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Three informational macromolecules in the cell
– DNA– RNA– Protein
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Replication:
DNA is duplicated
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Transcription:
information from DNA is transferredto RNA
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mRNA (messenger RNA):
encodes polypeptides
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tRNA (transfer RNA):
-Brings amino acids to ribosome in protein synthesis
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rRNA (ribosomal RNA):
plays role in protein synthesis
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Translation:
information in RNA is used to build polypeptides
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Eukaryote transcription
each gene is transcribed individually
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Prokaryotes transcription
multiple genes may betranscribed together
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Four nucelotides found in DNA
- – deoxyadenosine (A)
- – deoxyguanosine (G)
- – deoxycytidine (C)
- – deoxythymidine (T)
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Pyrimidine bases (single ring)
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Purine Bases (Two ring)
Adenine Guanine
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Backbone of DNA chain is alternating ______ and the pentose sugar ______
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Adenine–Thymine pair has ______ hydrogen bonds and Guanine–Cytosine pair has ______ hydrogen bonds
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denaturation
High heat breaks hydrogen bonds, causing denaturation
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Genome:
entire complement of genes in cell or virus
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Viruses Genetics
-genomes
-shape
- -contain either RNA or DNA genomes
- – Can be linear or circular– Can be single or double stranded
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Plasmids:
- -replicate separately from chromosome
- – Great majority are double stranded
- – Most are circular
- – Generally beneficial for the cell (e.g., antibioticresistance)
- – NOT extracellular, unlike virusesa genetic element that isexpendable and rarely contains genes required for growth under all conditions
- - Genetic information encoded on plasmids may confer a selective growth advantageunder certain conditions
- -In several pathogenic bacteria, virulence characteristics are encoded by plasmid genes
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Chromosome
genetic element with“housekeeping” genes– Presence of essential genes is necessary fora genetic element to be called a chromosome
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Avg gene length is ___ base pairs
1000
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episome
- plasmids that can integrate into the cell chromosome; similar to situation seen with prophages
- -essentially all can do this
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curing plasmids
Removal of plasmids from host cells can result from various treatments
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Conjugative plasmids
-can be transferred between suitable organisms via cell-to-cell contact between closely related, or distantly related bacteria (broad host range)
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Conjugal transfer controlled by ___ genes on plasmid
tra
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R plasmids
- – Resistance plasmids; confer resistance toantibiotics and other growth inhibitors(Figure 6.12)
- – Widespread and well-studied group ofplasmids
- – Many are conjugative
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4 characteristics of Virulence factors
- – Enable pathogen to colonize
- – Enable pathogen to cause host damage
- – Hemolysin-destruction of red blood cell
- – Enterotoxin-dehydration of intestinal wall (diarrhea)
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Bacteriocins
- – Proteins produced by bacteria that inhibit or kill closely related species or even different strains of the same species
- – Colicin, nisin
- - Genes encoding bacteriocins are often carried on plasmids
-
psuedomonas
- -famous bacteria for ability to eat anything due to plasmid genes
- -common soil bacteria
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Transposable Elements
- – Segment of DNA that can move from one site to another site on the same or a different DNA molecule
- – Inserted into other DNA molecules
-
Three main types of Transposable Elements
- • Insertion sequences
- • Transposons-multiple genes besides transpose genes
- • Special viruses
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3 DNA Replication components
- ? Templates and Enzymes
- ? The Replication Fork
- ? Bidirectional Replication and the Replisome
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semiconservative DNA replication
– Each of the two progeny double helices have one parental and one new strand
-
-
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Precursor of each nucleotide is a __________
deoxynucleoside 5′-triphosphate
-
Replication ALWAYS proceeds from the _′ end to the _′ end
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DNA polymerases
- DNA polymerases catalyze the addition of dNTPs
- - Five different DNA polymerases in E. coli –
- - DNA polymerases require a primer
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DNA polymerase III
primary enzyme replicating chromosomal DNA
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Primer made from RNA by ___
primase
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DNA synthesis begins at the ______ in prokaryotes
origin of replication
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Replication fork:
-zone of unwound DNA where replication occurs
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DNA helicase
unwinds the DNA
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Extension of DNA
- – Occurs continuously on the leading strand
- – Discontinuously on the lagging strand
- • Okazaki fragments are on lagging strand
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Transcription of genes
- -Only one of the two strands of DNA are transcribed by RNA polymerase for any gene
- - Genes are present on both strands of DNA, but only one of the strands at any given location has correct code
- RNA polymerase recognizes DNA sites and starts transcription at sites called promoters
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Transcription (DNA to RNA) is carried out by ___ ___
RNA polymerase
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RNA polymerase uses ___ as template
DNA
-
- RNA polymerase has ___ different subunits
five
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RNA precursors(4)
ATP, GTP, CTP, and UTP
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Promoters
- -site of initiation of transcription by DNA polymerase
- –Recognized by sigma factor (sub unit of RNA polymerase)
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transcription terminators
specific sites Transcription stops at
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Unlike DNA replication, transcription involves _______ units of DNA
(size)
- -smaller
- – Often as small as a single gene
- – Allows cell to transcribe different genes at different rates
-
Sigma factors recognize two highly conserved regions of promoter
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Pribnow box:
located 10 bases before the start oftranscription (-10 region)
-
35 region
located ~35 bases upstream of transcription
-
Termination of RNA synthesis is governed by a specific _____ sequence
DNA
-
Intrinsic terminators
- transcription is terminated without any additional factors
- -hairpin in mRNA followed by uuuuu
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Rho-dependent termination
Rho protein recognizes specific DNA stop sequences and causes a pause in the RNA polymerase
-
Unit of transcription
- -part of chromosome that is transcribed
- -can contain code for more than one gene
-
Most genes encode _______, but some RNAs are not translated (i.e., rRNA, tRNA)
proteins
-
Three types of rRNA:
- 16S, 23S, and 5S
- (s is a unit os size=svedburg)
-
2 very stable RNA types
rRNA and tRNA
-
tRNA cotranscribed with _____ or ______
-
mRNAs have ______ half-lives
- short
- (a few minutes or seconds)
-
Prokaryotes often have genes clustered together
– These genes are transcribed all at once as a single _____
mRNA
-
polycistronic mRNA
An mRNA encoding a group of cotranscribed genes (multygene)
-
2 types of functioning proteins in cell
- – Catalytic proteins (enzymes)
- – Structural proteins
-
Genetic code:
- a triplet of nucleic acid bases (codon) encodes a single amino acid
- – Specific codons for starting and stopping translation
-
Degenerate code:
- -multiple codons encode a single amino acid
- -many have 6 codons
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Anticodon
- -three bases of tRNA that recognize three complementary bases on mRNA
- - Fidelity of recognition process between tRNA and aminoacyl-tRNA synthetase is critical (Figure 6.34)
- – Incorrect amino acid could result in a faulty or nonfunctioning protein
-
Wobble:
- -irregular base pairing allowed at third position of tRNA (Figure 6.31)
- -first two letters of an amino acid code are the same
- -the third can vary creating a weaker bond with tRNA or a wobble
-
Stop codons:
terminate translation (UAA, UAG,and UGA)
-
Start codon:
translation begins with AUG (methionine)
-
Reading frame:
-triplet code requires translation to begin at the correct nucleotide because there are no spaces in code
-
Shine–Dalgarno sequence (ribosomal binding site):
sequence upstream of start sequence ensures proper reading frame
-
Open reading frame (ORF):
-AUG followed by a number of codons and a stop codon in the same reading frame
-
at least _____ tRNA per amino acid
one
-
– Bacterial cells have _____ different tRNAs
– Mammalian cells have ______ different tRNAs
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Specific tRNA for both a ______ and its _____ amino acid
-
tRNA and amino acid brought together by __________
(enzyme)
- aminoacyl-tRNA synthetases
- – ATP is required to attach amino acid to tRNA
-
tRNA is ______ in shape
cloverleaf
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Ribosomes: sites of ______ synthesis
– (amount) of ribosomes per cell
– Composed of two subunits ( ___and___ in prokaryotes)
– S = ______
– Combination of ____and _____
- E. coli has __ distinct ribosomal proteins that make up the sub units
- protein
- thousands
- 30S and 50S
- Svedberg units
- rRNA and protein
- 52
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Three main steps of translation
- 1. Initiation:
- 2. Elongation:
- 3. Termination:
-
Initiation:
- two ribosomal subunits assemble with mRNA
- • Begins at an AUG start codon
-
Elongation:
- -amino acids are brought to the ribosome and are added to the growing polypeptide
- • Occurs in the A and P sites of ribosome
- • translocation: movement of the tRNA holding the polypeptide from the A to the P site
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Translocation:
movement of the tRNA holding the polypeptide from the A to the P site
-
Release factors (RF):
- recognize stop codon and cleave polypeptide from tRNA
- -causes ribosome to break apart
-
Termination:
- occurs when ribosome reaches a stop codon
- • Release factors (RF): recognize stop codon and cleave polypeptide from tRNA
- • Ribosome subunits then dissociate
- • Subunits free to form new initiation complex andr epeat process
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