BIOL 326 E2

Chromosome characteristics

number, size, location of centromere, banding patterns

p

chromosome short arm

q

chromosome long arm

metacentric

centromere in middle

submetacentric

centromere slightly off center

acrocentric

centromere is significantly off center, but not at the end

telocentric

centromere at end; p may be nearly nonexistent

banding patterns

revealed when chromosomes are treated w/ stain

karyotype

photographic representation in which all of the chromosomes w/in a single cell are arranged in a standard fashion

chromosome numbering

according to size; Largest = smallest #

(sex chromosomes are just X and Y)

G banding

1. Chromosomes are treated w/ heat or proteolytic enzymes that partially digest chromosomal proteins

2. Chromosomes are exposed to Giemsa stain

3. Chromosomal regions that bind the Giemsa molecules heavily produce dark bands; in other regions, light bands are produced

dark G-bands

more tightly compacted regions

importance of banding

distinguishes chromosomes, detects changes in chromosome structure, assesses evolutionary relationships b/t species

euploid

organisms w/ a chromosome number that is an exact multiple of a chromosome set (ex/ fruit flies - 8 chromosomes, 2 sets = 4 chromosomes/set)

aneuploid

organisms w/ a chromosome number that is NOT an exact multiple of a set

trisomic

organism w/ three copies of a chromosome instead of 2 (2n+1)

monosomic

organism w/ one copy of chromosome instead of 2 (2n-1)

aneuploidy in humans

can cause miscarriage; ~50% of all spontaneous abortions are due to alterations in chromosome #

most common survivable trisomies

trisomy 13, 18, or 21 (down-syndrome), and sex chromosome abnormalities

trisomy 1

believed to either cause gametes to be inviable or lethal at such an early developmental stage that it prevents successful implantation of the embryo

trisomy X

X-chromosome inactivation (barr bodies) allows for the normal expression of most X-linked genes

meiotic nondisjunction

can occur during anaphase I or II

meiotic nondisjunction during A1

an entire bivalent migrates to one pole → 4 abnormal haploid cells

meiotic nondisjunction during A2

net result of 2 abnormal and 2 normal haploid cells

trisomic nondisjunction

if a gamete carrying an extra chromosome unites with a normal gamete

monosomic nondisjunction

if a gamete missing a chromosome is viable and participates in fertilization

complete nondisjunction

rare; all of the chromosomes undergo nondisjunction and migrate to one of the daughter cells

daughter cell w/ all chromosomes may complete meiosis and form two diploid cells, which give rise to diploid gametes

daughter cell w/ no chromosomes is nonviable

deletions and duplications

changes in the total amount of genetic material w/in a single chromosome

deletion

a segment of chromosomal material is missing causing the affected chromosome to be deficient in a significant amount of genetic material

deficiency

refers to the condition of a chromosome that is missing a region

duplication

occurs when a section of a chromosome is repeated w/in a chromosome

inversions and translocations

chromosomal rearrangements; total amount of material is unchanged

inversion

a change in the direction of the genetic material along a single chromosome

translocation

one segment of a chromosome becomes attached to a different chromosome/different part of the same chromosome

simple translocation

a single piece of chromosome is attached to another chromosome

reciprocal translocation

two different chromosomes exchange pieces, altering both of them

how deletions occur

a chromosome breaks in one or more places, and a fragment of the chromosome is lost OR

recombination occurs at incorrect locations b/t homologous chromosomes

terminal deletions

fragments w/ the centromere

non-terminal deletions

fragments w/out the centromere; lost bc they do not find their way into the nucleus after mitosis, resulting in degradation in cytosol

interstitial deletion

when two ends of a broken chromosome reconnect, and the central fragment is lost

deletions due to incorrect recombination

Result in one chromosome w/ a deletion and one w/ a duplication

how duplications occur

abnormal crossover events during meiosis; crossover may occur at misaligned sites on homologs

misalignment

occurs when a chromosome has repetitive sequences

repetitive sequences

two or more homologous segments that have identical or similar sequences

nonallelic homologous recombination

occurs at homologous sites (such as repetitive sequences), but the sites are not alleles of the same gene, resulting in one chromatid w/ a duplication and another w/ a deletion

deletion phenotypic consequences

usually produce detrimental effects on phenotype; larger deletions are more harmful bc more genes are missing

duplication phenotypic consequences

tend to be less phenotypically harmful than deletions; larger duplications are more harmful

gene family

two or more genes in a particular species that are similar to each other; occurs by duplication

copy number variation (CNV)

a type of structural variation in which a DNA segment (≥1000 bp) commonly exhibits copy number differences among members of the same species; occurs at the population level

how CNV occurs

may occur bc some members of a species carry a chromosome missing a gene or part of a gene OR

bc of nonallelic homologous recombination OR

bc of a duplication

pericentric inversion

if the centromere lies w/in the inverted region of the chromosome

paracentric inversion

if the centromere lies outside the inverted region of the chromosome

acentric fragment

piece of chromosome w/out any centromere - lost and degraded during cell division

dicentric chromosome

contains two centromeres, region connecting two centromeres is a dicentric bridge

balanced translocation

total amount of genetic material is unchanged; typically no phenotypic consequences

unbalanced translocation

significant portions of genetic material are duplicated/deleted; associated w/ phenotypic abnormalities and can be lethal

how balanced translocations occur

Mechanism 1:

1. Cells are exposed to agents that cause chromosomes to break

2. Broken ends lack telomeres and are therefore reactive

3. A reactive end readily binds to another reactive end (via DNA repair enzymes), so if multiple chromosomes are broken, reactive ends may join incorrectly to produce a reciprocal translocation

Mechanism 2: nonhomologous chromosomes may crossover and exchange pieces

how unbalanced translocations occur

occurs in offspring of parents with balanced translocation

nucleic acid

Term was derived from Friedrich Miescher's discovery of DNA in 1869

- He identified an unknown phosphorus-containing substance isolated from the nuclei of WBCs - he named it nuclein

- As the structure of DNA and RNA became better understood, it was determined they are acidic molecules bc they release H ions in solution and have a net negative charge at neutral pH

- Nuclein + acid = nucleic acid = DNA and RNA

genetic material criteria: information

genetic material must contain info necessary to construct an entire organism; blueprint for determining the inherited traits of an organism

genetic material criteria: transmission

during reproduction, the genetic material must be passed from parents to offspring

genetic material criteria: replication

genetic material must be copied to pass it from parent to offspring

genetic material criteria: variation

the genetic material must vary in ways that can account for phenotypic differences w/in each species

nucleotide components

at least one phosphate group, a pentose sugar, and a nitrogenous base

pentose sugars

deoxyribose (DNA) and ribose (RNA)

purines

double ring structures: adenine (A) and guanine (G)

pyrimidines

single ring structures: thymine (T), cytosine (C) (DNA), and uracil (U) (RNA)

phosphodiester linkage

attachment of phosphate to 3' carbon in one nucleotide and the 5' carbon in the next nucleotide

why DNA has directionality

all sugar molecules are oriented in the same direction

5' end

phosphate group

3' end

sugar hydroxyl (OH) group

DNA backbone

phosphates and sugar molecule; phosphate group connects two sugar molecules via phosphodiester linkage; negatively charged due to negative charge on each phosphate; bases project from the backbone

base pairing rules

A-T, G-C, A-U (RNA)

chargaff's rule

the amount of A in DNA = the amount of T & the amount of G = the amount of C

antiparallel arrangement

in a DNA double helix, one strand is 5' to 3' and the other is 3' to 5'

A-T

two hydrogen bonds

GC

three hydrogen bonds

helicase

breaks the h-bonds b/t DNA strands

topoisomerase II

alleviates positive supercoiling (overwounding)

single-stranded binding protein

keeps the parental strands apart

primase

synthesizes an RNA primer

DNA polymerase III

synthesizes a daughter strand of DNA

DNA polymerase II

proofreads the daughter strand of replicated DNA and corrects any base pairing errors

DNA polymerase I

removes the RNA primers and fills in w/ DNA

DNA ligase

covalently links the Okazaki fragments together

leading strand

continuous synthesis; one RNA primer is made at the origin, and then DNA pol III attaches nucleotides in 5' to 3' direction as it slides toward the opening of the replication fork

lagging strand

Discontinuous synthesis; RNA primers repeatedly initiate synthesis in 5' to 3' direction, away from the replication fork

okazaki fragment

segments of lagging strand; each contains a short RNA primer at the 5' end

completion of okazaki fragment synthesis

1. Removal of RNA primers by DNA pol I

2. Synthesis of DNA by DNA pol I in the region where the primers were removed

3. Covalent attachment of adjacent fragments of DNA by DNA ligase

replisome

Primosome + two DNA polymerase II

primosome

complex formed by DNA helicase and primase

termination of DNA replication in E. coli

1. there is a pair of termination sequences on the opposite side of the chromosome from oriC (origin of replication) known as ter sequences

2. The protein, termination utilization substance (Tus) binds to the ter sequences and stops the movement of the replication forks

3. One of the ter sequences, T1, prevents the advancement of the fork moving left to right

4. Another ter sequence, T2, prevents the advancement of the fork moving right to left

5. DNA replication ends when oppositely advancing forks meet, usually at T1 or T2

dNTP

nucleotide about to be attached to the growing strand; contains three phosphate groups attached at the 5' carbon atom of deoxyribose

how nucleotides are connected

1. dNTP first enters the catalytic site of DNA polymerase and binds to the template strand

2. Next, the 3' OH group in the nucleotide on the end of the growing strand reacts with the PO42- group on the dNTP

- Highly exergonic reaction resulting in a covalent bond b/t 3' and 5' end

- Formation of the bond causes the newly made strand to grow in the 5' to 3' direction

how proofreading occurs

occurs by the removal of nucleotides in the 3' to 5' direction at the 3' exonuclease site; after the mismatched nucleotide is removed, DNA polymerase resumes DNA synthesis in the 5' to 3' direction

telomeres

highly repetitive telomeric sequences w/in the DNA and the specific proteins that are bound to those sequences

telomerase

recognizes the sequences at the the end of eukaryotic chromosomes and synthesizes the telomeric sequences

introns

non coding intervening sequences

exons

regions of an RNA molecule that remain after splicing has removed the introns

origins of replication

chromosomal sites necessary to initiate replication; eukaryotic chromosomes contain many origins