Genetics Exam 2

Crossing over/Recombination

Genetic exchange between non-sister chromatids during Prophase I that results in chimeric chromatids

Linked Genes

Genes located in close physical proximity along a chromosome

What are the 3 forms of gamete formation that is exhibited during meiosis in double heterozygous individuals

• Independent Assortment

• Linkage without crossing over

• Linkage with crossing over

Complete Linkage

Production of Chimeric gametes due to crossing over occurs at a rate of 0%

Incomplete Linkage

Production of chimeric gametes due to crossing over at a rate greater than 0% but less than 50%

Annotated Genomes

Allows researchers to use resequencing techniques to make big quantities of genetic data which can be mapped using similarities to a reference genome

Contigs

Large units of continuous genetic sequence

How does crossing over differ from sister chromatid exchange?

Crossing over is essential for genetic recombination during meiosis, while SCE is a primarily repair-associated process with no effect on genetic diversity.

Explain how recombination frequencies between multiple genes can be used to generate a linkage map of a chromosome.

By combining multiple recombination frequencies, scientists build a chromosome map showing the relative positions of genes.

Why is a recombination rate greater than 50 cM undetectable using traditional linkage mapping?

A recombination rate greater than 50 centimorgans (cM) is undetectable using traditional linkage mapping because at this point, genes behave as if they are unlinked and assort independently, following Mendel’s second law.

Why is gene mapping using traditional methods error-prone for genes that are very near one another in physical distance along a chromosome?

For genes that are very close together, low recombination rates, statistical noise, interference, and undetected crossovers make traditional gene mapping less accurate. Modern molecular techniques (e.g., SNP mapping, whole-genome sequencing) provide better precision in determining gene order and distances.

Describe two reasons why genetic sequencing technology provides a more accurate map of chromosomal arrangement than linkage mapping?

Genetic sequencing is more precise because it measures actual DNA sequences and physical distances, rather than relying on recombination events, which can be influenced by biological variability.

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Nucleoid

Where bacterial DNA is kept; made of DNA, RNA, and protein

Bacterial Chromosome

Contains all essential genetic material for life

Plasmids

Small extrachromosomal circular DNA thagt replicated independently (replicons) from the bacterial chromosome

Transformation

Form of genetic exchange where bacteria takes up genetic material from the external environment and incorporate that material into their genome

Conjugation

Form of GE that requires direct cell-to-cell contact and allows for direct transfer of genetic material between two individual bacteria

Transduction

Form of genetic exchange where a virus (bacteriophage) captures genetic material from one bacterial host cell and inserts that genetic material into another bacterial cell

Fertility Factor (F Factor)

A plasmid that includes genes associated with conjugation

Interrupted Mating Technique

Determines the relative position of genes during conjugation transfer

Origination Point (O Point)

Occurs when F factor becomes integrated into the bacterial chromosome

What occurs after binary fission

One offspring cell genome inherits the parent allele and the other gets the new allele

What does transformation require?

Recognition and active uptake of exogenous genetic material

Auxotroph

Bacterial cultures with alleles that cause loss-of-function

Prototrophs

Bacterial culture that can live on minimal medium

Can cells with an Factor be a donor?

Yes

Which structure is this?

Ribose

Which structure is this?

2-Deoxyribose

What structure is this?

Nucleotide 5’ - Monophosphate

What structure is this?

Nucleotide 5’ - Diphosphate

What structure is this?

Nucleotide 5’ - Triphosphate

Which structure is this?

Nucleoside

Which structure is this?

Nucleotide

Polynucleotides

Oligonucleotides longer than 20 base pairs

What occurs in nucelotides?

The 5’ end terminates in phosphate bond to the C-5’ of the pentose sugar. The 3’ end terminate in the C-3’ of the pentose sugar (bound to hydroxyl group).

What is double stranded DNA composed of?

Two nucleotides with complementary bases

How many hydrogen bonds does adenine pair with thymine?

2

How many hydrogen bonds does guanine pair with cytosine?

3

Which direction does single stranded DNA (ssDNA) run to the other double stranded DNA (ssDNA)?

Antiparallel

Where is the minor groove located?

Between the phosphate backbones of complementary strands

Where is the major groove located?

Between successive twists of the double-stranded structure

RNA may form secondary structures via ____ between constituent nucleotides

Complementary base pairing

What are stem-loop structures?

Hairpin structures

What are pseudoknots?

two stem-loop structures in which half of one stem is intercalated between the two halves of another stem

Messenger RNA (mRNA)

Transcribed from DNA

Which do each of these letters match up to?

• A in DNA complements __ in mRNA

• C in DNA complements __ in mRNA

• G in DNA complements __ in mRNA

• T in DNA complements ___ in mRNA

• U

• G

• C

• A

What is the only RNA translated into proteins?

mRNA

Transfer RNA (tRNA)

Acts as a carrier molecule for amino acids during translation

Anticodon

One stem loop structure that includes a three-nucleotide sequence

Which end of the tRNA can attach to an amino acid

3’

Ribosomal RNA (rRNA)

Forms the primary structure of a ribosome

During translation which RNA acts as a template?

mRNA

During translation which RNA acts a carrier molecule for amino acids?

tRNA

Which RNA acts as staging ground (catalyst) in which all the components are arranged to promote polypeptide synthesis?

rRNA

Long non coding RNA (lncRNA)

Greater than 200 nucleotides in length

What can lncRNA do?

Perform regulatory functions within cells, modify gene expression, and be involved in epigenetic inheritance.

Small interfering RNA (siRNA) and micro RNA (miRNA)

Small oligonucleotide that may act as regulators of post-transcriptional expression (RNA silencing)

Denaturing

dsDNA being disassembled into ssDNA via heating

What does melting temperature increase based on?

Relative G-C content of oligonucleotides

Annealing

ssDNA being reassembled into dsDNA via cooling

DNA probes

artificially synthesized oligonucleotides with a known sequence that can be used to anneal to complimentary regions of ssDNA (molecular hybridization).

FISH

a form of molecular hybridization in which a probe bound to a fluorescent label is

used to mark the location of a specific sequence within the genome.

Electrophoresis

uses a matrix (usually an agarose gel) to differentiate oligonucleotides based on their migration rate through the matrix.

What are the three constituents of a nucleotide?

Pentose sugar, phosphate group, nitrogenous base

How does a nucleoside differ from a nucleotide?

Nucleosides don’t have a phosphate group

How does a DNA nucleotide differ from an RNA nucleotide?

A DNA nucleotide has deoxyribose sugar and thymine (T), while an RNA nucleotide has ribose sugar and uracil (U).

Describe base pair complementation patterns in DNA.

• Adenine (A) pairs with Thymine (T) using two hydrogen bonds.

• Cytosine (C) pairs with Guanine (G) using three hydrogen bonds.

Describe base pair complementation patterns in RNA.

• Adenine (A) pairs with Uracil (U) instead of thymine.

• Cytosine (C) still pairs with Guanine (G) using three hydrogen bonds.

• RNA can form complex secondary structures (e.g., hairpins) through intra-strand base pairing.

Why does G-C content affect melting temperature?

Higher G-C content increases melting temperature because G-C pairs form three hydrogen bonds, making the DNA more stable and requiring more heat to separate the strands.

What can act as template for replication of a second complimentary ssDNA polymer?

ssDNA

Semiconservative replication

dsDNA is split into ssDNA and replication occurs along each strand to create duplicate dsDNA polymers composed of one original and one newly synthesized strand.

DNA polymerase

protein complexes that catalyze synthesis of new DNA polymers (chain elongation) from deoxyribonucleoside triphosphates (dNTPs) in a 5′ to 3′ direction.

What always occurs in a 5’ - 3’ direction?

DNA synthesis

Replication fork

a split in the dsDNA where new strand synthesis can occur.

oriC

Where bacterial replication forks form at a locus

ter

Where bacterial replication terminates at a locus

DNA polymerase I, II, and III can all elongate a DNA polymer by not initiate a new one because they require a what?

Primer

What type of exonuclease activity do DNA polymerase I, II, and III, exhibit allowing for proofreading?

3’-5’

Proofreading

Excision of incorrectly matched polymerized nucleotides

Which DNA polymerase are involved in DNA repair?

II, IV, and V

Which type of exonuclease activity does DNA polymerase I exhibit allowing it to replace primer sequences?

5’-3’

What is DNA polymerase III also referred to as when actively dynthesizing DNA?

Holoenzyme

DnaA

a protein that binds to the oriC locus and helps destabilize complimentary bases (breaking hydrogen bonds) allowing for partial separation of dsDNA into ssDNA.

DNA helicase

a protein complex that assembles at the replication fork around the partially separated ssDNA

What does the DNA helicase and holoenzyme do?

DNA helicase travels along the replication fork and actively denatures the dsDNA as it progresses along the ssDNA strand, while the holoenzyme synthesizes a new complimentary strand in its wake.

Single-stranded binding proteins

bind the exposed ssDNA behind the DNA helicase to prevent reannealing to the

complimentary strand.

DNA gyrase

a protein that can make selective cuts to relieve torsion

Replisome

The template DNA, DNA polymerase, SSBs, DNA helicase, DNA gyrase, and additional associated proteins

RNA oligonucleotide

complimentary to the DNA sequence acts as a primer to initiate DNA synthesis

What is RNA synthesis directed by?

RNA polymerase (primase); does not require a free 3’ hydroxyl group to start RNA synthesis

What does DNA polymerase require in order to elongate?

A free 3’ hydroxyl group

Conitnous DNA synthesis occurs along which strand?

Leading strand

Discontinous DNA synthesis occurs along which strand?

Lagging strand

Which enzyme replaces the RNA primer with DNA, and what specific activity allows it to do so?

DNA polymerase I replaces the RNA primer with DNA using its 5′-3′ exonuclease activity, which removes the RNA nucleotides, and its 5′-3′ polymerase activity, which synthesizes the new DNA strand.

Why does the antiparallel nature of double-stranded DNA require different replication strategies for each template strand?

The antiparallel structure of DNA and the 5′ to 3′ directionality of DNA synthesis require different replication strategies:

• The leading strand is synthesized continuously in the same direction as the replication fork.

• The lagging strand is synthesized discontinuously in short fragments (Okazaki fragments) that are later joined by DNA ligase.

Okazaki Fragments

short polynucleotide segments of newly synthesized DNA on the lagging strand, which form because DNA polymerase can only synthesize in the 5′ to 3′ direction.

Why are Okazaki fragments necessary during DNA replication?

Okazaki fragments allow the lagging strand to be synthesized in short sections since DNA polymerase only works in the 5′ to 3′ direction.

What role does DNA ligase play in DNA replication after primer replacement by DNA polymerase I?

DNA ligase joins the individual Okazaki fragments by forming phosphodiester bonds between them after the RNA primer is replaced by DNA polymerase I.

What is chromatin, and how is eukaryotic DNA associated with it?

Chromatin is a complex of DNA bound to proteins in eukaryotic cells.