Chapter 13 Flashcards by Hailey Hendrickon

what is a genome?

The complete collection of genes in a
bacterial cell

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What is a gene?

A unit of heredity, a DNA sequence

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What is the central dogma?

the theory that genetic information flows from DNA to RNA to protein

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Bacteria are haploid/diploid

haploid

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What is a plasmid?

circular DNA that carries “accessory traits” and contribute to genetic diversity

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What are some traits that plasmids might carry?

New metabolism
Antibiotic resistance
Toxin production
Fertility Factors, etc.

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What are the differences between RNA and DNA?

RNA-
ribose
singe stranded
Uracil
DNA-
deoxyribose
double stranded
Thymine

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What are the 2 forms of DNA supercoiling?

Positive- winds more tightly
Negative- more common, underwound, loosens up for replication and transcription

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Explain bacterial DNA replication

the complimentary (antiparallel) strands separate and form template strands that are then used for replication.

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_____ replication from a single origin (bacterial DNA replication)

Bidirectional

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What is a replicon?

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

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What is the replisome?

12 proteins involved in replication. One replisome goes in either direction

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What direction is DNA synthesis going?

5’ to 3’

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DNA polymerase

catalyzes formation of complimentary strand

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What does DNA polymerase require?

-template
- primer
- Deoxynucleotide triphosphates (dGTP, dATP, etc.)

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helicase

unwinds DNA strands

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Single-stranded DNA binding proteins

coat single stranded DNA to protect it from damage

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Topoisomerases

relieve twist generated by the rapid
unwinding of double helix, prevents supercoiling.

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Primase

synthesizes short complementary strands of RNA primers (approximately 10 nucleotides) needed by DNA polymerase.

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What is different about the lagging strand?

synthesized in short segments called okazaki fragments- each one needs a new primer

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DNA polymerase 1

removes RNA primers and fills the gaps with DNA

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DNA ligase

bonds things together- specifically Okazaki fragments

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DNA polymerase 3

proofreads and removes incorrect bases

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Catenanes

form when topoisomerases
break and rejoin DNA strands to ease
supercoiling

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What is replication, transcription, and translation

replication= DNA-DNA transcription= DNA-->RNA translation=mRNA-->proteins

What direction is the template strand read in transcription

read in the 3' to 5' direction mRNA synthesis

complementary (sense strand)

same nucleotide sequence as mRNA

promoter

at start of gene- binding site for RNA polymerase

leader sequence

transcribed into mRNA but not proteins

Shine-Dalgarno sequence

important for translation initiation

trailer sequence

prepares R NA polymerase for terminator sequence.

tRNA

carries amino acids during protein synthesis

rRNA

molecules are components of ribosomes

mRNA

carries the message for protein synthesis.

Polycistronic

mRNA with multiple coding regions

Monocistronic

not common in eukaryotes. (one coding region)

The sigma factor

has no catalytic activity but helps the core enzyme recognize the start of genes

Sigma promoter

helps position the core enzyme at the promoter.

35 bp upstream

Sigma factor recognizes this sequence directing haloenzyme to “settle” here

10 bp upstream

Where DNA strands start to separate

what direction does RNA synthesis move

5' to 3' direction

describe elongation

RNA polymerase unwinds DNA and creates a transcription bubble which moves with the polymerase and is a mix of DNA:RNA

Transcription termination

occurs when RNA polymerase dissociates, intrinsic and factor-dependent (proteins)

structure of an amino acid

amino group, side chain, and carboxyl group

what bonds hold together amino acid polymer?

peptide bonds

start codon

AUG

stop codons

UGA, UAA, UAG

what is wobble?

loose base pairing, decreases effects of mutation, eliminates need for a unique tRNA for each codon

Direction of synthesis in translation

N--->C terminal

where does translation take place?

ribosomes

tRNA structure

clover shaped- anticodon (complementary mRNA strand) on anticodon arm

what catalyzes amino acid synthesis

Aminoacyl-tRNA synthetases, each specific to a certain tRNA

what is the A site

acceptor site- receives tRNA carrying amino acid

What is the P site

Peptidyl site- holds tRNA with growing polypeptide

what is the E site

Exit site- empty tRNA leaves ribosome

needed for initiation -binds to Shine-Dalgarno sequence (ribosome binding site). -Binds to 3’CCA end of aminoacyl-tRNA

16S rRNA

what initiates synthesis?

bacterial- N-formylmethionine-tRNA eukaryotes and archaea- methionine-tRNA

what are the 3 phases of elongation

-Aminoacyl-tRNA binding - Transpeptidation reaction (peptide chain moved from P to A) - Translocation

primary structure

amino acid sequence

secondary structure

alpha helices or beta sheets

tertiary

3D structure

quaternary

2 or more polypeptide strands interacting