Lecture 8

genetics

___ is the study of inheritance or the heredity of living things

parents, offspring

genetics is the transmission of biological properties (traits) from ___ to ___

genetics

___ studies how traits are transferred, how they are expressed and varied, how they are regulated, structured, and changed

genotype

A(n) ___ is the sum of all gene types; an organism’s distinctive genetic makeup.

phenotype

A(n) ___ is the expression of certain traits (structures or functions).

genotype, phenotype

Organisms contain more genes in their ___ than are manifested in the ___ at any given time.

chromosomes

___ contain genetic material necessary to reproduce an organism; compacted complexes of DNA and proteins

histone, IHF

Chromosomes are compacted complexes of DNA and proteins; typically in Eukaryotes they are ___, while Prokaryotes have ___ (the second answer is an acronym)

genome

___ comprises most of the genetic material that an organism possesses.

nuclear, mitochondrial, chloroplast

Alternate genetic materials: single (haploid) circular chromosome in bacteria; ___ chromosomes in eukaryotes, ___ genome in animals, ___ genome in plants, plasmids in bacteria; DNA or RNA in virus’ genomes.

nucleoid

The bacterial chromosome is found in a region of the cell called the ___.

membrane, cytoplasm

The nucleoid is not bound by a ___; DNA is in direct contact with the ___; transcription and translation are coupled.

nucleotides

Bacterial chromosomal DNA is usually a circular molecule that is a few million ___ in length

7, 4, 3, 4

There are ___ different variants of genetic materials present in the virion; ___ are single stranded; ___ are DNA; ___ go through second processes to become mRNA.

viral

___ genomes vary in size from a few thousand to more than a hundred thousand nucleotides (hint: suffix is -al).

megavirus chilensis

The largest virus by genome size (currently) is ___ ___; also largest capsid by volume ~440nm; the genome is ~1,300,000 bp long.

porcine circovirus

The smallest virus by genome size (currently) is ___ ___; the genome is ~1,800 bp long; and only has 3 ORF’s.

circular, linear, segmented

The 3 organizations of genomes: ___, ___, and ___ (alphabetical order).

hemagglutinin, neuraminidase

___ (HA) and ___ (NA) are the ability for the virus to get out of cell 

shift, drift

When a chicken is infected with two strains of a virus, the DNA from each virus can be packed into new combinations when being re-put into the newly formed capsid:

Antigenic ___: a whole new antigen profile that can escape the immune system bc its never seen it before.

Antigenic ___: usually responsible for new vaccinations each year, your immune system just delays in noticing it.

This all happens when you have segmented genomes.

RNA, DNA

Nucleotides are important macromolecules in both: ___ is less stable than ___ because of the extra hydroxyl group which can be activated more easily (both are similar acronyms).

nitrogenous

In DNA, ___ bases attach by covalent bonds at the 1’ position of the sugar.

purines, pyrimidines

In DNA, ___ and ___ join with complementary bases by hydrogen bonds (alphabetical).

DNA

___ can be easily unzipped to access the information encoded by the bases.

adenine, thymine, guanine, cytosine

In DNA, the pairing of bases is dictated by the formation of hydrogen bonds between bases, called Chargoff’s Rule: ___ (A) always pairs with ___ (T) and ___ (G) always pairs with ___ (C)

hydrogen

Between DNA strands (between Cytokines and Guanine, Thymine and Adenine) are ___ bonds.

replication

The overall process of DNA ___ is semi-conservative

replication, daughter

DNA ___: Strands of the existing DNA molecule separate, copy one strand, and produce two complete ___molecules.

daughter, parent

After DNA replication, each ___ molecule is “identical” to the ___ in composition.

new, parent

After replication, neither strand is completely ___; each has a template of the ___ and a new copied daughter strand.

DNA replication

The importance of ___ ___: when we know how things work we can break them, if they can kill the ability to replicate DNA they can kill the cell.

primosome

DNA helicase and primase are physically bound to each other to form a complex called the ___: this complex leads the way at the replication fork.

replisome

The primosome is physically associated with two DNA polymerase III holoenzymes to form the ___.

DNA polymerase III

___ ___ ___ can not begin synthesizing a chain of nucleotides on its own; can only add nucleotides to an already existing chain; can only add nucleotides in the 5’ to 3’ direction (the first answer is an acronym, the third is a roman numeral)

helicase

DNA ___ is like a zipper for DNA, it breaks hydrogen bonds and separates the DNA; If your DNA breaks when doing this it is bad.

topoisomerase, primase

___: cuts the pressures for the unzipping.

___: primes replication process, puts down RNA primer, is the start of the synthesis of DNA.

Leading strand: is continuous.

3, 5, 5, 3

DNA’s enzyme polymerase III can identify a mismatched nucleotide and remove it from the daughter strand; uses a ___’ to ___’ exonuclease activity to digest the newly made strand until the mismatched nucleotide is removed; DNA synthesis then resumes in the ___’ to ___’ direction. (All answers are numbers)

exonuclease

At the 3′ ___ site, the strand is digested in

the 3′ to 5′ direction until the incorrect nucleotide is

removed.

decatenation

After replication, the two circles (catenates) are linked together; separated through ___ via topoisomerase.

central dogma

The ___ ___ is the flow on information in the cells.

mRNA, rRNA, tRNA

DNA transcripts to ___, ___, and ___ (alphabetical similar answers)

transcription, translation

Micro RNA, interfering RNA, antisense RNA, and riboswitches regulate ___ and ___ (alphabetical order).

initiation

___ is the first step of transcription.

promoter region

___ ___: initiates transcription; is two sequences of DNA just behind the gene to be transcribed; provides the signal for RNA polymerase to bind to the DNA.

initiation codon

___ ___: where the RNA polymerase begins its transcription.

scrunching

“DNA ___”: the DNA helix unwinds, the polymerase first pulls the early parts of the DNA into itself; gives the rest of the process energy.

promoters

The nucleotide sequence of ___ differs only slightly from gene to gene, with all promoters being rich in adenine and thymine.

elongation

___: proceeds in the 5’ to 3’ direction; mRNA is assembled by the addition of nucleotides that are complementary to the DNA template.

termination

___: polymerases recognize another code that signals the separation and release of the mRNA strand, or transcript.

mRNA

The smallest ___ might consist of 100 bases; the average ___ has maybe 1,200; the large ___ may consist of several thousand (all same acronym answer).

regulatory

___ RNAs: Micro RNAs (miRNA), Anti-sense RNAs, Riboswitches, Small interfering RNAs (siRNA)

primer

___ RNAs: operative in both prokaryotic and eukaryotic.

ribozymes

___ are enzymatically active RNAs.

messenger, transfer, ribosomal

RNAs involved in translation: ___ RNA (mRNA), ___ RNA (tRNA), and ___ RNA (rRNA).

anti sense

___-___ RNA: is the opposite sequence of the target, reduces degradation of RNA

riboswitches

___: pieces of DNA that will self dimerize.

Transcription: DNA —> ___

Translation: ___ —> Polypeptide

(same answer)

codon

Untranslated region: regions before start ___ and after the stop ___

Start ___: segment of first three actively translating

___: a group of three nucleotides

Stop ___: segment of last three actively translating; informs to stop translation

(all same singular answer)

nucleotides, degenerate

Codon: groups of three ___ encode which amino acid is added to peptide chain; 64 different triplet codes and 20 amino acids.

___ code: amino acids are represented by several codons.

wobble

___: only the first two nucleotides are required to encode the correct amino acid, and the third nucleotide does not change its sense.

tRNA

The six steps of translation: (1) entrance of ___ 1 and 2, (2) formation of peptide bond, (3) discharge of ___ 1 at E site, (4) first translocation, (5) formation of the peptide bond, (6) discharge of ___ 2, second translocation, enter ___ 4 (all same answer)

translation, transcription

In bacteria, ___ of mRNA starts while ___ is still occurring (coupled)

Polyribosomal

___ complex: mRNA is long enough to be fed through more than one ribosome; permits the synthesis of hundreds of protein copies from the same mRNA transcript; occurs only in prokaryotes (transcription/translation occur in cytoplasm).

tertiary

In translation, before the peptide is released from the ribosome, it begins folding on itself to achieve its biologically active ___ structure

cofactors, quaternary

Posttranslational modifications: some must have the starting amino acid (formyl methionine) removed; ___ must be added to proteins destined to become enzymes; some join other proteins to form ___ structures

prokaryotes, eukaryotes, eukaryotes

In ___ AUG codes for a different form of methionine called formylmethionine (prokaryotes or eukaryotes).

In ___ mRNAs code for just one protein (prokaryotes or eukaryotes).

In ___, transcription takes place in the nucleus and must pass through pores in the nuclear membrane to the cytoplasm for translation (prokaryotes or eukaryotes).

introns, exons

Eukaryotic genes do not exist uninterrupted…

___: intervening sequence of bases that do not code for a protein

___: coding regions that will be translated into proteins

mRNA

Processing ___: transcription of the entire gene, series of adenosines added to ___, spliceosome cuts through intron-exon junctions, exons are the joined end to end, ___ is translated.

spliceosome

___: a type of RNA and protein that recognizes the intron-exon junctions and enzymatically cuts through them

control mechanisms

___ ___ ensure that genes are active only when their products are required.

substrate

Many operons encoding enzymes that act in catabolism are inducible (turned on) by the presence of the ___.

anabolic

Repressible operons contain genes coding for ___ enzymes and are repressed (turned off) by the product synthesized by the enzyme.

enzymes

___ are only produced as they are needed and prevent the waste of energy and materials.

operons

___: typically found in bacteria; coordinated set of genes controlled by the same promoter(s); generally all regulated as a single unit; can be either inducible or repressible

lac operon

___ ___ accounts for the regulation of lactose metabolism in E. coli.

regulators, locus

Features of the lac operon: ___, control ___, and structural ___ (2nd and 3rd answers the same).

regulator

___(s): a gene that codes for a protein capable of repressing the operon (a repressor) and, distantly, a gene that codes for a protein capable of activating the operon (an activator).

control locus

___ ___: composed of the promoter (recognized by RNA polymerase) and the operator, a sequence that acts as an on/off switch.

structural locus

___ ___: made up of three genes, each coding for a different enzyme needed to catabolize lactose.

repressed

No lactose in the environment —> lac operon is ___.

induced

Lactose present in the environment —> lac operon is ___.

phenotypic

When bacteria turn on or off a complement of genes that leads to obvious ___ changes.

heritable

Phenotype is generally ___, meaning that it can be passed down to subsequent generations.

phase variation

___ ___ can occur during the process of turning on genes mediated by regulatory proteins

immune system, surfaces, environments

Most often applied to traits affecting the bacterial cell surface: describes the ability of bacteria to change components of their surface marked for targeting the host’s ___ ___; influences the bacterium’s ability to attach to ___; allows microbes to adapt to, and stick in, different ___.

horizontal gene transfer

___ ___ ___: transfer of DNA from one organism to another that did not directly come from parental organisms.

plasmids

Horizontal gene transfer typically involves ___: chromosomal “fragments.”

plasmids

___: small, circular pieces of DNA that contain their own origin of replication; can replicate independently of the bacterial chromosome; can contain genes that confer useful traits (ex: antibiotic resistance)

conjugation

Factors involved with ___: donor cell with pilus, fertility plasmid in donor, both donor and recipient alive, bridge forms between cells to transfer DNA.

transformation

Factors involved with ___: free donor DNA (fragment), Live and competent recipient cell.

transduction

Factors involved with ___: donor is lysed bacterial cell, defective bacteriophage is carrier of donor DNA, live recipient of same species as donor.

direct, indirect, indirect

Horizontal Gene transfer:

Conjugation is ___ (direct or indirect)

Transformation is ___ (direct or indirect)

Transduction is ___ (direct or indirect)

direct contact

In Horizontal Gene Transfer Conjugation: mode of genetic exchange in which a plasmid or other genetic material is transferred by a donor to a recipient cell via ___ ___.

conjugate

Both gram-positive and gram-negative cells can ___.

fertility

Gram-negative conjugation: ___ (F’ factor) allows the synthesis of a conjugative pilus; the recipient cell has a recognition site on its surface; contact is made when a pilus grows out from the F+ cell, attaches to the surface of the F- cell, contracts, and draws the two cells together.

plasmid

F+: cell that has the ___.

F-: cell that lacks the ___.

donor, recipient

The process of gram-negative conjugation: the ___ (F+) cell makes a copy of its F factor, transmits this to a ___ (F-) cell, turns it into an F+ cell capable of producing a pilus and conjugating with other cells.

high, recombinant

___-frequency ___ (HFR) donors: F plasmid becomes integrated into the F+ donor chromosome; when F plasmid is replicated it begins to transfer to the recipient cell; some chromosomal genes get transferred to the recipient; all of the plasmid genes may or may not be transferred.

positive

Gram-___ conjugation: an opening is created between two adjacent cells, replicated DNA passes across from one cell to another.

conservative

Conjugation is a ___ process in which the donor bacterium retains (“conserves”) a copy of the genetic material being transferred.