UF BSC2010 Exam 2 (updated)

Genotype

An organism's genetic code

Phenotype

An organism's physical traits; caused by genotype

Chromosome

Where genetic material is carried

chromosome disclaimer

chromosomes stereotypically look like X shape (aka has 2 sister chromatids)

but can look just like an l shape (so just 1 chromatid)

so both sides of the picture are chromosomes (just single vs double stranded types or unreplicated vs replicated)

XX vs XY chromosome

XX = female

XY = male

Aneuploidy & 2 types

= abnormal # of chromosomes

types:

trisomy = 2n +1 (one extra chromosome)

monosomy = 2n - 1 (one fewer chromosome)

Polyploidy

= having an extra *set* of chromosomes

types:

triploidy = 3 sets

tetraploidy = 4 sets

Sister chromatids

The 2 strands shown in a replicated chromosome

Centromere

Point of attachment of sister chromatids

Homologous Chromosomes

Pair of separate chromosomes that are the same size & appearance

Alleles

Different versions of the same gene

Mutation

Accidental change to DNA

Silent mutation

Does not result in a functional change

Codon

Sequence of 3 bases

Sense codons

Codons that DO code for amino acids

-they've got the sense to

Missense mutation

Result in a change in an amino acid

-ex: GAU codes for aspartic acid, while GUU codes for valine so a change from GAU to GUU results in diff amino acid

Nonsense mutation

Insertion of premature stop codon

- so NO sense codon, stops before it gets to code

Loss-of-stop mutation

When stop codon is changed to sense codon

Frameshift mutation

When 1 or 2 bases (3 is different mutation) are inserted in a sequence, thus moving the reading frame

-Can be insertion or deletion

Mismatch Mutation & Repair

Corrects incorrect bases after replication ends

mRNA (messenger RNA)

The message/blueprints for making protein

- Copies genetic instructions from nucleus & acts as messenger (tells what the order of amino acids is/how to build the given protein)

tRNA (transfer RNA)

The delivery truck for making proteins

-Top side carries correct amino acid to growing polypeptide strand & bottom side (called anticodon bc opposite the codon) binds to mRNA to read its instructions

tRNA shape

funky T

-ignore labels on picture (just know general shape & amino acid on top, anticodon on bottom)

Anticodon

Where the tRNA binds to mRNA (lines up w/ codon that mRNA has, hence called ANTIcodon)

rRNA (ribosomal RNA)

The factory where mRNA and tRNA come together (looks like seat)

-rRNA glues them the amino acids together (once tRNA brings them over) to form chain

Protein synthesis

2 steps: transcription & translation

Transcription

RNA -> DNA

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Coding vs template strand

Coding = Strand with the same sequence as the mRNA (except U is switched for T)

Template = strand complementary to the coding strand- read by RNA polymerase

What happens after transcription/ during post-transcriptional processing?

1) Guanine cap (g-cap) is added to 5' end of pre-mRNA to protect mRNA

2) Poly-A tail of 100-200 molecules (long ass chain of just A) is added to 3' end of pre-mRNA (again to protect the strand)

3) RNA splicing occurs

-Introns are cut out of spliced genes, extrons remain (names annoyingly backwards)

Intron

Junk, sequence of nucleotides that are transcribed but REMOVED from pre-mRNA after transcription

Extron

Nucleotide sequences that are not removed after transcription

-Glued by spliceosomes

Spliceosomes

The scissors and glue for pre-mRNA

-Cuts introns out & glues extrons together to form mature mRNA

-"splice" = join

Code for the "start codon"

Amino acid: Methionine (MET)

Sequence: AUG

3 sequences for "stop codon"

UAA, UAG, UGA

Translation

mRNA -> protein

Polypeptide synthesis: A site

(Aminoacyl) entry site

-Where incoming charged tRNA meets the ribosome (rRNA's seat job)

Polypeptide synthesis: P site

(Peptidyl) binding site

-Where the amino acid brought by the tRNA is actually attached to the growing polypeptide chain (rRNA does its gluing job)

Polypeptide synthesis: E site

Exit site, where tRNA molecules move to be released by the ribosome

overall: tRNA shifts right to left (EPA)

Processes that can occur in post-translational processing

Glycosidation, Phosphorylation and Proteolysis

Glycosidation

Addition of a sugar

Phosphorylation

The addition of phosphate group

Proteolysis

Breakdown of proteins

Pyrimidines

C, T, U

- have only one ring

Purines

A, G

-two ringed

"PURe As Gold)

Central Dogma

DNA -> RNA -> Protein

aka Replication -> Transcription -> Translation

(the flow of genetic info transformation)

Origins of Replication

Site DNA replication begins, where proteins attach to the DNA and form "replication bubbles"

Replication Fork

Formed as a result of "replication bubbles", DNA replication proceeds in both directions here

Amplification

Artificial process that increases/amplifies DNA

- Used in lab, not part of normal process (forced)

Leading vs lagging strand

Leading = runs 5' to 3' so synthesized normally

Lagging = runs 3' to 5' so keeps falling behind bc enzyme keeps backtracking to synthesize small segments in 5' to 3' direction

Initiation, Elongation, & Termination disclaimer

Initiation, Elongation, & Termination are the 3 general steps (in that order) that occur for DNA replication, transcription, & translation (so occurs 9 times total)

Semi conservative

DNA Replication is this

-when new DNA is formed, one strand (template strand) is "old" (dark blue) and the other is "new" (light blue) aka some old is conserved

Synthesis of leading vs lagging strand

Leading -> Continuous

Lagging -> Discontinuous (synthesis occurs in small segments aka okazaki fragments)

Helicase

Unwinds the double helix

Primase

Makes RNA primers that are necessary for DNA polymerase (primase makes short starting point of 3 bases & polymerase builds off of it)

DNA polymerase

Adds nucleotides to both strands during DNA replication

Ligase

An enzyme that "glues" two fragments of DNA to make a single fragment

end-replication problem

every time a chromosome is made, the next one is shorter

Telomeres

Junk nucleotide sequences that repeat hundreds of times at the end of chromosomes to protect them

- Solution to the end replication problem- protects chromosome bc this is cut off instead of important info

similar function to Poly A (protect ends)

Telomerase

Build telomeres

-Only in sex cells not somatic cells (why aging occurs, body cells worn down)

Mitosis

Cell division for somatic (body) cells that produces 2 identical diploid cells

who does mitosis & meiosis

eukaryotes do (aka animals, plants, fungus- everybody but bacteria)

- prokaryotes don't (aka bacteria) bc don't have membrane-bound organelles to divide

Meiosis

Cell division for germ/sex cells that produces 4 different haploid cells

- 2 parts (meiosis 1 and meiosis 2 each w/ their own PMAT)

- haploid because 2 gametes fuse together to form diploid zygote (1 + 1 = 2)

Symmetrical vs Asymmetrical cell division

Sym- A single cell produces 2 identical cells of the same size and contents

Asym- A single cell produces a second cell unlike the first cell

Asexual vs sexual reproduction

Asexual = A single parent produces identical offspring

Sexual = 2 parents produces different offspring

Binary Fission

How single-celled prokaryotes reproduce- is a form of asexual reproduction

Binary fission & who does it

Prokaryotes (bacteria) cell division

- classic example of asexual reproduction

Gamete vs Zygote

gamete = sex cell

-From mom or dad (egg or sperm)

zygote = 2 gametes together

- both egg & sperm

- z comes later in alphabet

Fertilization

Process in which haploid gametes from meiosis are combined to form a diploid zygote

Cancer

Uncontrollable cell division

Binary Fission Steps

1) Signal to initiate 2) DNA replication 3) DNA segregation 4) Cytokinesis

ori vs ter site in replication

ORI site = replication starts (ORIgin of replication) vs replication ends at TER site (TERminus of replication)

Karyotype

A display of the chromosome pairs of a cell arranged by size and shape.

Kinetochores

protein structures on the centromeres, the microtubules latch onto these to drag chromosome

sister chromatids vs homologous chromosomes

Chromatin

the material chromosomes are made of

Centrosome

Regions associated with spindle fiber formation and spindle poles during mitosis.

Are the organizing center for microtubules in cell and sites for synthesis and replication of microtubules

Centrioles

Hollow microtubule rings arranged perpendicular to each other- have same structure as cilia and flagella in that they are made of 9 pairs of microtubule doublets arranged in a circle

Cell Cycle Order

G1, S(synthesis), G2, M(mitosis)

Interphase

Period of cell's life where doing normal functions- 90% of cell's life cycle.

Interphase: G1 phase (growth 1)

Normal functions & prepares for cell division as grows up

- most time of life spent here

Interphase: G0 Phase

Cell "exits" interphase to rest

-goes back to normal functions, but not preparing for cell division bc lacks nutrients for the process

Interphase: S (synthesis) phase

DNA is replicated

Interphase: G2 phase (growth 2)

Cell grows & produces proteins in preparation for Mitosis

M phase (mitosis)

Cell division (includes the PMAT stages)

G1S checkpoint inhibitor

Rb (retinoblastoma protein)

- when present, cell cycle is inhibited at that checkpoint

Ploidy at diff Stages

G1 = 2 diploid

S = 2 to 4 diploid (bc replication) transition

G2 = 4 diploid

Meiosis 1 = 2 haploid

Meiosis 2 = 1 haploid (end result)

Alleles vs Locus

Locus are where alleles resides (DNA at each locus varies so different phenotypes are caused like brown vs blue eye color)

- you inherit one allele from each parent

Mendel Laws (for true-breeding bc Mendel got lucky w/ that)

Law of Segregation = each parent has their own copy of a gene/allele, but due to segregation, only one is passed down to child (2->1)

-ex: tall & short mom & dad -> tall kid

Law of Independent Assortment = genes are handed down independent of one another

- ex: stem color & size are independent

Law of Dominance = dominant & recessive rules

ex: T vs t

Probability Calculations P(A or B) & P(A and B)

P(A or B) = P(A) + P(B)

P(A and B) = P(A) x P(B)

Dependent/Linked vs Independent/Unlinked Assortment

Dependent = Loci assort together, inherited as one unit

- loci close to each other on the same chromosome

- ex: if have R allele then also have Y allele vs if have r allele also have y allele

Independent = loci don't affect each other (9:3:3:1)

- loci on entirely diff chromosomes or far apart on same chromosome

Diplontic vs haplontic life cycle

Diplontic = Organism is diploid & gametes are haploid

Haplontic = Organism is haploid & gametes are diploid

- named after whatever it spends its life as

Prophase (mitosis)

1) Nucleolus disappears

2) Chromosomes condense

3) Mitotic spindle & centrosomes form

Prometaphase (Mitosis)

small stage between prophase & metaphase (not mentioned in PMAT acronym tho)

1) Nuclear envelope breaks down

2) Spindles attach to centromeres at kinetochores

Metaphase (mitosis)

Chromosomes line up in the middle of the cell at the "metaphase plate" or "equator"

Anaphase (Mitosis)

Cell elongates, chromosomes are split in half into sister chromatids and dragged to opposite sides

Telophase (Mitosis)

1) Spindle breaks down

2) Nucleoli reform

3) Chromosomes uncondense

*basically the opposite of Anaphase*

Cytokinesis

2nd component of mitosis (M phase): splits a cell into two parts

- looks similar to telophase but the distinction is that they fully separate here