AP Genetics Review Why do cells divide? The continuity of life is based on the reproduction of...

AP Genetics Review

Why do cells divide?

• The continuity of life is based on the reproduction of cells: cell division

• Cells divide to:– Reproduce– Renewal– Repair– Replacement– Make new cells

Organization of Genetic Material

• DNA: our genetic material, our genes

• Chromatin: DNA and proteins

• Chromosomes: thread-like structures in the nucleus that are made of chromatin

• Genome: all of our DNA

Chromosome Duplication

• Before a cell can divide, chromosomes must duplicate.

• Each duplicated chromosome has two identical sister chromatids, attached at a centromere.

Phases of the Cell Cycle

• Interphase: 90% of the cell’s life, during which growth, protein synthesis, and chromosome duplication occurs. Has 3 sub-phases:

• G1 phase: “first gap” the cell grows

• S phase: “synthesis” chromosomes duplicate• G2 phase: “second gap” the cell grows some

more and prepares for division

Phases of the Cell Cycle

• The other phase is the Mitotic Phase (M) during which the cell divides. It has 2 sub-phases:

• Mitosis: when the nucleus divides• Cytokinesis: when the cytoplasm and the rest

of the cell divides

The Phases of Mitosis

• Prophase• (Prometaphase)• Metaphase• Anaphase• Telophase• Cytokinesis

Binary Fission• Prokaryotes (bacteria and

Archea) reproduce by binary fission, meaning “division in half.”

• Bacteria have one chromosome, which is a a big circle, which reproduce starting at the origin of replication.

• After DNA is duplicated, the plasma membrane pinches inward and a new cell wall grows between the daughter cells.

Kinases and Cyclins• Kinases are enzymes that

active or inactive proteins of the cell cycle

• Cyclins are proteins that must be attached to kinases to be active; they are cyclin dependent kinases (Cdks)

• MPF “maturation-promotion factor” triggers G2

How cells grow

• Cells don’t grow if they are over-crowded, which is called density-dependent inhibition

• Most cells are anchorage dependent which means that they must be attached to something to grow

• Cancer cells are NEITHER of these things, they are cells growing out of control wherever they want.

Inheritance of Genes

• Genes are segments of DNA. Copies of genes (with some differences due to crossing over) are passed from parents to children.

• Gametes are sex cells, eggs and sperm, that carry genes from one generation to the next.

• During fertilization, gametes unite to form a zygote, which develops into an embryo, then a fetus, and then a newborn.

Karyotypes

• A karyotype is a picture of all 23 pairs of chromosomes (duplicated to be 46) arranged in order from 1 23.

• Homologous chromosomes are pairs; one from Mom and one from Dad

Types of Chromosomes

• 22 pairs of our chromosomes are autosomes, non-sex chromosomes.

• 1 pair of our chromosomes are called sex chromosomes, and determine gender.

• Women = XX• Men = XY

Diploid vs. Haploid

• Diploid Cells:• 2n• 46 chromosomes• Somatic cells (body cells)• 2 sets of chromosomes• 2n = 46• Skin, nerve, muscle...all

body cells• Zygotes

• Haploid Cells:• n• 23 chromosomes• Gametes only• Egg and sperm• 1 set of unduplicated

chromosomes• n=23• Sex cells

Meiosis• Meiosis is cell division that reduces the number

of sets of chromosomes from two to one, creating gametes (eggs and sperm).

• It ONLY happens in the ovaries and testes.

The process of meiosis

• Meiosis happens in two steps, Meiosis I and Meiosis II.

Stages of Meiosis I:Prophase IMetaphase IAnaphase ITelophase I and Cytokinesis

Stages of Meiosis II:Prophase IIMetaphase IIAnaphase IITelophase II and Cytokinesis

Prophase I

• 90% of meiosis• Chromosomes condense• Crossing over occurs:

DNA in non-sister chromatids mix and match; resulting in genetic variation of offspring

• Tetrads are held together at chiasmata

Crossing Over• Duplicated homologous

chromosomes connect, this is called synapsis.

• Pieces of DNA swap, called crossing over.

• All 4 chromatids together make a tetrad.

• Each tetrad has at least one site of chiasma, where crossing over occurs.

Anaphase I

• The chromosomes begin to move to the poles.• Sister chromatids remain attached!

Anaphase II

• Centromeres of each chromosome separate, and sister chromatids start moving apart.

Mitosis vs. Meiosis

Mitosis• Cells divide once• No crossing over• Two daughter cells made• Daughter cells are identical

to each other and parents• Daughter cells are 2n• Occurs in somatic cells

Meiosis• Cells divide twice• Crossing over (prophase I)• Four daughter cells made• Daughter cells are all

different from each other and parents

• Daughter cells are n• Occurs in ovaries/testes• Makes gametes

Why is crossing over important?• During Prophase I, crossing over occurs and

produces genetic variation.• This produces recombinant chromosomes, that

carry genes (DNA) from two different parents• Powers natural selection/evolution: all

individuals are different and the most fit survive to reproduce

• Makes species more “hardy,” if bad things happen, at least some will have adaptations that help them survive.

Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings

• From his experimental data, Mendel deduced that an organism has two genes (alleles) for each inherited characteristic

– One characteristic comes from each parent!!!

9.3 Mendel’s principle of segregation describes the inheritance of a single characteristic

P GENERATION(true-breedingparents)

F1 generation

F2

generation

Purple flowers White flowers

All plants have purple flowers

Fertilization among F1 plants(F1 x F1)

3/4 of plantshave purple flowers

1/4 of plantshave white flowers

Figure 9.3A


• A sperm or egg carries only one allele of each pair– The 2 alleles for

a gene separate during gamete formation, and each gamete gets a different one

– This is the law of segregation

GENETIC MAKEUP (ALLELES)

P PLANTS

F1 PLANTS(hybrids)

F2 PLANTS

PP pp

All P All p

All Pp

1/2 P 1/2 p

EggsP

p

P

PPp

Sperm

Pp Pp

pp

Gametes

Gametes

Phenotypic ratio3 purple : 1 white

Genotypic ratio1 PP : 2 Pp : 1 pp

Figure 9.3B


Law of Independent Assortment

• Another law Mendel discovered is the Law of Independent Assortment which says that each allele segregates independently from another (traits aren’t linked unless they are on the same chromosome)


Genotype and Phenotype

• A genotype is the genetic make-up of an individual, expressed in letters. (BB, Bb, bb)

• A phenotype is the physical appearance of an individual, determined by his or her genotype. (black, brown, short, tall, etc)


Purple flowers, P, are dominant to white, p.

• Show a Punnett Square crossing a homozygous purple flower with a heterozygous purple flower.

• PP x Pp

• What are the genotypic and phenotypic ratios?


Incomplete Dominance

• In incomplete dominance, the heterozygous genotype produces a phenotype that is in between the dominant and recessive ones.

• For example, if RR makes red flowers, and rr makes white flowers, then Rr makes PINK flowers (instead of red).


Co-Dominance

• Co-Dominance- when both alleles are expressed in the phenotype, an example blood type AB.


Dihybrid Crosses

• Instead of crossing just one trait, dihyrbrid crosses show the crossing of two separate traits.


Pedigrees

• Pedigrees are used to trace traits through a family tree.

• Circles are girls, squares are boys.

• Filled in circles and squares represent individuals affected by a disease.

• A horizontal line connecting the symbols represents marriage, vertical lines represent offspring.


Everything that’s left over…

• A testcross is done to figure out an unknown genotype. The mystery genotype is crossed with a homozygous recessive individual.

• A carrier is heterozygous for a disease but does not show symptoms. They CAN pass it on to offspring.


Other types of inheritance

• Pleiotropy: Genes can affect more than one phenotype (sickle-cell and malaria)

• Epistasis: One gene affects how a second gene is expressed

• Polygenic Inheritance: Many genes affect one phenotype (skin color)


Sex-linked diseases

• Any gene located on a sex chromosome is called a sex-linked gene.

• Examples include color blindness, baldness, hemophilia, and muscular dystrophy.

• These recessive diseases usually affect men more than women.


The importance of chromosomes

• In 1902, the chromosomal theory of inheritance began to take form, stating: genes have specific locations (loci) on chromosomes, and you randomly get one chromosome from each parent.


Linked Genes

• Genes on the same chromosome tend to be inherited together “linked genes”

So why do offspring look different from parents?


Independent Assortment

• The phenotypes of the parents are called parental types.

• The offspring, with new and different phenotypes, are called recombinant types or recombinants.

• This happens because offspring receive one chromosome from each parent, and end up looking different.


Linkage Mapping

• Based on a linkage map, one can assume: the farther apart 2 genes are, the more likely a crossover will occur between them, therefore the recombination frequency is higher.


Linkage Mapping

• A linkage map is a genetic map based on recombination frequencies.

• Units are called map units and show the distance between genes.

• 1 map unit = a 1% chance of recombination.

• If two genes are 50 map units apart, how likely is recombination?

Abnormal Chromosome Number• Nondisjunction is when chromosomes do not separate

correctly during meiosis.

• This causes an abnormal chromosome number, called aneuploidy

• Trisomy is when you have 3 chromosomes instead of 2 (2n + 1)

• Monosomy is when you have 1 chromosome instead of 2 (2n – 1)

• Polyploidy is having more than one complete set of chromosomes

• If any of the above organisms survive to birth, it will have major developmental abnormalities

Alterations of chromosome structure

• Deletion: chromosomal fragment is deleted

• Duplication: a chromosomal fragment is doubled

• Inversion: chromosomal fragment gets reversed

• Translocation: chromosomal fragments get switched around

What is DNA?

• DNA stands for deoxyribonucleic acid.• DNA is what makes our genes, and

along with protein, makes our chromosomes.

• It encodes our hereditary information.• It directs the development of our

anatomical, physiological, and behavioral traits.

The Structure of DNA

DNA is a double helix.It is a polymer made of

monomers called nucleotides.

Each nucleotide is made of a nitrogenous base, a pentose sugar called deoxyribose, and a phosphate group.

The backbone of DNA is called “sugar phosphate” and has bases attached to it like rungs of a ladder.

The Structure of DNA

DNA is “right handed” and curves to the right.

Hydrogen bonds hold the bases together

The 5’ end has a phosphate group

The 3’ end has an OH group

Strands always line up with one 5’ strand face up attached to a 3’ strand

Purines

Purines are nitrogenous bases with 2 organic rings.

G and A are purines

Pyrimidines

Pyrimidines are nitrogenous bases with only 1 organic ring

Cytosine and thymine

DNA Replication

DNA replicates during the S phase of interphase, prior to cell division (mitosis).

DNA replication is semi-conservative, meaning that new DNA strands are made of one new daughter strand attached to one old parent strand.

DNA Replication

DNA polymerases are special enzymes that add complementary bases to the unzipped DNA.

DNA Replication

DNA replication can ONLY go from 5’ to 3’

So replication is antiparallel, one strand elongates normally, called the leading strand.

The other is going away from the replication fork, called the lagging strand.

DNA Replication

As the bubble of replication grows, the lagging strand is made bit by bit in fragments, called Okazaki fragments.

These are eventually joined by an enzyme called DNA ligase.

From Gene to Protein

• The “Central Dogma of Molecular Biology” is DNA RNA protein

• Meaning that our DNA codes our RNA which provides instructions for making protein

• Proteins (you may remember) do many things: structure, support, communication, transportation, enzymes etc.

Transcription and Translation

• Transcription is the synthesis of RNA from DNA

• Translation is the synthesis of a polypeptide (protein) from RNA.

Codons

• Proteins are made of amino acids.

• Each amino acid is coded for by a triplet of nucleotides called a codon.

• For example, AGT = serine

• There are only 20 amino acids, but 64 codons.

Transcription: DNA to RNA

• First, RNA Polymerase unzips a strand of DNA.

• Transcription can only go from 5’ to 3’

• RNA Polymerase II attaches to DNA at a promoter

• The portion of DNA being transcribed is called a transcription unit

Transcription: DNA to RNA

• RNA is now synthesized, as base pairs are added to the unzipped DNA strand.

• RNA is ribonucleic acid. It is a single helix. Instead of T (thymine) RNA has U (uracil).

• So every A in DNA now pairs with U (instead of T).

• The RNA that is made is called mRNA which stands for messenger RNA.

RNA splicing

• Some of the RNA isn’t needed to code for proteins, so it is cut out through RNA splicing.

• The non-coding regions that are cut out are called introns, the coding portions the cell needs are called exons.

• Little molecules called small nuclear ribonucleoproteins, snRNA, join with a molecule called a spliceosome to slice the RNA.

Translation: RNA to protein

• The mRNA now leaves the nucleus and binds to a ribosome, where protein synthesis occurs.

• As it passes through the ribosome, tRNA (transfer RNA) molecules, each carrying an amino acid, begin to form a long chain of amino acids.


• At one end of tRNA is a triplet code called an anticodon which matches the mRNA.

• At the other end of the tRNA is an amino acid.


• The ribosome where this all happens has two pieces, and is made of proteins and RNA called ribosomal RNA (rRNA)

• The subunits are called “large” and “small”

Operons

• Genes that can be turned on or off as needed.

• The switch that does this is a segment of DNA called an operator.

• Along with an operator, there is a promoter and some enzymes that make up the operon.

• Repressors turn off an operon

• Inducers turn on an operon

Trp operon

• Tryptophan is an amino acid that is usually produced by the body but can be turned off. This is a “repressible operon”

Lac operon

• The lac operon is usually off but can be stimulated (induced) and is therefore called an “inducible operon.”

• The lac operon functions in the digestion of lactose, milk sugar.

AP Biology

Points of control The control of gene

expression can occur at any step in the pathway from gene to functional protein1. packing/unpacking DNA

2. transcription

3. mRNA processing

4. mRNA transport

5. translation

6. protein processing

7. protein degradation

AP Biology

How do you fit all that DNA into nucleus?

DNA coiling & folding double helix nucleosomes chromatin fiber looped

domains chromosome

from DNA double helix to condensed chromosome

1. DNA packing

AP Biology

Nucleosomes “Beads on a string”

1st level of DNA packing histone proteins

8 protein molecules positively charged amino acids bind tightly to negatively charged DNA

DNA packing movie

8 histone molecules

AP Biology

DNA packing as gene control Degree of packing of DNA regulates transcription

tightly wrapped around histones no transcription genes turned off heterochromatin

darker DNA (H) = tightly packed euchromatin

lighter DNA (E) = loosely packed

H E

AP Biology

DNA methylation Methylation of DNA blocks transcription factors

no transcription genes turned off attachment of methyl groups (–CH3) to cytosine

C = cytosine nearly permanent inactivation of genes

ex. inactivated mammalian X chromosome = Barr body

AP Biology

Histone acetylation Acetylation of histones unwinds DNA

loosely wrapped around histones

enables transcription genes turned on

attachment of acetyl groups (–COCH3) to histones

conformational change in histone proteins transcription factors have easier access to genes

AP Biology

RNA interference Small interfering RNAs (siRNA)

short segments of RNA (21-28 bases) bind to mRNA create sections of double-stranded mRNA “death” tag for mRNA

triggers degradation of mRNA

cause gene “silencing” post-transcriptional control turns off gene = no protein produced

siRNA

AP Biology

initiation of transcription

1

mRNA splicing

2

mRNA protection3

initiation of translation

6

mRNAprocessing

5

1 & 2. transcription - DNA packing - transcription factors

3 & 4. post-transcription - mRNA processing

- splicing- 5’ cap & poly-A tail- breakdown by siRNA

5. translation - block start of translation

6 & 7. post-translation - protein processing - protein degradation

7 protein processing & degradation

4

4

Gene Regulation

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