Midterm Final Review Part II. Somatic CellsGametes Body cells Diploid (2n): 2 of each type of...

Midterm Final Review

Part II

Somatic Cells Gametes• Body cells• Diploid (2n): 2 of each

type of chromosome• Divide by mitosis

• Humans: 2n = 46

• Sex cells (sperm/egg)• Haploid (n): 1 of each

type of chromosome• Divide by meiosis

• Humans: n = 23

Phases of the Cell Cycle

Phases of the Cell Cycle The mitotic phase alternates with interphase:

G1 S G2 mitosis cytokinesis Interphase (90% of cell cycle)G1 Phase: cell grows and carries out normal functionsS Phase: duplicates chromosomesG2 Phase: prepares for cell division M Phase (mitotic)Mitosis: nucleus dividesCytokinesis: cytoplasm divides

Mitosis: Prophase Metaphase Anaphase Telophase

Cell Cycle Control System• Checkpoint = control point where stop/go signals

regulate the cell cycle

Major Checkpoints1.1. GG11 checkpoint checkpoint (Most important!)

– Controlled by cell size, growth factors, environment– “Go” completes whole cell cycle– “Stop” cell enters nondividing state (G0 Phase)

• Nerve, muscle cells stay at G0; liver cells called back from G0

2.2. GG22 checkpoint checkpoint• Controlled by DNA replication completion, DNA mutations, Controlled by DNA replication completion, DNA mutations,

cell sizecell size

3.3. M-spindle (Metaphase) checkpointM-spindle (Metaphase) checkpoint– Check spindle fiber (microtubule) attachment to chromosomes

at kinetochores (anchor sites)

Internal Regulatory Molecules

• Kinases (cyclin-dependent kinase, Cdk): protein enzyme controls cell cycle; active when connected to cyclin

• Cyclins: proteins which attach to kinases to activate them; levels fluctuate in the cell cycle

Internal Regulatory Molecules

MPF = maturation-promoting factor• specific cyclin-Cdk complex which allows cells

to pass G2 and go to M phase

• Growth Factor: proteins released by other cells to stimulate cell division

• Density-Dependent Inhibition: crowded cells normally stop dividing; cell-surface protein binds to adjoining cell to inhibit growth

• Anchorage Dependence: cells must be attached to another cell or ECM (extracellular matrix) to divide

External Regulatory Factors

Cancer Cells

Cancer: disorder in which cells lose the ability to control growth by not responding to regulation.

• multistep process of about 5-7 genetic changes (for a human) for a cell to transform

• loses anchorage dependency and density-dependency regulation

Normal Cells Cancer Cells

Cancer cells• Some have abnormal #’s of chromosomes

Karyotype of Metastatic Melanoma

Types of Reproduction

ASEXUAL• Produces clones

(genetically identical)• Single parent• Little variation in

population - only through mutations

• Fast and energy efficient• Eg. budding, binary

fission

SEXUAL• Meiosis produces

gametes (sex cells)• 2 parents: male/female• Lots of

variation/diversity• Slower and energy

consumptive• Eg. humans, trees

Homologous Chromosomes in a Somatic Cell

Meiosis = reduction divisionMeiosis = reduction division

• Cells divide twicetwice• Result: 4 daughter

cells, each with half as many chromosomes as parent cell

Events Unique to Meiosis I (not in mitosis)

1. Prophase I: Synapsis and crossing over

2. Metaphase I: pairs of homologous chromosomes line up on metaphase plate

3. Anaphase I: homologous pairs separate sister chromatids still attached at centromere

Sources of Genetic Variation:1. Crossing Over

– Exchange genetic material

– Recombinant chromosomes

Sources of Genetic Variation:2.Independent Assortment of Chromosomes

– Random orientation of homologous pairs in Metaphase I

Sources of Genetic Variation:3. Random Fertilization

– Any sperm + Any egg– 8 million X 8 million = 64 trillion combinations!

Mitosis Meiosis Both are divisions of cell nucleus

• Somatic cells• 1 division• 2 diploid daughter cells• Clones• From zygote to death• Purpose: growth and repair• No synapsis, crossing over

• Gametes• 2 divisions• 4 haploid daughter cells• Genetically different-less than

1 in 8 million alike• Females before birth follicles

are formed. Mature ova released beginning puberty

• Purpose: Reproduction

MENDELMENDEL’’S PRINCIPLESS PRINCIPLES

1. Alternate version of genes (allelesalleles) cause variations in inherited characteristics among offspring.

2. For each character, every organism inherits one allele from each parent.

3. If 2 alleles are different, the dominantdominant allele will be fully expressed; the recessiverecessive allele will have no noticeable effect on offspring’s appearance.

4.4. Law of SegregationLaw of Segregation: the 2 alleles for each character separate during gamete formation.

– dominant (P), recessive (p)• homozygous = 2 same alleles (PP or pp)• heterozygous = 2 different alleles (Pp)– Phenotype: expressed physical traits– Genotype: genetic make-up

TestcrossTestcross: : determine if dominant trait is homozygous or heterozygous by crossing with recessive (pp)

Law of Independent Assortment:Law of Independent Assortment:• Each pair of alleles segregates (separates) independently

during gamete formation• Eg. color is separate from shape

Extending Mendelian GeneticsThe relationship between genotype and phenotype is rarely simple

Complete Dominance: heterozygote and homozygote for dominant allele are indistinguishable•Eg. YY or Yy = yellow seed

Incomplete Dominance: F1 hybrids have appearance that is between that of 2 parents•Eg. red x white = pink flowers

Blood Typing

Phenotype(Blood Group) Genotype(s)

Type A IAIA or IAi

Type B IBIB or IBi

Type AB IAIB

Type O ii

Mendelian Inheritance in Humans

Pedigree: diagram that shows the relationship between parents/offspring across 2+ generations

Woman = Man = Trait expressed:

Sex-linked genes

• Sex-linked gene on X or Y• Females (XX), male (XY)

– Eggs = X, sperm = X or Y• Fathers pass X-linked genes to daughters, but not

sons• Males express recessive trait on the single X

(hemizygous)• Females can be affected or carrier

X-InactivationX-InactivationBarr body = inactive X chromosome; regulate gene dosage in females during embryonic development

• Cats: allele for fur color is on X

• Only female cats can be tortoiseshell or calico.

Genetic Recombination: production of offspring with new combo of genes from parents

• If offspring look like parents parental types• If different from parents recombinants

Linked genes: located on same chromosome and tend to be inherited together during cell division

Crossing over: explains why some linked genes get separated during meiosis

• the furtherfurther apart 2 genes on same chromosome, the higher higher the probability of crossing over and the higherhigher the recombination frequency

Calculating recombination frequency

Linkage Map: genetic map that is based on % of cross-over events

• 1 map unit = 1% recombination frequency• Express relative distances along chromosome• 50% recombination = far apart on same chromosome

or on 2 different chromosomes

NondisjunctionNondisjunction: chromosomes fail to separate properly in Meiosis I or Meiosis II

NondisjunctionNondisjunction

• Aneuploidy: incorrect # chromosomes– Monosomy (1 copy) or Trisomy (3 copies)

• Polyploidy: 2+ complete sets of chromosomes; 3n or 4n– Rare in animals, frequent in plants

A tetraploid mammal. Scientists think this species may have arisen when an ancestor doubled its chromosome # by errors in mitosis or meiosis.

Chromosomal Mutations

Chromosomal Mutations

Exceptions to Mendelian inheritance• Genomic imprinting: phenotypic effect of gene

depends on whether from M or F parent• Silence genes by adding methyl groups to DNA

(methylation)

Exceptions to Mendelian inheritance

• Some genes located in organelles– Mitochondria, chloroplasts,

plastids– Contain small circular DNA

• Mitochondria = maternal inheritance (eggs)

Variegated (striped or spotted) leaves result from mutations in pigment genes in plastids, which generally are inherited from

the maternal parent.

Frederick Griffith (1928)

Conclusion: living R bacteria transformed into deadly S bacteria by unknown, heritable substance

Avery, McCarty, McLeod (1944)– Tested DNA, RNA, & proteins in heat-killed

pathogenic bacteria– Discovered that the transforming agent was

DNA

Hershey and Chase (1952)

• Bacteriophages: virus that infects bacteria; composed of DNA and protein

Protein = radiolabel SProtein = radiolabel SDNA = radiolabel PDNA = radiolabel P

Edwin Chargaff (1947)

Chargaff’s Rules:• DNA composition varies

between species• Ratios:

– %A = %T and %G = %C

Rosalind Franklin (1950’s)

• Worked with Maurice Wilkins• X-ray crystallography = images of DNA• Provided measurements on chemistry of DNA

James Watson & Francis Crick (1953)

• Discovered the double helix by building models to conform to Franklin’s X-ray data and Chargaff’s Rules.

Structure of DNA

DNA = double helix– “Backbone” = sugar +

phosphate– “Rungs” = nitrogenous

bases

Structure of DNA

Nitrogenous Bases– Adenine (A)– Guanine (G)– Thymine (T)– Cytosine (C)

• Pairing:– purine + pyrimidine– A = T– G Ξ C

purine

pyrimidine

Structure of DNA

Hydrogen bonds between base pairs of the two strands hold the molecule together like a zipper.

Structure of DNA

Antiparallel: one strand (5’ 3’), other strand runs in opposite, upside-down direction (3’ 5’)

DNA Comparison

• Double-stranded• Circular• One chromosome• In cytoplasm• No histones• Supercoiled DNA

• Double-stranded• Linear• Usually 1+ chromosomes• In nucleus• DNA wrapped around histones

(proteins)• Forms chromatin

Prokaryotic DNA Eukaryotic DNA

Replication is semiconservative

DNA Replication

Leading strand vs. Lagging strand

Proofreading and Repair

• Mismatch repair: special enzymes fix incorrect pairings

Nucleotide Excision Repair

• DNA polymerases proofread as bases added

• Nucleotide excision repair:– Nucleases cut damaged

DNA– DNA poly and ligase fill in

gaps

Telomeres: repeated units of short nucleotide sequences (TTAGGG) at ends of DNA

• Telomeres “cap” ends of DNA to postpone erosion of genes at ends (TTAGGG)

• Telomerase: enzyme that adds to telomeres– Eukaryotic germ cells, cancer cells

Telomeres stained orange at the ends of mouse chromosomes

Telomeres & Telomerase

1 Gene = 1 polypeptide or RNA molecule

A Summary of Protein Synthesis

1 gene = 1 polypeptide or 1 RNA molecule1 gene = 1 polypeptide or 1 RNA molecule

DNA RNA• Nucleic acid composed of

nucleotides• Double-stranded• Deoxyribose=sugar• Thymine• Template for individual

• Nucleic acid composed of nucleotides

• Single-stranded• Ribose=sugar• Uracil• Helper in steps from DNA to

protein• Types: mRNA, pre-mRNA,

tRNA, rRNA, snRNA, srpRNA, siRNA

The Genetic Code

The Genetic Code

64 different codon combinations

This code is universal: all life forms use the same code.

Reading frame: groups of 3 must be read in correct groupings

1. Initiation

Transcription factors must recognize TATA box before RNA polymerase can bind to DNA promoter

Eukaryotes:TATA box = DNA sequence (TATAAAA) upstream from promoter

2. Elongation

• RNA polymerase adds RNA nucleotides to the 3’ end of the growing chain (A-U, G-C)

3. Termination

RNA polymerase transcribes a terminator sequence in DNA, then mRNA and polymerase detach.

It is now called pre-mRNA for eukaryotes.

Prokaryotes = mRNA ready for use

Additions to pre-mRNA:• 5’ cap (modified guanine) and 3’ poly-A tail (50-520

A’s) are added

• Help export from nucleus, protect from enzyme degradation, attach to ribosomes

RNA Splicing

• Pre-mRNA has introns (noncoding sequences) and exons (codes for amino acids)

• Splicing = introns cut out, exons joined together

RNA Splicing

• SpliceosomeSpliceosome = snRNP + Proteins• Remove intronsintrons and join exonsexons• RibozymeRibozyme = RNA acts as enzyme

Why have introns?• Some regulate gene activity

• Alternative RNA SplicingAlternative RNA Splicing: produce different combinations of exons– One gene can make more

than one polypeptide!– 20,000 genes 100,000

polypeptides

Translation:1. Initiation

• Small subunit binds to start codon (AUG) on mRNA• tRNA carrying Met attaches to P site• Large subunit attaches

2. Elongation

3.Termination• Stop codon reached and translation stops• Release factor binds to stop codon;

polypeptide is released• Ribosomal subunits dissociate

Protein Folding• During synthesis, polypeptide chain coils and

folds spontaneously• Chaperonin: protein that helps polypeptide

fold correctly

Types of Ribosomes• Free ribosomes: synthesize proteins that stay

in cytosol and function there• Bound ribosomes (to ER): make proteins of

endomembrane system (nuclear envelope, ER, Golgi, lysosomes, vacuoles, plasma membrane) & proteins for secretion– Uses signal peptide to target location

Cellular “Zip Codes”• Signal peptide: 20 AA at leading end of

polypeptide determines destination• Signal-recognition particle (SRP): brings

ribosome to ER

The Central Dogma

Mutations happen here

Effects play out here

Mutations = changes in the genetic material of a cell

• Large scale mutations: chromosomal; always cause disorders or death– nondisjunction, translocation, inversions,

duplications, large deletions• Point mutations: alter 1 base pair of a gene

1. Base-pair substitutions – replace 1 with another• Missense: different amino acid• Nonsense: stop codon, not amino acid

2. Frameshift – mRNA read incorrectly; nonfunctional proteins

• Caused by insertions or deletions

Sickle-Cell Disease = Point Mutation

Prokaryotes vs. Eukaryotes

Prokaryotes Eukaryotes• Transcription and

translation both in cytoplasm

• DNA/RNA in cytoplasm• RNA poly binds directly to

promoter• Transcription makes mRNA

(not processed)• No introns

• Transcription in nucleus; translation in cytoplasm

• DNA in nucleus, RNA travels in/out nucleus

• RNA poly binds to TATA box & transcription factors

• Transcription makes pre-mRNA RNA processing final mRNA

• Exons, introns (cut out)