Genetics Exam II

Types of Sex Determination

XX-XO

XX-XY

ZZ-ZW

Haplodiploploidy

XX-XO Sex Determination

Females are XX, males are X- (only one x chromosome and heterogametic sex); grasshoppers

XX-XY Sex Determination

Females are XX, Males are XY; mammals

ZZ-ZW Sex Determination

Males are ZZ, Females are ZW; birds, snakes, butterflies, etc

Haplodiploploidy Sex Determination

Males have a haploid set (like walking sex cells), and females have diploid sets. Ants, bees, wasps (colonial animals)

Heterogametic Sex

Sex that can produce two different types of gametes with respect to sex chromosomes

Homogametic Sex

Sex that produces one type of gamete with respect to sex chromosomes

Genic Sex Determination

No sex chromosomes, only sex-determining genes; found in plants, fungi, fish

Environmental Sex Determination

Environmental factors determine sex: temperature in turtles

Aneuploidy

Abnormal number of chromosomes (autosomal or sex chromosomes)

Non-disjunction

When chromosomes fail to separate properly during mitosis, meiosis I or meiosis II

Aneuploidy vs. Polyploidy

In aneuploidy, one or several chromosomes are affected. In polyploidy, all chromosomes are affected.

Aneuploidy

An abnormal number of chromosomes in a cell. In mammals, aneuploidy is tolerated in sex chromosomes but not in autosomes

Polyploidy

Cell has an entire extra set or set of chromosomes (more than two)

Non-disjunction in meiosis I

Results in all four gametes being affected. Two gametes are n+1, and two gametes are n-1

Non-disjunction in meiosis II

Results in two normal gametes and two affected gametes. One affected gamete is n+1, one affected gamete is n-1.

Turner Syndrome

XO chromosome in females (only one X), caused by non-disjunction → aneuploidy

Klinefelter syndrome

XXY or XXXY or XXYY, in males

Dosage compensation

The amount of protein produced by X-linked genes and randomly inactivated in two sexes

Experimental Evidence for DNA

Franklin and Wilkins used X-ray diffraction to display the structure of DNA, and then Watson and Crick used their findings to realize it was a double-helix structure.

Structure of DNA

Two polynucleotide strands wound around each other, forming a double helix. Sugar phosphates make the outside backbone and nitrogenous bases make the “rungs of the ladder.”

Structure of Polynucleotide Strands

A string of nucleotides linked through phosphodiester bonds in a directional manner. Two polynucleotide strands are antiparallel and have complementary base pairings

Nucleotide

Basic building block of nucleic acid, consists of a nitrogenous base (CGAT/U), a five-carbon sugar (ribose/deoxyribose), and a phosphate group

Purines

Nitrogenous bases with two rings

“AGgies are pure:” Adenine and Guanine

Pyrimidines

Nitrogenous bases with one ring

“Pyramids are CUT:” Cytosine, Uracil (in RNA) and Thymine

Phosphate group

Gives nucleic acid an overall negative charge. Attaches to 5’ carbon of the nucleotide, and then also connects to 3’ carbon of other nucleotide’s sugar via a phosphodiester bond,

Van der Waal’s attractions

Small, very weak attractions between adjacent base pairs that cause DNA’s twist in the helix

Bacterial Chromosome

Most bacterial genomes have a single circular DNA molecule (therefore considered haploid). DNA appears as a clump called the nucleoid.

DNA Packaging in Prokaryotes

1. Twist of the double helix

2. Supercoiling: topoisomerases add/remove turns in the coil

DNA Packaging in Eukaryotes

1. Twist of the double helix

2. Formation of the nucleosome

3. 30nm fiber: nucleosomes fold up to produce 30nm fiber

4. 300nm fiber

   1. 30nm fiber loops around scaffold proteins to form 300nm-length fibers

5. 300nm fiber compresses to form 250nm-wide fiber

6. 250nm-wide fiber coils to form chromosome

Nucleosome

8 histone proteins with 2 loops of DNA around it

Semi-Conservative

DNA Replication is semi-conservative: one strand from the original DNA, and one newly made strand

Modes of DNA Replication

Theta replication (prokaryotes)

Linear replication (eukaryotes)

Theta Replication

1. Two strands are separated at the (one) origin of replication

2. A replication bubble is formed

3. DNA unwinds

4. Bidirectional replication using two replication forks

Results in two circular DNA molecules

Occurs in prokaryotes

Linear Replication

1. Strands are separated at MULTIPLE origins of replication

2. DNA is unwound

3. Two replication forks move bidirectionally

Occurs in eukaryotes

Requirements of DNA polymerase

1. Substrate (ATCG) must be in triphosphate form, because breaking off 2 phosphates releases energy required later

2. Must have a template strand

3. Requires an available 3’ hydroxl group → RNA primer, to attach to; because polymerase can only add nucleotides to 3’ end

Which direction does DNA synthesis occur?

5’ to 3’; polymerase adds nucleotides to 3’ OH of new strand

3 Stages of DNA Replication

Initiation, elongation, termination

DNA Replication Initiation

1. Initiator protein binds to origin of replication

2. DNA Helicase unwinds the helix by breaking the bonds

3. Single-strand binding proteins keep the DNA helix open

4. Gyrase relieves strain outside the replication bubble by cutting strands then gluing back together

5. Primase synthesizes RNA primers, which are complementary and antiparallel to each template strand

Initiator protein

Binds to origin and separates strands of DNA to initiate replication

DNA Helicase

Unwinds DNA at replication fork

Single-strand binding proteins

Attaches to single-stranded DNA to hold it open

DNA gyrase

Cuts and reseals DNA to release torsion tension from unwinding replication fork (think of unwinding yarn from the center: what happens to either end of the gap?)

DNA primase

Synthesizes a short RNA primer to provide a 3’ hydroxl (OH) group for DNA polymerase to attach DNA nucleotides

DNA polymerase III

Elongates a new nucleotide strand from 3’ in prokaryotes. Breaks off 2 phosphate groups from nucleotide (they are in triphosphate form) and uses that energy to synthesize phosphodiester bond to new template (attaches nucleotide via phosphodiester bond from previous 5’ carbon to phosphate to new nucleotide’s 3’ OH group)

DNA polymerase I

Removes RNA primers and replaces them with DNA (in prokaryotes)

DNA ligase

Joins Okazaki fragments by gluing gaps shut

DNA Replication Elongation

1. Nucleotide sequence is copied from template strand to new strand of DNA

2. DNA polymerase III (in prokaryotes) catalyzes phosphodiester bond formation between adjacent nucleotides

3. Strand synthesis

4. DNA polymerase I (in prokaryotes) replaces RNA primer with DNA (cuts it out and adds DNA instead)

5. DNA ligase covalently joins successive Okazaki fragments together via a phosphodiester bond (glues gaps shut)

DNA Replication Termination

Occurs when two replication forks meet (in prokaryotes)

Telomeres

Ends of linear chromosomes that do not encode gene and consist of repeated nucleotides, these are replicated by telomerase to avoid shortening of DNA during replication

Telomerase

A ribonucleoprotein that replicates the ends of chromosomes (telomeres) to extend them. Active in adult somatic cells, stem cells, and cancer cells

3 Types of RNA

translation RNA, messenger RNA, and ribosomal RNA. mRNA is the only type that’s translated. They’re present in both eukaryotes and eukaryotes

Gene

A stretch of DNA that codes for a protein or an RNA molecule. Basic hereditary unit for all life

Transcribed and highly regulated

Regulatory Gene

Any gene that codes for an RNA or protein that IS involved in regulation of the expression of other genes

Structural genes

Any gene that codes for an RNA or a protein that is NOT involved in regulation of other genes

Regions of a Gene

Promoter, RNA coding region, and terminator. Common to all genes

Promoter region

Region to which RNA polymerase binds, NOT transcribed

RNA Coding Region

Region that is transcribed to an RNA molecule

Terminator

Region that halts transcription, is transcribed and “kicks off” RNA polymerase

Core promoter

RNA polymerase binds here, always present

Regulatory promoter

bound by special proteins (“transcription factors”) that block transcription (not always present!)

Enhancers

Turn on gene expression and increase the rate of transcription

Silencers

Turn expression of a gene “off”

Cis-acting element

Part of DNA; ex. regulatory promoters

Trans-acting element

Binds to DNA; ex. RNA polymerase

Consensus sequences

A short stretch of common nucleotide sequences

-10 and -35 are most important in bacteria