Micro Exam 3

genetics

science that studies the inheritance/heredity of biological characteristics of life forms (different levels)

organism

expression of characters in an organism/cell, transmission of characters from one to the next

molecular

genetic element/unit that is made of DNA and carries genes

genotype

a unique set of genes

phenotype

the observable characteristics that result from the genes carried by an organism

DNA IS ______

antiparallel

binary fission must be _____ for replication into daughter cells

accurate

semi-conservative model of DNA replication

Double helix separated to two strands

each act as a template for the synthesis of the new complementary strand

result: each double helix will have one old and one new strand

GOAL: to make identical copies of each strand of DNA

DNA replication requires

many enzymes

the three stages of DNA replication

initiation, elongation, termination

Initiation

proteins bind to begin the replication process

elongation

addition of nucleotides

termination

end of DNA replication

DNA replication occurs

at specific nucleotide sequence called origin of replication oriC. Various proteins bind to begin the replication process. Prokaryotic chromosomes generally have one origin of replication (approximately 245bp and rich with A and T). Eukaryotic chromosomes may have multiple origins

step 1 (initation)

RELAX the supercoiled circular DNA chromosome

step 2 (initation)

HELICASE binds to ORI and UNWINDS and SEPARATES the two DNA strands by breaking the hydrogen bonds between the base pairs

step 3 (initiation)

Short SINGLE-STRANDED BINDING PROTEINS (SSBP) bind to the unwound/separated DNA strands

Step 4 (initiation)

Generate short RNA PRIMERS on each strand of DNA by RNA PRIMASE

DNA polymerase III

Adds complementary bases in the 5’ to 3’ direction. DNA polymerase requires a free 3’-OH group to form a phosphodiester bond between the 3’-OH end and the 5’ phosphate of the next nucleotide. Requires a primer which provides a free 3’-OH end. Requires a template strand. It can proofread, decreasing the number of errors that occur in the newly synthesized strand

step 5 (elongation)

Binding of DNA POLYMERASE III to each strand of DNA at the 3' end of the RNA primer. DNA polymerase III can ONLY add nucleotides onto the 3’-OH group of the new strand so with RNA primers in place… GOOD TO GO!

step 6 (elongation)

DNA POLYMERASE III begins to proceed down the strand of parental DNA synthesizing a new strand of DNA by adding complementary nucleotides

step 7 (elongation)

DNA polymerase III can continue to move down the strand following the helicase without stopping (CONTINUOUS SYNTHESIS). DNA Polymerase III is a holoenzyme that consists of two identical parts joined together. PROBLEM: But the parts of the enzyme want to move in opposite directions!

step 8 (elongation)

Because the lagging strand is produced through DISCONTINUOUS SYNTHESIS, it is made in fragments: Okazaki fragments

Ozaki fragments

the fragments of the lagging strand, composed of fragments of RNA & DNA with gaps in between. But the goal is to make a continuous copy of DNA!

step 9 (elongation)

Digest the RNA primers on each Okazaki fragment and replace it with DNA using DNA POLYMERASE I

step 10 (elongation)

DNA LIGASE is used to repair the gaps and join the fragments of the lagging strand

termination

There are specific sequences associated with termination (ter sequences)

After replication, the two circular chromosomes are interlocked, or concatenated

Topoisomerase IV

introduces a double-stranded break allowing the circular DNA chromosomes to separate

DNA Replication - Eukaryotes

• Many of the enzymes have the same functions but have different names

• Eukaryotes have DNA polymerase δ (lagging strand) and DNA polymerase ε (leading strand)

• RNase H removes the RNA primer

Telomerase

• adds nucleotides to the 3’ end of the chromosome

• Contains a catalytic part and a built-in RNA template 

Telomeres

region of noncoding repetitive sequences at each end of the chromosome

protect the DNA from getting lost during replication process

Plasmid Replication

• A single strand is nicked at the double-stranded origin site. DNA polymerase III begins synthesis of the new strand using the un-nicked strand as a template

• The nicked strand gets displaced.

• Both strands get the gaps fixed.

• The nicked strand is replicated by RNA polymerase introducing a primer and the rest filled by DNA polymerase III.

The Central Dogma

Flow of genetic information

Gene expression

process of transcription and translation. Synthesis of a specific protein that is encoded in the gene.

Ribonucleic Acid

• Mainly involved in the process of protein synthesis (translation) and its regulation

• Typically, single-stranded and is made of ribonucleotides

ribonucleotide

a phosphate group, five-carbon sugar called ribose, and a nitrogenous base

messanger RNA

Singlestranded, Repeating phosphate sugar backbone attached to single nitrogen bases, Use of uracil instead of thymine

ribosomal RNA

Ribosomes are composed of rRNA and protein. rRNA has enzymatic activity (peptidyl transferase)

transfer RNA

Short (90-70 nucleotides), Stable RNA with extensive intramolecular base pairing; contains an amino acid binding site and an mRNA binding site, Carries the correct amino acid to the site of protein synthesis in the ribosome 

transcription

• Requires DNA template, RNA polymerase, Transcription Factors, Ribonucleotides 

• RNA polymerase binds to promoter region upstream of the gene

• RNA polymerase adds nucleotides complementary to the template strand of a segment of DNA in the 5′ to 3′ direction

• Uracil is placed as adenine’s complement (no thymine in RNA)

template strand

the strand that WILL BE transcribed and contains the genetic information needed to make a protein

nontemplate strand

the strand that is NOT transcribed

transcription initiation

The transcription machinery, which includes the enzyme RNA POLYMERASE binds to

the promoter region on the DNA strand

• Transcription Machinery Complex → key protein in the complex… the enzyme RNA POLYMERASE

at the end of elongation

RNA POLYMERASE continues down the template until it encounters the terminator sequence,

which causes the polymerase to release from the template

RNA polymerase generate a _______ TRANSCRIPT

messanger RNA

termination of transcription is signaled by

the presence of a repeated nucleotide sequence on the DNA template, causing RNA polymerase to stall and release from the DNA template, freeing the RNA transcript.

• After transcription has completed, then the DNA double helix will completely reanneal.

translation

• mRNA (nucleotides) is “read” and converted into a polypeptide (amino acids)

• Second step in gene expression

• mRNA is read in groups of three nucleotides : codon

• The relationship between mRNA codon and its corresponding amino acid is called the genetic code

Redundancy (degeneracy)

allows for misreading of the nucleotide without affecting the protein

genetic code ( 61 ____ codons)

sense

sense codons code for

an amino acid and includes start codon AUG

stop codons (nonsense)

terminate protein synthesis (there are 3)

A protein’s primary structure (its sequence of amino acids) determines

its shape and function

ribosomes are composed of

catalytic rRNAs (called ribozymes) structural rRNA and ribosomal proteins (polypeptides)

CCA is a

amino acid binding end

anticodon end

three-nucleotide sequence that bonds with an mRNA codon

translation requires

mRNA ribosomes tRNAs amino acids various enzymatic factors

polyribosome (or polysome)

structure containing an mRNA with multiple associated ribosomes

In bacteria and archaea

transcription and translation occurring at the same time

A site

aminoacyl - location at which incoming aminoacyl-tRNA base pair with the mRNA codon

P site

peptidyl - location at which the amino acid is transferred from its tRNA to the growing polypeptide chain

E site

exit - location at which the “empty” tRNA sits before being released back into the cytoplasm

initiation

the 30S ribosome subunit binds to the mRNA. the anticodon on the initiator tRNA associates with the start codon on the mRNA. the 50S ribosome subunit joins to create the full ribosome

elongation

A new tRNA enters the A site and matches its anticodon with the mRNA codon. A peptide bond forms between amino acids, transferring the growing chain to the tRNA in the A site (this is catalyzed by peptidyl transferase). The ribosome then moves along the mRNA (5’ → 3’), shifting the tRNAs: the empty tRNA moves to the E site and exits, while the tRNA with the growing chain moves to the P site. This cycle repeats to continue building the protein.

termination

elongation continues until a stop codon reaches the A site. Since no tRNA matches a stop codon, the polypeptide chain is released. The ribosome then disassembles, and its parts can be reused. Some proteins are further modified after translation (post-translational modifications).

protein cleavage

Removal of portions of a protein in order to allow it to become active or travel to certain cellular locations or be secreted from the cell 

protein folding

Tertiary and quaternary structure in order to give the protein its 3-dimensional shape 

chemical modifications

Addition of phosphates, lipids or sugars to specific amino acids of a protein

gene regulation

• Not all genes are expressed at the same time.

• Not all genes are regulated

• Many genes are expressed constitutively, which are constantly being expressed

  • HOUSEKEEPING GENES

  • Enzymes that are needed in large amounts for the cell’s major life processes

promoter

Region of DNA that is recognized by RNA polymerase, initiating transcription

operator

DNA sequence located between the promoter region and the first coding gene (region that is recognized and bound by regulatory proteins/transcription factors)

operon

Group of genes with related functions and transcribed under one promoter

induction

The process that turns on transcription

inducer

Small molecule that activates transcription

repression

Mechanism that inhibits transcription

repressor

Protein that inhibits transcription (binds to operator)

mutation

Organism that may have a recognizable change in phenotype compared to wild type

mutant

Heritable change in the DNA sequence of an organism

wild type

Phenotype most commonly observed in nature

silent mutations

(NO change to amino acid) - no effect on protein

missense mutations

(change to a different amino acid)

nonsense mutations

(change that generates a STOP codon)

frameshift mutation

insertions or deletions of nucleotides that are not multiples of 3

insertion mutation

(addition or one or more nucleotides)

deletion mutation

(removal of one or more nucleotides)

spontaneous mutation

mistakes made during DNA replication, in the absence of any mutation-causing agents. a change or changes in the DNA arising from an error during DNA replication which occurs RANDOMLY

induced mutations

mutations due to exposure to a mutagen (chemical agents or radiation). results from exposure to a MUTAGEN (physical or chemical reagents) that interacts with DNA in a disruptive manner

carcinogens

agents that cause cancer

chemical mutagens

interact directly with DNA as a nucleotide analogs or modifying nucleotide bases

nucleotide analogs

structurally similar to normal nucleotide bases, can be incorporated into DNA during replication

conjugation

bacterial “sex” = the transfer of genetic material by DIRECT CONTACT

transformation

naked DNA is taken up from the environment

transduction

bacteriophage serves as a carrier of DNA from a donor bacterium to a recipient bacterium

fomites

Inanimate objects that may contain microbes and aid in disease transmission

critical items

used inside the body, often penetrating sterile tissues or the

blood stream

degerming

gentle scrubbing and/or swabbing (physical removal) of living tissue (e.g. the skin) with chemicals (antiseptics) to REDUCE the number of microorganisms

sterilization

 the COMPLETE removal/destruction of ALL microbial life (including bacterial endospores)

disinfection

the destruction of MOST but NOT all microbial life on INANIMATE surfaces through the use of chemicals, termed DISINFECTANTS, or heat

antiseptics

the destruction of MOST but NOT all microbial life on

LIVING skin or tissue through the use of chemicals termed _______

aseptic technique

Precautionary measures taken to avoid contamination of a

sterile surface or solution

sanitation

the cleaning of inanimate objects with chemical disinfectants or heat in order to REDUCE the number of microbes and achieve safe public health levels