strands to break leading to chromosome fragmentation 

chemical mutagens- they change nucleotide sequences by inserting base analogues 

frame shift mutagens- they are flat nucleotides that slip between bases, causing base pairs to be displaced so the DNA unwinds

base-altering chemicals- they deaminate and remove amino groups (NH2) from the nitrogenous bases AGC.