Bio1A MT2

Chromosomes copying

semi conservative mechanisms, parental strands copies to form hybrid duplex

Replication

• Bidirectionally on circular bacteria

• Linear eukaryotic chomosomes

Primase

special RNA, makes short oligonucleotide on leading and lagging template strand, initiating replication by seperate chromosome replication DNA polymerase

Meselson- Stahl experiment

conclusion: DNA replication is semiconservative- each new molecule has one old strand and one new strand

Helicases

Uses ATP to unwind the parental duplex ahead of the fork

Topoisomerase

Relieves supercoiling ahead of the fork

Primase

Makes short RNA primers on leading and lagging templates

DNA pol III

Main replicative polymerase; extends primers on leading and lagging strands

DNA pol I

Repair- type polymerase; replace RNA primers with DNA on the lagging strand

DNA ligase

Seals the nick between adjacent okazaki fragments

Gene expression

DNA→mRNA(transcription)→protein(translation)

RNA is always sythesized

5’ → 3’, starting with a 5’ triphosphate

Prokaryotic transcription - Initiation

RNA polymerase + regulatory proteins bind the promoter, unwind the DNA helix, and start the RNA chain.

Prokaryotic transcription - Elongation

The transcription "bubble" moves along the DNA. DNA re-anneals behind the polymerase, which displaces the 5′ end of the new mRNA.

Prokaryotic transcription - termination

A termination signal releases the finished mRNA.

Prokaryotic transcription - result

mRNA is ready to use immediately (no processing needed).

Eukaryotic transcription

More complex

• Eukaryotes use many more proteins to control initiation, and the transcript must be processed before it is a mature mRNA:

• 5′ cap added (a modified nucleotide)

• 3′ poly-A tail added

• Splicing: non-coding introns are removed; coding exons are joined

Why exons matter:

exons often correspond to independent protein domains, so splicing and shuffling exons is a way to build new proteins from existing modules.

Mutation - Silent

• point mutation, often in the 3rd codon position

• Effect: no amino acid change (because of degeneracy)

Mutation - Missense

• point mutation, often in the 1st or 2nd position

• Effect: one amino acid substituted

Mutation - nonsense

• point mutation creates a stop codon

• Effect: premature chain termination (truncated protein)

Mutation - frameshift

• insertion or deletion of 1 or 2 bases

• effect: reading frame shifts so every downstream codon changes

Translation - mRNA

• carries the codons; threads along the small ribosomal subunit

Translation - tRNA

• adapter molecule: one end carries the amino acid, the other reads the codon

Translation - Ribosome

• Two large RNA-protein subunits that assemble the polypeptide

Translation - GTPases

• Organize each stage; initiation, elongation, termination

tRNA

• Folds into a cloverleaf (base-paired secondary structure) and then a compact tertiary shape.

• The anticodon loop base-pairs with the mRNA codon.

• The 3′ end (3′-OH of the terminal adenylate) is where the amino acid attaches.

• Specific enzymes recognize each tRNA and attach the correct amino acid.

Ribosome - Site A

• Acceptor (aminoacyl) site

• What sits there: incoming charged tRNA

Ribosome - Site P

• Peptidyl site

• What sits there: tRNA holding the growing peptide chain

Ribosome - Site E

• Exit site

• What sits there: free (uncharged) tRNA leaving

Genetics

is the scientific study of heredity and variation

Heredity

is the transmission of traits from one generation to the next

Variation

is demonstrated by the differences in appearance that offspring show from parents and siblings

Genes

are hereditary units made of DNA that parental cells transmit to their progeny cells

Most DNA is packaged into _, each of which is one very long double-stranded DNA molecule

chromosomes

asexual reproduction

somatic cells divide to give rise to two genetically identically progeny cells via mitosis and cytokinesis

sexual reproduction

genes are recombined and passed to the next generation via reproductive cells called gametes (sperm and eggs)

Human have

46 chromosomes in the nuclei of their somatic cells (all cells of the body except gametes): 22 pairs of autosomes and 1 pair of sex chromosomes (2n=46). We are diploid (2n), except for our gametes, which are haploid (n).

Centromere

the constricted region (“waist”) of a chromosome

Chromatid

one of the two identical halves of a chromosome after DNA replication (after DNA replication, a chromosome is Replicated composed of two identical chromatids) chromatids

Interphase (~90% of the cell cycle)

G1 Phase (”first gap”)

S Phase (“synthesis”) - End; replication

G2 Phase (”second gap”)

G1 phase

Metabolic activity and growth

S phase

Metabolic activity, growth, and DNA synthesis

G2 phase

Metabolic activity, growth, and preparation for cell division

Mitosis

Distribution of chromosomes into two identical nuclei

Cytokinesis

Division of the cytoplasm

G2 and M checkpoints

ensure that a cell is ready to divide

The Human life cycle

Haploid vs Diploid cells

• Haploid: having a single set of unpaired chromosomes

• Diploid: containing two complete sets of homologous chromosomes, one from each parent

4 Key Ideas about Meiosis

1. Law of Segregation: The maternal and paternal copies of a given chromosome (or gene) separate during meiosis and end up in different gametes at random (with equal probability).

2. Law of Independent Assortment: The maternal and paternal chromosomes of any homologous pair segregate into gametes independently of all other homologous pairs of chromosomes.

3. Crossing Over: Maternal and paternal chromosomes exchange genetic information during Prophase I.

4. Meiosis is like a slot machine that produces 4 genetically distinct haploid cells!

Number of combinations

possible when chromosomes assort independently into gametes is 2 n, where n is the haploid number

Random fertilization

adds to genetic variation because any sperm can fuse with any unfertilized egg

Prophase I

homologous chromosomes align and are held together tightly by a protein complex

Synapsis

crossing over occurs between chromatids on the aligned homologous chromosomes, which results in (a) genetic recombination between maternal and paternal homologous chromosomes and (b) formation of chiasmata

Anaphase

cohesins are cleaved along the chromosome armsto allow homologs to separate. Cohesins are cleaved at the centromeres in Anaphase II to allow replicated chromatids to separate.

Three mechanisms contribute to genetic variation in sexual life cycles

independent assortment of chromosomes, crossing over, and random fertilization

Gregor Mendel

described the law of segregation and the law of independent assortment

Why pea plants

• There are many true-breeding varieties of pea plants with different characters (flower color, seed color, morphology, etc.)

• Each variant for a character is called a trait (for example, purple vs. white)

• Peas have a short generation time

• Peas produce a lot of offspring (progeny)

• Mating can be controlled; pea plants can self-pollinate or can be cross-pollinated

Mendel’s model to explain his results

1. There are alternative versions of heritable factors (genes) that we call alleles

2. Two copies (alleles) of a gene are inherited by an individual, one from each parent

3. If the alleles differ, then the dominant allele determines the appearance of the individual; the other allele is recessive

4. The law of segregation: the two alleles separate from each other during gamete formation and end up in gametes

• an egg or sperm gets only one of the two alleles present in the parent

• this is explained by the behavior of chromosomes in meiosis!

Mendel’s law of independent assortment

• Mendel’s second law states that each pair of alleles segregates independently of any other pair of alleles during gamete formation

• In terms of meiosis, this law simply states that each pair of homologous chromosomes follows Mendel’s first law (the law of segregation) without influence of other chromosomes

• This law applies only to genes on different, nonhomologous chromosomes or those that are very far apart on the same chromosome

• Genes located near each other on the same chromosome tend to be inherited together

Testcross

can distinguish the possible genotypes of individuals with the dominant phenotype

Pedigrees

family trees

Carrier

person who is heterozygous for a recessive, inherited disorder

Incomplete dominance

Neither allele is completely dominance

Codominance

two dominant alleles affect the phenotype in separate, distinguishable ways

More than two alleles

this is true for most genes

Epistasis

the phenotypic expression of one gene affect that of another

Polygenic inheritance

additive effect of two or more genes on a single phenotypic character

Why fruit flies (Drosophila melanogaster)?

• Fruit flies have a short generation time (2 weeks)

• Fruit flies produce a lot of offspring (progeny)

• Mating can be controlled, but unlike pea plants, fruit flies must be crossed

• Fruit flies have only four pairs of chromosomes, which can be seen with a microscope

• In the early 1900’s, Morgan isolated mutants that could be easily distinguished from the wild type

wild type

• the most common phenotype observed in natural populations (“in the wild”)

• Each gene is given a gene symbol that usually describes the mutant phenotype: w for white eyes

  • the wild-type allele denotes with a plus: w+

  • A recessive mutant allele is shown in lowercase: w

Sex-linked genes

(genes on sex chromosomes) exhibit unique patterns of inheritance

Sex determination

in mammals and many other animals has a chromosomal basis

Inheritance of X-linked genes in humans

• A gene that is located on either sex chromosome is called a sex-linked gene

• Some disorders are caused by recessive alleles on the X

chromosome in humans:

• Color blindness (mostly X-linked)

• Duchenne muscular dystrophy

• Hemophilia

For a recessive X-linked trait to be expressed,

• a female needs two copies of the allele (homozygous)

• a male needs only one copy of the allele (hemizygous)

For a recessive X-linked trait to be expressed

• a female needs two copies of the allele (homozygous)

• a male needs only one copy of the allele (hemizygous)

Cells don’t need every protein all the time, so they save energy by__?

Turning genes on only when needed

Operon

a group of genes with related function that are transcribed together from one promoter

Promoter

where the RNA polymerase binds

Operator

the “switch” site where a repressor can bind and block transcription

Regulatory gene

makes the repressor protein (trpR or lacI)

Structural genes

encode the enzymes

trp operon

Job: make the amino acid tryptophan

Genes: trpE, trpD, trpC, trpB, trpA

No tryptophan

repressor is inactive→operon ON→cell makes tryptophan

Tryptophan present

it acts as a corepressor and binds the repressor→repressor ACTIVE, binds the operator→operon OFF

Lac operon

Job: digest lactose into galactose+glucose. Genes: LacZ, LacY (permease), LacA (transacetylase). The repressor gene is LacI.

No lactose

Lacl repressor is active and binds the operator→ operon OFF (white colonies on X-gal)

Lactose present

lactose becomes allolactose (the inducer), which binds Lacl and inactivates it→operon ON (blue colonies)

Lacl and Trp

sequence-specific DNA-binding proteins, also called transcription factors

Lacl forms

a tetramer, and its α-helices contact the operator DNA

Binding a small signal molecule (inducer or corepressor) __

changes whether the protein binds DNA

Glucose high→

cAMP low→CRP inactive

Glucose low→

cAMP high→cAMp binds CRP→active CRP binds the lac promoter and helps RNA polymerase bind

Differential gene expression

Different cell types express different genes, even though they all have the same DNA

Chromatin

A mix of DNA and protein

Eukaryotic regulation points

Chromatin unpacking, transcription, RNA processing, transport, mRNA degradation, translation, protein processing, protein degradation

Nucleosome

DNA wrapped around a core of histone proteins

Histone tails

Parts of histones that stick out of the nucleosome and can be chemically modified

Heterochromatin

Highly condensed chromatin that is generally not expressed

Euchromatin

Loose, open chromatin that is accessible to transcription factors and RNA polymerase

Histone acetylation

Chemical modification of histone tails that loosens chromatin and promotes transcription